Software Developer - Phytozome

Software Developer 3/4 - Phytozome - 74226
Organization: GN-Genomics

The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting opportunity available for an experienced Software Developer / Engineer to support the Phytozome group. The Phytozome group in the JGI Plant Genomics Program is responsible for the annotation and analysis of plant genomes, and for providing both internal and external users with visualization, querying and data access capabilities to facilitate progress in fundamental, biofuel and climate-related Plant science. The Phytozome website and associated databases and analysis tools provide JGI’s collaborators and the broader plant biology community with intuitive and powerful interfaces to access and explore plant genomic data. As the JGI anticipates a massive increase in RNA-Seq and resequencing output, we have an opportunity for an experienced developer to help us enhance and expand Phytozome to host even more plant genomes and their annotations, and to develop new databases and interfaces to support users’ exploration of plant genomic diversity and gene expression data.

Under broad supervision, the ideal candidate will develop, implement, test, integrate and deploy new and/or existing software components of the Phytozome system for the visualization and querying of plant genomic and related data. They should demonstrate detailed knowledge and strong technical ability in web user interface design concepts and implementation, data modeling, and database schema design, as well as extensive familiarity with standard genomic sequence data types and analysis methods.

The selected candidate will be hired at the Software Developer 3 or 4 classification level depending upon the candidate's level of experience and qualifications. Position reports to the Phytozome Group Lead.

Specific Job Duties

Essential

• Work as a member of the Phytozome development team to create, maintain and extend the suite of visualization, backend, and data management tools that support the public interface to the JGI’s Plant Genomics program.
• Create and maintain database-backed web applications for the display and querying of genomic data.
• Evaluate the suitability of third party open source tools (e.g. GMOD) versus in-house development to provide desired functionality to Phytozome.
• Optimize the Phytozome user experience by constantly monitoring and improving backend data retrieval performance (as determined by benchmarking) and front-end usability (as determined by user surveys and best practices).
• Follow best practices for software version control, documentation, testing and release engineering.

Marginal

• Work with Phytozome/Metazome internal and external user community and Scientific Advisory Board to prioritize new feature requests, and provide accurate estimates of implementation timelines.
• Assist in the preparation of manuscripts, tutorials and conference presentations based on Phytozome.
• Work with JGI’s Systems group to anticipate hardware needs for increasing data set sizes and expanded functionality.

Essential duties for the Software Developer 4 - In addition to the job duties described above, the Software Developer 4 will:

• Operate at a higher level of independence and responsibility when carrying out assignments.
• Will serve as a technical lead and key contributor called upon to solve highly technical, complex problems.

Key Success Factors

Essential -

• B.S. in technical or scientific field (or equivalent experience) and a minimum of five years programming experience.
• Minimum five years experience and demonstrated success designing and implementing bioinformatics analysis systems and software in a scientific or technical environment, e.g., University, National Laboratory, corporate R&D.
• Familiarity with standard genomic sequence data repositories (e.g, GenBank, SwissProt) and functional classification databases and ontologies (e.g., KEGG, Panther, Metacyc, GO).
• Solid experience programming with object-oriented Perl and Java.
• Advanced knowledge of SQL and relational database design.
• High degree of comfort developing on, and for, linux systems.
• Demonstrated experience developing database-backed applications and experience with web technologies including: Apache, Tomcat, CGI programming, JDBC, JAXB, GWT, AJAX.
• Ability to effectively learn and apply new technical concepts to troubleshoot and solve problems and challenges of a diverse scope.
• Effective interpersonal communication and presentation skills.
• Effective time management, organization, and planning skills.
• Ability to work effectively in a diverse team environment.

Desirable -

• M.S./Ph.D. in Molecular Biology, Genetics or related field.
• Mathematical sophistication to understand algorithmic concepts behind sequence alignment, gene family clustering, and phylogenetic tree building.
• Experience with the management and visualization of gene expression and genomic diversity data.
• Solid understanding of statistics.
• Experience developing software that includes or interacts with GMOD and bioperl components.
• Working knowledge of Python and PHP.

Essential Qualifications for the Software Developer 4 - In addition to the qualifications listed above, the Software Developer 4 requires:

• A minimum of eight years related experience.
• Demonstrated ability to solve highly complex problems and work independently on end-to-end implementation and maintenance of software projects through multiple releases.

How To Apply: Apply directly online and follow the instructions to complete the application process.

Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.

2013 GMOD Meeting Survey

As we are trying to plan for next years GMOD meeting, we would like to decide between two venues as soon as possible. To help us decide, we've put together a simple survey. We are asking your help in deciding between:

• San Diego, California in January before or after the Plant and Animal Genomes meeting
• Cambridge, England in April before or after the International Society of Biocurators meeting.

Each option has its upsides: the Plant and Animal Genomes is a large meeting attended by several members of the GMOD community, so it would likely have a fairly high attendance. On the other hand, having a meeting in Cambridge would make it easier for European members of the GMOD community to attend. Please share your thoughts with us and take this survey.

Bioinformaticians @ FDA

A conceptually new computational cloud paradigm of High performance Integrated Virtual Environment (HIVE) is being developed at Food and Drug Administration (FDA) Center for Biologics Evaluation and Research (CBER) for High Throughput Sequencing (HTS) XL-data storage and analysis.

A team of professional Bioinformaticians, DB developers, WEB programmers is being assembled for this purpose. The team will be responsible for implementing a Sequence Read Archive (SRA) Library and computational biology analytics tools within HIVE cloud.

Bioinformatician tasks will include programming of computational biology tools, development of new algorithms, adapting existing tools to the HIVE cloud.

Education

• Ph.D in Physics/Math/Biology/Biostatistics or related field

Skills

• 2+ years in C/C++ is required. Must have developed a tool/program.
• Expertise in fundamental mathematical models/algorithms
• Solid understanding of bioinformatics concepts: alignments, strings and trees, sequences, clustering methods, biostatistics
• GMOD or Galaxy experience is a significant plus
• Ability to work in different operating systems: Linux, Windows, Mac; development environments: Visual Studio, Eclipse, GCC/GDB;
• Experience in developing parallel and/or multithreaded programs a plus
• Understanding of client/server infrastructure
• Experience with Java, SQL, scripting languages is a plus

Background

• Scientific background in Mathematics, Physics, Chemistry or Biology is a significant plus.
• Having publications in reviewed journals is a significant advantage

Environment

• Ability to work in a collaborative team of highly skilled professionals is a must
• Ability to independently work on parts of a project and implement/maintain libraries and tools associated with sub-projects is a key
• Will be interacting with scientist and regulatory personnel to understand and translate requirements into computationally executable tasks

Please contact Vahan Simonyan to apply, or if you have questions.

JBrowse 1.3.0 released

JBrowse version 1.3.0 has arrived!

We have a long list of improvements in this release, some of which have been a long time coming. It’s full speed ahead from here: more major new features are just around the corner!

This release comes in two flavors: the “minimal” release (http://jbrowse.org/releases/JBrowse-1.3.0-min.zip - 2.0M) that includes only the software and documentation necessary to format your own data and run the browser, and the “full” release (http://jbrowse.org/releases/JBrowse-1.3.0-full.zip - 4.7M) that includes the developers’ test suite, more sample data files, and developer documentation.

One important note about browser support: as of this 1.3.0 release, JBrowse no longer supports Microsoft Internet Explorer 6.

Please see the blog post for the full list of new features.

Robert Buels

Lead Developer
JBrowse - http://jbrowse.org

Xenbase Hiring Two Developers

Best skiing in the world at your doorstep (and great science too!)

Position 1, entry level developer

Xenbase, the Xenopus model organism database is looking for a strong skiier/rider software developer to join our team in Calgary. Good Java and Javascript skills are essential. Database and/or perl would be a plus but isn’t essential. This developer will work on interfaces that allow our 1,000 daily users to interrogate our database on Xenopus genomics, cell and developmental biology.

Applicants should be based in North America and eligible to work in Canada (under NAFTA this includes USA and Mexico). A BS or BA in computer science is preferred, but other technical certifications in software development would also be fine.

Position 2, senior software developer

Xenbase, the Xenopus model organism database is looking for an experienced skiier/rider senior software developer to join our team in Calgary. The rocky mountains are an hour from town, with incredible skiing, backcountry and camping. The city itself has over million people and has lots to do when you are not skiing working. In addition to building interfaces using Java the senior developer will manage, upgrade and customize a variety of perl based data pipleines and also optimize and customize our genome browsing tools. Good DNA and protein sequence alignment skills are essential. Experience with GMOD tools such as Gbrowse would be sweet, as would experience with the UCSC browser, e-utilities, RNA-seq and ChIP-seq data.

Xenbase imports a wide range of data on Xenopus genomics and biology. This data is processed by automated systems and also by a team of data curators who do all the things that our pipelines can’t- like read the scientific literature and mark it up using software interfaces that you will help improve.

If you would like more info on either position please get in touch with the database director, Jeff Bowes bowes [at] ucalgary.ca

Friedberg Lab Hiring

Department of Microbiology, Miami University Oxford, Ohio: Scientific Programmer/Specialist to implement and maintain a genomic database web site; implement data management tools including relational database management applications for efficient storage and retrieval of genomic data; perform other duties as related to the position such as data and project management to ensure data are being processed in an efficient and timely manner; contribute to writing scientific manuscripts. See also here

Required qualifications: BS or BA in Computer Science, bioinformatics, or a related discipline; demonstrated programming experience, particularly in Python and SQL databases; demonstrated web programming experience; knowledge of Linux/Unix; excellent spoken and written communication and documentation skills.

Preferred qualifications: Advanced degree (M.Sc. or Ph.D) or equivalent in Computer Science, Bioinformatics, Molecular Biology or a related discipline; experience in development of bioinformatic algorithms; knowledge of R programming; experience in development of or contribution to open source projects; experience in collaborative software development such as the use of version control software, writing and following software specifications, participation in code review; knowledge of basic molecular biology; experience with genomic browser programming, such as GMOD or equivalent.

Candidates should send a CV or resume and have three letters of reference sent separately to Dr. Iddo Friedberg at Friedberg.lab.jobs ‘at’ gmail ‘dot’ com. Screening of applications begins April 14, 2012 and will continue until the position is filled.

Miami University is an affirmative action/equal opportunity employer with smoke-free campuses. Consumer Information http://www.miami.muohio.edu/about-miami/publications-and-policies/student-consumer-info/. Hard copy upon request.

See also here: [1]

ZFIN Software Dev Manager

ZFIN, the zebrafish model organism database, is an international bioinformatics organization looking for a software development project manager. The person who fills this staff position will work with a team of computer scientists and biologists to design, develop, and maintain the biological model organism database for zebrafish. ZFIN supports GBrowse and InterMine deployments.

ZFIN is located at the University of Oregon in Eugene, Oregon. Eugene is a green community with short commutes, a laid back environment, and a low cost of living. The position provides excellent benefits and stable funding.

See the full job posting for duties and responsibilities, minimum and preferred qualifications, and how to apply.

Openings at Galaxy

Wants You!

Want to work on one of the fastest growing open source bioinformatics projects around? The Galaxy Project, a highly successful high throughput data analysis platform for Life Sciences with over 15,000 users worldwide, is hiring.

• The Taylor Lab in the Biology and Mathematics & Computer Science at Emory University is looking for software engineers and postdoctoral scholars to work on the Galaxy Project.
  • We are seeking software engineers with expertise in distributed computing and systems programming, web-based visualization and visual analytics, informatics and data analysis and integration, and bioinformatics application areas such as re-sequencing, de novo assembly, metagenomics, transcriptome analysis and epigenetics. These are full time positions located in Atlanta, GA. See the official posting for full details.
  • Postdoctoral applicants should have expertise in Bioinformatics and Computational Biology and research interests that complement but extend the lab's current interests: The Galaxy project; distributed and high-performance computing for data intensive science; vertebrate functional genomics; and genomics and epigenomic mechanisms of gene regulation, the role of transcription factors and chromatin structure in global gene expression, development, and differentiation. See the announcement for full details.
• The Nekrutenko Lab at the Huck Institutes of Life Sciences at Penn State is seeking highly opinionated and biologically inclined Postdoctoral researchers within the Galaxy Project to develop best practices for analysis of next-generation sequencing data in all areas of Life Sciences where NGS is used. Successful candidates will join a vibrant research group at the Center for Comparative Genomics and Bioinformatics at Penn State University.

Please send your CV to jobs@galaxyproject.org.

GMOD Community Support Specialist

Opening for the GMOD Community Support Specialist

Are you fascinated by genomics and bioinformatics? Are you passionate about collaborative open-source software? Do you enjoy teaching and working with scientists? Are you a natural communicator?

The Generic Model Organism Database project (GMOD) is a collection of open source software tools for creating and managing biological, and particularly genomic, databases. GMOD has a large, highly distributed, and dynamic community of software users and developers. The University of North Carolina at Chapel Hill has an opening for a GMOD Community Support Specialist, to be based at the US National Evolutionary Synthesis Center in Durham, North Carolina, while serving the international community of GMOD users.

Job Description: The incumbent will present tutorials; organize short courses, conference sessions, GMOD meetings and other community building activities; survey user needs; liaise between users and developers on GMOD mailing lists; and oversee the community wiki and news feeds. The incumbent will collaborate closely with the GMOD Coordinator (Scott Cain, The Ontario Institute for Cancer Research) and other distributed personnel. See GMOD Community Support for more background. The position offers a competitive salary and the incumbent will receive a comprehensive benefits package as an SPA employee within the UNC system. Funding is anticipated to be available for three years.

Qualifications: Required qualifications include: excellent written and verbal communication skills; team orientation with strong interpersonal skills. Preferred qualifications include: an MS or PhD in biology, computer science or related field; three or more years of experience with genome database administration or curation, preferably in a GMOD environment; at least one year of experience with web content management, ideally using MediaWiki; freedom to travel 5-15 weeks/yr.

To Apply: Please provide a cover letter and CV, including contact information for three references, to Hilmar Lapp, Assistant Director of Informatics, NESCent, at hlapp@nescent.org. Inquiries may be addressed to H. Lapp by email or by phone at 919.668.5288.

Registration Open for GMOD 2012 Meeting

Registration for the April 2012 GMOD Meeting is now open. Please go to http://gmod2012.eventbrite.com/ to register. If you register before March 7, the fee is $40; after March 7, the fee goes to $50. Also, if you register before March 7 you will be entered in a drawing for GMOD swag.

I am very excited for this meeting. It is occurring right after the Biocuration meeting just down the street. I am also very pleased the the keynote speaker will be Deanna Church from NCBI. If you would like to present at the meeting, either contact me or edit the meeting page directly to add your suggested topic.

Scott Cain

Textpresso Software Developer

Textpresso (http://www.textpresso.org), a search engine for biomedical literature and text mining project, and a GMOD Component, is seeking candidates to fill the position of a software developer.

Basic qualifications include:

• BS in a field of science or engineering.
• Documented experience in software development.
• Experience with the majority of the following languages: Perl, C/C++, Java, Javascript, Ajax, jQuery.
• Familiarity with web application frameworks.
• Experience managing and configuring Linux systems and webservers.
• Proficiency in protocols used for web-publishing such as HTML, XML, XSLT, CSS.
• Knowledge about database management systems and similar software such as PostgreSQL or MySQL.

Thanks and Happy Holidays,

Hans-Michael Muller

modENCODE Data Access Webinar

modENCODE project aims to provide the biological research community with a comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. Data Coordination Center for modENCODE is conducting a series of webinars with the next one, "Understanding worm and fly chromatin modification data" scheduled on Thursday Dec 1, 12:00 EST (Eastern US time). This online webinar will introduce participants to the data obtained in experimental studies of various histone modification marks and chromatin binding proteins, also showing how to visualize and download these data from the modENCODE web site/FTP. Space is limited so advance registration is necessary. Please email help@modencode.org to reserve your spot. More details and the schedule are at http://wiki.modencode.org/project/index.php/DCC_Usability_webinars

Peter Ruzanov

Intern @ Aniseed: work on Chado

Develop modules for a Chado-based Model Organism Database dedicated to the developmental biology in tunicates.

Background:

Our team combines various techniques of molecular and cellular biology, bioinformatics, and mathematical modeling to decipher and formalize the embryonic development of animals. The team is composed of experimental biologists and computer scientists.

To integrate these heterogeneous data of gene expression, genomic sequences, anatomical and quantitative description of embryology, we have developed the Aniseed system (Ascidian Network for In Situ Expression and Embryological Data). This sophisticated information system is being rewritten using Chado and then extended.

Internship Projects:

We are proposing to host up to three students in the team located in the Research Center on Macromolecular Biochemistry (CRBM) in Montpellier. The working language in the lab is English. Internships are paid.

Each intern will work on the development of a new Chado module of Aniseed. The development of each module will include the formalization of biological data and their interactions with data already represented in the database, modification/extension to the schema, use/adaptation of ontologies, and the development of interfaces to graphically represent the data and mine them. The data considered include:

• SELEX-seq DNA-binding specificities for a large fraction of ascidian transcription factors obtained by the team
• Data from ChIP-seq/RNA-seq experiments
• Signal transduction pathways/networks

Development of a module for data curation (manual annotation and verification) is also proposed.

Expected Skills:

The projects are primarily intended for students with a training in computer science, or biologists who have a very good practice of software development. The candidates are expected to have team spirit, autonomy, dynamism and creativity. Interest in molecular biology is highly desirable, and some basic knowledge of biology would be welcome. Given the international nature of the project, a command of English sufficient to understand technical seminars, annotating code, and present the work is requested. Computer skills required are:

• Knowledge of relational databases (PostgreSQL, MySQL). Knowledge of Chado would be an asset.
• OOP / Languages: PHP 5 (Jelix framework), Perl, XML
• Control of web interfaces PHP / HTML / Apache, IDE: NetBeans
• Experience in web-service (XHTML, HTML, CSS, XML)
• Linux OS

Contact:

Patrick Lemaire <patrick.lemaire@crbm.cnrs.fr> and Cyril Martin <cyril.martin@crbm.cnrs.fr>

BioMart Special Issue in Database

I am very pleased to announce the publication of the DATABASE special issue dedicated to the BioMart project

http://www.oxfordjournals.org/our_journals/databa/biomart_virtual_issue.html

BioMart is a unique open source data federation technology that provides unified access to distributed databases storing a wide range of data. This DATABASE issue recognizes BioMart's outstanding contributions to bioinformatics and documents the achievements of the BioMart community, which has grown impressively over the last ten years to become what it is today, a collaboration between numerous database projects on five continents: Asia, Australia, Europe, North America and South America.

I would like to thank and congratulate the BioMart community on this impressive achievement. This issue would have not been possible without their dedication, expertise, passion and enthusiasm.

Arek Kasprzyk

GMOD Workshop Jan 23-25

A GMOD Workshop is being held 23-25 January in Český Krumlov, Czech Republic, as part of the Advanced Topics Workshops immediately following the Workshop on Genomics.

This will be a 3-day focused workshop experience on the installation, usage and development of a subset of GMOD Components. Particular attention will be provided to the use of Chado for genomic feature annotation, and JBrowse, GBrowse and WebApollo for for viewing, creating and editing genomic annotations in graphical environments.

→ The official application deadline has been extended to December 15.

However, later registration will be accepted dependent on availability. The registration fee is $600 USD (payment terms provided upon acceptance).

FYI: The Workshop on Genomics features some Galaxy content, and is still accepting application as well.

Scott Cain

Galaxy Development Workshop Jan 23

Update: This workshop has been canceled.

A one day Galaxy Developer Workshop has been scheduled for 23 January in Český Krumlov, Czech Republic, immediately following the Workshop on Genomics, (which also features Galaxy content and is still taking applications).

This workshop is aimed at:

IT and Bioinformatics staff

Galaxy is an easy to use, web-based tool that enables your researchers to perform data integration and analysis, in house, without handholding from you. This workshop will teach you how to install your own instance of Galaxy, either on your local compute infrastructure, or on the cloud.

Bioinformatics tool developers

Galaxy provides mechanisms for integrating your own tools and the tools of others into Galaxy instances. This workshop will cover how to define your tools in Galaxy, and how to then make those definitions available for installation in any Galaxy instance, thus making your tools much more accessible to the research community.

This workshop also includes contributed talks from participants. If you have a topic of interest to the workshop’s audience, then please submit a short (500 words or less) abstract along with your registration. Topics do not have to be directly related to Galaxy, but they should be of interest to those working with the integration, analysis, and sharing of large biological datasets.

15 December is the preferred registration deadline. However, later registration will certainly be accepted dependent on availability. The registration fee is $200 USD (payment terms provided upon acceptance).

Dave Clements

PS: Plans for the 2012 Galaxy Community Conference are coming along nicely. Dates are July 25-27 in Chicago, Illinois.

ZFIN Project Manager Wanted

ZFIN, the zebrafish model organism database, located at the University of Oregon is looking for a highly qualified software development project manager. The person who fills this position will work with a team of computer scientists and biologists to design, develop and maintain a dynamic bioinformatics database infrastructure that includes GBrowse and InterMine deployments. The final candidate must successfully complete a criminal background check

The essential functions of this position include:

• Supervise technical staff (9 direct reports) ensuring equal growth opportunities and facilitating skills development.
• Manage project plans and schedules.
• Work with staff to establish software project development standards.
• Ensure development process consistency and compliance with standards.
• Meet regularly with the data curation manager to co-ordinate planning efforts and review progress.
• Ensure adequate support for existing and future infrastructure.
• Help team members to resolve technical and non-technical problems.
• Facilitate communication within and between teams.

Minimum qualifications:

• Bachelor's degree in computer science or a related technical field. Master's preferred.
• 3+ years experience managing software development projects.
• Proven experience using formal software methodologies.
• Familiarity with relational database systems and Java programming environment.
• Strong interpersonal skills, written, and verbal communication.
• Demonstrated organizational skills.
• Knowledge of biology is a plus.

Send resume with names and phone numbers of 3 references to

Or FAX to 541-346-4548. The UO is an AA/EO/ADA institution committed to cultural diversity. Candidates who promote and enhance diversity are strongly desired. Applications received by November 10, 2011 receive first consideration. The position will remain open until filled.

WormBase Is Hiring

WormBase is hiring! You want to do web architecture development in support of a project essential to basic biomedical research.

The Ontario Institute for Cancer Research seeks an agile and adaptable software engineer with a broad skill set and an interest in applying it to scientific problems. You will assist the team in designing and implementing a scalable architecture and web interface to a vast array of biological data supporting a global community of researchers. This position will be based in Toronto, ON, Canada.

We're looking for someone excited about science, computers, and technology. You're comfortable working with big data and moving information between formats, systems, and platforms. You are passionate about trending technology and social media and how they might enhance the scientific process. You can work within the constraints of legacy systems when required and in proposing and evaluating new alternatives when warranted. In the past, you’ve confronted issues related to scalability and data management and have created demonstrable solutions resolving them.

As a web developer, you possess a broad range of skills that you've used to generate maintainable and stable solutions. You've deployed or considered things like EC2, Hadoop/Hoop/HBase/HDFS, Map/Reduce, and NoSQL variants for data management and analysis. You speak Perl fluently, know what Moose look like, have heard of Catalyst, use MySQL and interact with it via ORMs, and love git. You actually enjoy writing documentation and tests. You're not a designer, but can write HTML and CSS when necessary, know some Javascript and the basics of Ajax. When required, you can jump in and help out on a variety of tasks that might not immediately fall under your purview as the needs of the project evolve. Strong candidates will have an understanding of modern biological concepts and familiarity with open source bioinformatics tools like BioPerl and GBrowse. Those from other non-biological science backgrounds but with strong software engineering skills will also be considered.

We're a small, dedicated, distributed team. You should work well independently, and be receptive to exchanging ideas via IM, Google Hangouts, Skype, social media outlets, conference calls, and email threads. In short, excellent communication skills are assumed.

Experience:

Bachelors degree in Computer Science, Bioinformatics, Biology or related field with a minimum of three years experience. On the upper end, a Masters or PhD with 3-5 years suitable experience.

Please send resumes and vitaes to Todd Harris (todd@wormbase.org).

Questions?

• email me at todd@wormbase.org
• call me on skype: toddharris.phd
• find me on google+/gchat: toddwharris
• read a blog post about the position
• see the official job posting at OICR

GBrowse Version 2.40 Released

GBrowse version 2.40 is now available for downloading from SourceForge and CPAN.

Here is the recent changelog:

• Quash a few uninitialized variable warnings when bringing up track configuration dialog.
• Fix inability to toggle visibility & favorite status of plugin tracks from the track titlebar.
• Added caching of inverted configuration file data structure to speed up track rendering on really huge configuration files with many stanzas. Cache structure is stored in /tmp/bio_graphics_ff_cache_$UID
• Add ability to save and restore named snapshots of current state.
• Changed behavior of render slave to a prefork model. Activate by including PREFORK=5 (or other desired number of servers) in /etc/default/gbrowse-slave.
• Added support script for Amazon cloud image: gbrowse_attach_slaves.pl creates slave instances for AMI ami-c6ca31af.
• Change default tmpfile location to /var/tmp/gbrowse2 (was /tmp/gbrowse2).

The most significant change is actually the third from the top, which improves speed dramatically when used with data sources that have lots of complex track definitions.

Lincoln Stein

Ergatis Release v2r16

There has been a new release of Ergatis and dependent software packages. The install tarballs are on Sourceforge. For full list of changes since last release, see the CHANGELOG.

Highlighted changes from the CHANGELOG:

• Several new components
  • genbank2fasta, nucmer-detla-filter, nucmer-show-snps, snp-add-gene-info, blast_lgt_finder, btab2taxon, insert_pmarks_in_scaffolds
• Prokaryotic Pipeline Updates
  • Blastable databases are automatically generated during loading steps.
  • PFunc: added more rules for cleaning common names post-annotation
  • run_prok_pipeline.pl script now automatically adds pipeline comments when used
• Added scripts to util to download various types of sequence files (genbank, pep, seq, etc) from Chado DB.

Any bugs/feature requests should be addressed on the Sourceforge site.

Chado Version 1.2 Released

I am pleased to announce the release of Chado version 1.2. It is available at:

http://sourceforge.net/projects/gmod/files/gmod/chado-1.2/

and the change log is listed below. There are two items of special interest in this release:

1. The natural diversity module is included in this release. It is intended for capturing a variety of experimental data related to diversity, including phenotype and genotype assays, and collections like crosses and field collection.
2. It now ships with a tool to aid in updating the schema from previous versions of Chado (from version 1.0 or better). See Updating_Chado for more information on this tool.

Please follow up with comments or problems with this release to the schema mailing list.

Thanks,

Scott

Changes in Chado 1.2:

• Added some error checking to gmod_fasta2gff3.pl (Rob)
• Updated Bio::Chado::Builder to detect recent versions of go-perl. They no longer have .pl at the end of the go2fmt script name (Rob)
• The GFF3 bulk loader will now ignore ##sequence-region directives; previously, their presence caused the loader to fail (Scott)
• added a check for the nodes file downloaded from NCBI. There have been cases of missing nodes/parents. Code dies if parent is missing. User must check the nodes file. This needs further investigation with NCBI taxonomy. (Naama)
• Fix the code in the gff-bridge in the sequence module so that GFF dumping from GBrowse will work correctly (Scott)
• Added a cvprop table to capture things like obo file version from a loaded cv. (Scott)
• Removed the "DB:" prefix from all of the names of databases that go into the db table. (Scott)
• Removed the dependency on Log::Log4perl (it was overkill for what it was being used for) (Scott)
• Bumped the version to 1.2 because of the new schema module. (Scott)
• Added gmod_chado_properties.pl to examine the chadoprop table and return values on the command line (like the schema version) (Scott)
• Added gmod_update_chado.pl to update the schema automatically, and added a make target (make update) to make updating easier. (Scott)
• Removed cell_type ontology from 'make ontologies' list as it wasn't loading via stag_storenode.pl at release time (Scott)

New InterMine and MOD funding

An NHGRI grant that funded a collaboration between InterMine and three of the major Model Organism Databases (MODs) has been renewed and expanded.

The new InterMOD funding is for three years and now includes MGI (mouse) and WormBase (worm) who will each set up and host an InterMine instance. These will work alongside the existing InterMine developments at SGD (yeast), RGD (rat) and ZFIN (zebrafish).

A major aim of the new project is to provide stronger links and cross organism querying between the MODs involved and to make query APIs available to bioinformaticians.

Meeting Almost Full, Free Workshops

There are only a few spots remaining for the October 12-13 GMOD meeting in Toronto Canada. The slate of talks is growing and this will certainly be an interesting meeting. See the meeting page for more information about the meeting, including the two keynote speakers we will have.

To register, go to the meeting registration page at EventBrite.

While you are there, you register for the free workshops on the following day:

1. BioMart from 9:00 to 12:30
2. Galaxy from 9:00 to 2:00
3. MAKER from 2:30 to 5:00

Space is limited for them too, so register as soon as you can. You do not need to attend the main GMOD meeting to attend one of the workshops.

See you in October,

Scott Cain

CARD

New Database Announcement

The Michael G. DeGroote Institute for Infectious Disease Research and the laboratory of Dr. Gerry Wright at McMaster University, Canada announces the beta release of The Comprehensive Antibiotic Resistance Database (CARD; arpcard.mcmaster.ca). CARD is a bioinformatic database of antibiotic resistance genes, their products and associated phenotypes that uses Chado and a custom Antibiotic Resistance Ontology as its core organizing principle. It serves as a basis for organizing antibiotic resistance molecular data and as a platform for de novo annotation of new genomic and metagenomic DNA sequence information.

Andrew McArthur

UC Davis Courses this September

The UC Davis Bioinformatics Core is offering a number of courses this month that are of interest to GMOD:

Go to the UC Davis registration site and click on Start Registration for full information about each course. Space is limited (an NGS analysis course is already full).

Dave Clements

dictyBase is Hiring

We have an open position for a Bioinformatics Software Engineer at dictyBase. The job involves developing web application and middleware for
chado database as well as integration of various gmod tools (gbrowse, intermine, apollo, biomart, pathway tools etc..).
See the official posting for full details.

Galaxy is Hiring

The Galaxy project currently has open positions in both the Penn State and Emory University groups.

Penn State: System administrators/analysts

The Nekrutenko Lab at the Huck Institutes of Life Sciences at State is currently recruiting system analysts/administrators with experience in building and maintaining complex performance compute environments. The areas of immediate need include:

• Storage balancing and tiered storage
• Virtualization
• Schedulers
• Deployment of Galaxy instances and dependence management
• Relational databases and query optimization
• User management

A minimum of 5 year experience with UNIX/Linux system administration is required. Applicants should submit a CV and list of references to jobs@galaxyproject.org.

Emory University: Software Engineers and Post-Docs

The Taylor Lab in the Biology and Mathematics & Computer Science at Emory University is looking for software engineers and postdoctoral scholars to work on the Galaxy project.

We are seeking software engineers with expertise in distributed computing and systems programming, web-based visualization and visual analytics, informatics and data analysis and integration, and bioinformatics application areas such as re-sequencing, de novo assembly, metagenomics, transcriptome analysis and epigenetics. These are full time positions located in Atlanta, GA. See the official posting for full details.

Postdoctoral applicants should have expertise in Bioinformatics and Computational Biology and research interests that complement but extend the lab's current interests: The Galaxy project; distributed and high-performance computing for data intensive science; vertebrate functional genomics; and genomics and epigenomic mechanisms of gene regulation, the role of transcription factors and chromatin structure in global gene expression, development, and differentiation. See the announcement for full details.

Tripal v0.3.1b released

The Tripal development group has released an updated version of Tripal, version 0.3.1b. The new release provides the following:

• Multiple bug fixes including several for loading of FASTA, GFF and OBO files.
• The GFF loader has been expanded to support the majority of the GFF3 specification.
• An updated Tripal tutorial is now available and hosted on the GMOD website
• A VirtualBox virtual machine is now available for download on the Tripal website that has Tripal/Drupal/Chado pre-installed ready for data loading and customization.
• A version of the Tripal tutorial is available for the virtual machine image
• The extension modules for Blast, KEGG, GO, Interpro and Unigene have all been updated for this new version and are also available for download.

Thanks to everyone who indicated problems and provided suggestions.

ISB Leadership Nominations Open

The International Society for Biocuration (ISB) is a professional organization about and for biocuration. GMOD and ISB have a strong relationship and the April 2012 GMOD Meeting will be colocated with ISB's 2012 Biocuration conference.

The 2011 ISB Executive Committee elections are next month and we are now taking nominations. The Executive Committee has 9 positions, 5 of which will be on this year's ballot. Terms are for 2 years and committee members can run for reelection.

This is a great way to become directly involved with the work of the society, and contribute to the decisions that are taken on behalf of the biocuration community. However it also requires a commitment of a certain amount of time to the role. Typically this involves attending monthly teleconference meetings (1 hour) and following up on any action points from meetings, as well as promoting the ISB's activities to members and non-members.

If you are interested or have questions, please contact the ISB Nominating Committee at isbelection@gmail.com, or see the call for nominations.

Thanks,

Dave Clements

on behalf of the ISB Nominating Committee:

Maria Costanzo, Dave Clements, Dawn Field, Mike Livstone, and Michele Magrane

October GMOD Registration Open

Registration for the October 2011 GMOD Meeting is now open. Please go to http://gmod.eventbrite.com/ to register. If you register before September 13, the fee is $40; after September 13, the fee goes to $50. Note that due to space limitations, the attendance for the meeting is limited to 40 people.

Scott Cain

October 2011 GMOD Meeting

I am pleased to formally announce pre-registration for the upcoming GMOD community meeting which will take place October 12-13 in Toronto, Ontario, Canada, hosted by the Ontario Institute for Cancer Research. While the meeting page is still under construction, the registration page should be available by the end of next week, along with information about the keynote speaker(s) and logistics like hotels. In the mean time, I urge you to go to the meeting page and add suggested topics and talks to the appropriate section.

Finally, the meeting itself will be limited in size, so when registration is open, I urge you to register as soon as possible, since I may need to close registration when we are full.

Thanks and I look forward to seeing you in Toronto,

Scott Cain

GMOD @ BOSC 2011

A tentative schedule for the 2011 Bioinformatics Open Source Conference (BOSC) has been published and it features at least 8 GMOD related talks, covering Galaxy, InterMine, BioMart, WebApollo, SADI for GMOOD, and the project as a whole.

BOSC is being held as a satellite to ISMB/ECCB 2011. If you are giving a GMOD related talk or poster at any ISMB/ECCB event, please add it to the ISMB/ECCB 2011 page.

Thanks,

Dave Clements

Galaxy Project

Galaxy Workshops @ USC, June 23-24

There will be two Galaxy workshops at the University of Southern California (USC) later this month. Both are presented by Jeremy Goecks of Emory University and the Galaxy team. Both workshops are open to the public:

Galaxy: A web‐based workbench for interactive and reproducible analysis of high‐throughput sequencing data, Thursday, June 23, 2011

At Aresty Auditorium, Harylene J Norris Cancer Research Tower, USC Health Science Campus, 1450 Biggy Street

Registration is free, but required.

Progress and Challenges in Developing a Web-based Platform for Computational Biomedical Research, Friday, June 24, 2011

See USC ISI AI Seminar Page for details on time and location.

The recent reliance on computation in biology has created an informatics crisis for biomedical researchers: computational resources are often difficult to use, communicating techniques and experiments is challenging, and reproducibility is very limited. Galaxy is one approach for addressing these problems. Galaxy is a popular Web-based platform for performing accessible, reproducible, and transparent genomics research. Galaxy provides a collaborative environment for performing complex analyses with automatic and unobtrusive provenance tracking; these features allow transparent sharing of both the precise computational details underlying an analysis and also intent, context, and narrative. Based on experiences with Galaxy, Jeremy will discuss some open problems that might be addressed using artificial intelligence methods and techniques.

Tripal v0.3b Released

We are excited to announce the release of v0.3b of Tripal. This new version sports many new improvements, including the following features:

• Web-based Data Loaders (OBO, GFF, FASTA)
• Web-based Chado Installation
• Support for the Chado Stock Module
• Support for Feature/Stock Properties, Synonyms, Database References and Relationships
• Integration of Tripal with Drupal Views
• Fully customizable Page Layouts (Little to No HTML or PHP needed)
• Change in the default layout of Chado content pages
• An improved, well defined Tripal API with online documentation.

Tripal can be downloaded from the Tripal website.

There is also

• A more detailed list of new functionality
• analysis modules that previously were packaged with Tripal are now downloadable as separate extensions.
• Installation instructions
• upgrade instructions
• A tutorial based on a pre-release version of v0.3b

Please post any issues or questions about this new version to the Tripal Mailing List

Stephen Ficklin

ISGA 1.3.2 Released

ISGA 1.3.2 is now available for download.

With this release, we have moved our development and downloads to SourceForge. For the time being, installation instructions will still be hosted at the CGB.

To reiterate the changes in 1.3.2 compared to the previous version of ISGA available for download -

• New Prokaryotic Annotation Pipeline Release:
  • All calls to wu-blast programs have been replaced with NCBI blast
  • We have enabled the pathway image output for Asgard
  • Reference databases have been updated
  • Improved validation and auto-correction of Fasta input
  • Streamline output-generation and include more information in summary files

• Other New Features:
  • Pipelines are now modular and can be installed independently of the ISGA installation process
  • Workbench interface has been standardized to make adding new tools easier
  • Added PhyloEGGS tool for studying gene clusters across phylogenies of prokaryotes.
  • Added ability to "upload" files to ISGA by providing a URL
  • Fixed several instances where large files were read in entirety into memory

Cheers,

Chris Hemmerich

GMOD @ Arthropod Genomics 2011

For the fourth year in a row, there will be GMOD related workshops at the 2011 Arthropod Genomics Symposium, June 9-12, 2011, in Kansas City, Missouri, United States.

• Genome Project 101: We’ve got an assembly! Now What?

Thursday, June 9, 4:00-6:00pm, Scott Cain, Dave Clements

• Comparative genomics with the generic synteny browser (GBrowse_syn): Configuration and display of various co-linearity data types.

Saturday, June 11, 10:30-Noon, Sheldon McKay

GMOD has a strong presence in the arthropod community and many GMOD users will also be attendance. Watch the Arthropod Genomics 2011 GMOD page for additional talks and posters as the conference approaches.

See you in Kansas City!

Scott Cain, Dave Clements, and Sheldon McKay

Migration to git

Today we will start the process of migrating several of the source code repositories for GMOD projects from SourceForge svn to GitHub. The first repository to move will be the GBrowse repository (called "Generic-Genome-Browser" in the SourceForge repository), which will be moved on Thursday afternoon. Please refrain from committing changes to the SourceForge repository after 2:00PM EDT to avoid losses as a result of the move. After the move is complete, it will be announced here and on the GBrowse mailing list, and help page for using git will be set up.

Scott

OK, GBrowse and Bio-Graphics are done. For each, I replaced their master branches in svn with a MOVED.txt file that contains the URL of the repository on GitHub.

GBrowse on Github: https://github.com/gmod/gbrowse

Bio-Graphics on Github: https://github.com/GMOD/Bio-Graphics

The conversions look pretty good to me, all the branches and tags seem

to have come though fine. Please let me know if you find any problems!

Rob

Mediawiki Software Update

On Tuesday, May 10, the software that powers gmod.org, MediaWiki, will be undergoing a software upgrade and enhancement. We will be moving away from using locally created login accounts at gmod.org and instead will start using OpenID for new users. If you already have an account on the gmod.org wiki, it will remain active and you won't have to do anything. New users will be able to log in with OpenID or have an account created for them by a wiki admin.

OpenID accounts are fairly ubiquitous, with Google, Yahoo and Wordpress all providing OpenID credentials to their users, with other providers listed here. This move to OpenID should combat wiki spam that has been a problem for the last several months.

In addition to OpenID, we plan to also provide a set of Semantic MediaWiki extensions to make documenting and categorizing software easier; that should happen some time this week as well.

The planned down time for the wiki at gmod.org will start at 2:00 PM EDT and hopefully will not last very long at all (less than an hour).

Pathway Tools Flux Balance Tutorial

A workshop on the new Pathway Tools module for generating and refining metabolic flux models using the method of flux-balance analysis (FBA) will be held at SRI in Menlo Park, CA from June 21-22. FBA models are steady-state quantitative models of the metabolic network that can be used for predicting growth phenotypes under different nutrient conditions and under gene knock-outs. Pathway Tools includes support for SBML.

The purpose of the workshop is to describe the use of this new module in significant detail, to offer advice on strategies for refining FBA models, and to assist attendees in hands-on refinement of Pathway Tools based FBA models.

More details and registration are available online.

A remote online attendance option for the tutorial is available.

Please feel free to repost this announcement to any interested parties.

Regards,

Tomer Altman

Pathway Tools Training Coordinator

FlyBase jobs

FlyBase jobs

FlyBase currently has 2 job openings.

• Software Engineer - Department of Biology, Indiana University
• Senior Database Programmer - Molecular and Cellular Biology, Harvard University

Entagen Bioinformatican Wanted

Genomics Computational Biologist/Software Engineer

Email info@entagen.com with CV if interested.

Entagen (http://www.entagen.com) is a leading provider of specialized software platforms and custom software development services to biomedical research and development (R&D) organizations.

We are looking for a new member of our Boston-area based team. The successful applicant will play a key role in the development of computational approaches to the management and analysis of large-scale sequence data sets from existing sources and next-gen sequencing experiments.

Strong programming skills and deep knowledge of sequencing data and bioinformatics tools are essential.

The ideal candidate will have experience with the following things:

• The GMOD tool set
• Bioinformatics data formats and tools
• Scripting languages: Perl, Python and/or Ruby
• Java and/or Groovy/Grails programming
• Javascript/AJAX programming
• Databases (SQL and/or NoSQL)
• Linux/Unix programming, maintenance, administration

An MA/MS or Ph.D. in bioinformatics is preferred but not required. Salary will be commensurate with experience.

Entagen offers competitive salary and benefits package, including health, 401K, vision and dental coverage. You will work in a fun and creative environment with a talented group of individuals that have a passion for building great software systems.

Entagen is an equal opportunity employer, dedicated to a policy of nondiscrimination in employment on any basis including race, gender, color, age, religion and/or national origin.

Note: Please re-apply if you sent an email to the info@entagen.com address. This address wasn't routing correctly.

Positions @ Bayer CropScience

1. BioAnalyst Scientist:

You will provide support in various activities: Next Generation Sequencing (NGS) data analysis, expression data (microarrays) analysis, genomics and biological networks. The successful applicant should have a PhD or equivalent experience in (plant) genetics and/or genomics. Computer skills are not mandatory but knowledge of bioinformatics applications is required. Excellent communication skills and the ability to support and train researchers with genomics data analysis is essential.

More information: BioAnalyst Scientist

Interested in any of this position? You can apply here or send your CV to Laurent Viau

2. Bioinformatics Researcher:

You will oversee the management of -omics data (genomics, phenotypics, proteomics, metabolomics, ...), investigate the emerging methodologies/technologies in the bioinformatics domain and participate in the evaluation and implementation of new bioinformatics software. Applicants should hold a Master degree (or higher) in a relevant field of Computational Biology/Bioinformatics with at least 3 years of successful experience in bioinformatics project management. Knowledge of any of the following languages is required: Java, Python, PERL as well as knowledge about plant biology and bio-analysis is required.

More information: BioInformatics Researcher

Operating language in the company is English.

Interested in any of these positions? You can apply here or send your CV to Yann-Francois Bizouerne

Erick Antezana

JBrowse is Hiring

The lead developer on the JBrowse team is moving on to pastures new: Mitch Skinner has accepted an offer to work at an exciting new medical genomics startup (which will, for the moment, remain nameless, but keep an eye out for their launch sometime in the next year).

Mitch hopes to continue contributing to JBrowse, but this also leaves an

open position in the core team. Accordingly, we are now hiring.

Full details of the position can be found here:

http://biowiki.org/JBrowseJob

Galaxy Events: April 2011

There are a number of Galaxy-related events going on this month:

• Intro to Galaxy workshops, April 6 at University of Pittsburgh, Dan Blankenberg
• Dynamically Scalable, Accessible Analysis for High-Throughput Sequence Data, April 13 talk at BioIT World, Boston, Enis Afgan
• NBIC Galaxy Hackathon, April 13-14, Belgium; this is now full but they are still accepting proposals to work on.
• Early registration closes for 2011 Galaxy Community Conference, April 24. Register early and save 20%.

Dave Clements
Galaxy Project

Account Creation Temporarily Disabled

Due to overwhelming wiki-spam over the last few weeks, new account creation has been disabled temporarily while we assess methods of controlling the spam. In the meantime, new accounts can still be created by any of the SysOps for the wiki, including Scott Cain. Sorry for any inconvenience.

Scott Cain

GMOD Americas 2011 Report

GMOD Americas 2011 is now over. Almost 60 people participated in one or more events during the week.

The newly offered Introduction to GMOD session introduced the GMOD big picture to over 20 attendees. The two-day March 2011 GMOD Meeting featured group discussions, Eric Stone's talk on the challenges of the Drosophila Genetic Reference Panel, and 15 other talks on project status and direction, component updates, and best practices. The Satellite Meetings were more popular than ever before, with over 20 people participating. Finally, 2011 GMOD Spring Training course offered 25 participants five days of hands-on training on installing, configuring and using popular GMOD components. This GMOD course featured new sessions on InterMine and SOBA as well as updated sessions on Apollo, Chado, Galaxy, GBrowse, GBrowse_syn, JBrowse, MAKER, and Tripal. Feedback on the events will be published shortly.

Don't despair if you missed this event as the the next GMOD meeting is scheduled for October, 2011 at the Ontario Institute for Cancer Research (OICR) in Toronto, Canada. OICR was the site of the July 2008 GMOD Meeting and is the home of the BioMart and GBrowse projects.

See you in October,

Scott Cain and Dave Clements

march 2011 meeting twitter hashtag

Follow the GMOD March 2011 Meeting on Twitter at #gmod11

Planned downtime for gmod.org

At 4:00PM today, gmod.org will have a brief downtime for some software updates. It should not be gone long.

Updated: Time change to 4:00 PM EST today.

InterMine 0.96 Release

InterMine 0.96 is now released.

The new version adds a flexible way of embedding results from InterMine queries in other web pages using JSONP and a new InterMine JavaScript library. You can see a demo of this functionality here.

There are several other enhancements and fixes, see the full release notes and the upgrade instructions if you are migrating from an earlier release.

Regards,

The InterMine developers.

GMOD Helpdesk Position Open

Opening for a USER SUPPORT SPECIALIST

Are you fascinated by genomics and bioinformatics? Are you passionate about collaborative open-source software? Do you enjoy teaching and working with scientists? If so, then this position is for you.

The Generic Model Organism Database project (GMOD, http://gmod.org) is a collection of open source software tools for creating and managing biological, and particularly genomic, databases. GMOD has a large, highly distributed, and dynamic community of software users and developers. The University of North Carolina at Chapel Hill has an opening for a GMOD user support specialist, to be based at the US National Evolutionary Synthesis Center ([1]) in Durham, North Carolina, while serving the international community of GMOD users.

Job Description:

The GMOD user support specialist will maintain online documentation; respond to mailing list help requests; present tutorials; organize short courses, conference sessions and other community building activities; survey user needs, and recruit members of the community to assist with these functions. The incumbent will collaborate closely with the GMOD Coordinator (Scott Cain, The Ontario Institute for Cancer Research) and other distributed personnel. See GMOD Help Desk for more background on the activities of the user support specialist. The salary range is $68,906 to $82,687, depending on qualifications, and the incumbent will receive a comprehensive benefits package as an SPA employee within the UNC system.

Qualifications:

Required qualifications include: excellent written and verbal communication skills; team orientation with strong interpersonal skills. Preferred qualifications include: an MS or PhD in biology, computer science or related field; three or more years of experience with web programming and relational database management systems; three or more years of experience with genome database administration or curation, preferably in a GMOD environment; at least one year of experience with web content management, ideally using MediaWiki; freedom to travel 5-15 weeks/yr.

To Apply:

Please provide a cover letter and CV, including contact information for three references, to Hilmar Lapp, Assistant Director of Informatics, NESCent, at hlapp@nescent.org, and submit materials through the UNC HR website. Inquiries may be addressed to H. Lapp at by email or by phone at 919.668.5288.

Galaxy Conf. Abstracts Due Feb 28

Abstracts are now being accepted for the 2011 Galaxy Community Conference being held 25-26 May, at the Conference Centre De Werelt in Lunteren, The Netherlands. This year the conference is co-organized by the Netherlands Bioinformatics Centre (NBIC). The conference features two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your research. If you have or intend to deploy Galaxy, or if you are a tool developer or a data provider then you are strongly encouraged to attend.

Deadlines

Please contact me if you have any questions, and hope to see you in the Netherlands!

Dave Clements

Galaxy Project

GMOD Wiki Migration Complete

I am pleased to announce that the migration of the GMOD wiki is now complete, and I believe that all of the functionality in the new wiki replicates the old. In fact, the only major change as a result of this move is with respect to the RSS feed that this news item is a part of. The main differences are two fold:

1. The News page is now a collection of individual news items on the site, whereas the old News page was really one very long page, making editing it somewhat fragile. The new system should be much more robust.
2. The URL for the RSS news feed has changed, though mod_rewrite is being used on the server to transparently translate requests for the old feed into the new one. The URL for the new News feed is http://gmod.org/wiki?title=Special%3ANewsChannel&format=rss20&limit=50&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed

The procedure for creating a news entry is described at the bottom of the News page.

I would like to sincerely thank Dave Clements for his considerable help getting this new News page and feed set up.

Scott Cain

March 2011 GMOD Meeting

Registration is now open for the March 2011 GMOD Meeting. This meeting is part of GMOD Americas 2011, a week long event that includes a day of Satellite Meetings, a GMOD Course (already full), and for the first time, an Introduction to GMOD session the night before the meeting for GMOD newcomers. GMOD Americas 2011 events are being held at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States.

As with previous GMOD meetings, this meeting will have a mixture of project talks, component talks, and user talks. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now. For examples of what happens at a GMOD meeting, see the writeup of the September 2010 GMOD Meeting, or any previous meeting. GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project.

Registration for the March 2011 GMOD Meeting is

• $80 on or before February 18
• $95 after February 18

Please register early, both to save money, and ensure a spot. You are also strongly encouraged to sign up for (or propose) a Satellite Meeting. Details on transportation, suggested lodging, and other logistics are on the GMOD Americas 2011 page.

This meeting, and all GMOD Americas 2011 events, are jointly sponsored by NESCent and the Galaxy Project.

Dave Clements

Galaxy Project

Openings @ Xenbase

We have two openings (ID #9338 and #9339) for bioinformatician / software developers at Xenbase, the model organism data for the Xenopus research community. Required skills are Java, SQL, and object-oriented development. Xenbase is a GMOD user and applicants with BioPerl, Chado, GBrowse and/or Textpresso experience are strongly encouraged to apply.

Xenbase is located in Calgary, Alberta and is part of the University of Calgary.

Please see the job postings for further details.

Jeff Bowes

Xenbase

GMOD @ PAG 2011

GMOD will have a stronger presence then ever at the Plant and Animal Genome Conference (PAG 2011), being held January 15-19 in San Diego. This includes, for the first time, an all day GMOD Workshop on Wednesday, January 19th, featuring extended talks on

• MAKER: An easy to use genome annotation pipeline
• Galaxy: Analyze, Visualize, Communicate
• JBrowse: A Next Generation Genome Browser
• Tripal: A Construction Toolkit for Online Genomic Databases
• GMODviews: A web-based knowledge-base and user-configurable interface for GMOD databases and tools, including Tripal, GBrowse, and Chado DBs
• GBrowse_syn: The Generic Synteny Browser

PAG 2011 will also feature workshops and tutorials covering

• BioMart: Ensembl and Ensembl Genomes
• GBrowse: The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse
• CMap: Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses

Plus at least 25 more talks and posters about or using Pathway Tools, GBrowse, Galaxy, Cmap, Apollo, Chado, GBrowse_syn, JBrowse, BioMart, MAKER, Tripal, and the GMOD Evo Hackathon.

Many GMOD users and GMOD developers, including Stephen Ficklin (Tripal), Carson Holt (MAKER), Barry Moore (SOBA, MAKER), Dan Blankenberg (Galaxy), Mitch Skinner (JBrowse), Ken Youens-Clark (CMap), Mike Caudy (GMODviews), Rob Buels (Bio::Chado::Schema, GBrowse_syn), and Scott Cain (Chado, GBrowse, ...) will be attending PAG this year. Please seek each other out.

Dave Clements

Galaxy Project

PS: In addition, three of the GMOD developers (Dan, Mitch, Scott) are also available to visit organizations in the San Diego area during the meeting.

GMOD Roadshow in San Diego

GMOD will have a large number of representatives at Plant and Animal Genome (PAG) in San Diego this month. Three of them,

• Dan Blankenberg of the Galaxy project,
• Mitch Skinner, lead JBrowse developer, and
• Scott Cain, GMOD Project Coordinator

are available to visit organizations in the San Diego area during the conference.

If you would like to arrange a visit with Dan, Mitch, and/or Scott to discuss Galaxy, JBrowse, or any other GMOD Components, please contact Dan, Mitch and Scott directly.

Dave Clements

Galaxy Project

New GMOD.org Beta site

We have begun the process of migrating the gmod.org wiki from it server in Cold Spring Harbor to a pair of load balanced servers at the Ontario Institute for Cancer Research. The only major change in functionality is the RSS feed for news. While there still will be a news feed, it will be powered by a different Mediawiki extension (hopefully, a better one!). Please spend a little time over there testing the site and let me know if you run into any issues. Note that any additions made to the beta site will be lost when the final transition is made!

Thanks,

Scott Cain

Software Requirements V2.0

The proposed revisions to GMOD's software membership requirements have been approved.

The Version 2 requirements are:

• Meets a common need
• Useful over time
• Configurable and Extensible
• Open source license for all users
• Interoperable with existing GMOD Components
• Commitment of support
• Publicly archived mailing list (new)
• Publicly accessible code repository (new)

The revised requirements were discussed at the September 2010 GMOD Meeting, and on GMOD Mailing Lists. Not surprisingly, these uncontroversial revisions were approved in both forums (and even on Twitter).

Thanks for your help and input,

Dave Clements

GMOD Help Desk

GMOD Evo Hackathon Report

The GMOD Evo Hackathon was held November 8-12 at NESCent. The 30 participants self-organized into eight groups with at least one group addressing each of the event's three objectives. The outcomes for each group are summarized below.

GMatchbox

Worked on establishing a common database backend and JSON-based API for comparative genomics data, using several visualization tools (including JBrowse and GBrowse_syn) as targets. Will enable sharing of comparative data in multiple tools from multiple sources.

GBrowse_syn2

GBrowse_syn is built on and takes advantage of the GBrowse genome browser code and config files. However, it did not work well with GBrowse2, due to significant architectural changes. This group refactored GBrowse2 to naturally support GBrowse_syn. This work will also enable several other GBrowse1-only applications (SynView, Primer Designer, ...) to be ported to GBrowse2 as well. Two participants also became core GBrowse_syn developers.

JBrowse_syn

This group set out to extend JBrowse to be a comparative genomics browser. The group removed the existing "single genome" assumption from the code and successfully displayed several genomes in parallel. Several participants also became familiar with JBrowse code and architecture.

PhyloBox

PhyloBox is a flexible and fast web based tree visualization program. At the hackathon the PhyloBox team extended PhyloBox in numerous ways to make it a "widget" that can interact with other widgets. PhyloBox documentation was also created.

Integration PhyloBox JBrowse Integration

The group is the perfect example of the interaction that can happen at a hackathon. They worked with the JBrowse_syn, PhyloBox and GMatchbox groups to enable integration of these three technologies. This group was very helpful at getting teams to work together.

Natural Diversity and Phenotypes in Chado

This group focused on two outcomes, both relating to Chado. The first was a prototype Rails application that provided a web interface to the new Natural Diversity module in Chado. This was built on top of the emerging Chado on Rails project. The second was a better understanding, slight refactoring, and updated documentation for Chado's phenotype module.

Galaxy + HyPhy

Galaxy is both a workflow system and a means of persisting computational pipelines and results. This group worked on improving Galaxy's ability to integrate interactive tools, using HyPhy as the prototype application. The Galaxy and HyPhy code bases were modified to support this.

BioPerl

This subgroup worked on improving tree handling in BioPerl. Specifically, they addressed the handling of very large trees or large numbers of small trees. BioPerl now supports storing such trees in a lightweight database instead of in memory.

Dave Clements
GMOD Help Desk

GMOD Project Statistics Page

A GMOD Project Statistics page has been created as a place to find and record information about interest in and adoption of GMOD. This includes info on downloads, source code repository updates, mailing list traffic and membership, web site traffic, event attendance, and course applications. The numbers are pretty impressive, and the most impressive graphs (growth in mailing list volume) aren't even there yet.

If you have any statistics related to the project or GMOD Components, please add them to the Project Statistics page.

Dave Clements

GMOD Help Desk

Opening @ Cancer Research UK

The BioMart-related position that was advertised in October has been reopened.

There is an opening for a bioinformatician at the Barts Cancer Centre for Molecular Oncology and Imaging working on the Pancreas Expression Database:

... contribute to the development of the pancreatic cancer bioinformatics platform and tools. Working mainly with BioMart, the successful candidate will be expected to address bioinformatics needs related to the update, maintenance and expansion of the pancreatic expression database (www.pancreasexpression.org) to set up the Bioinformatics Infrastructure. The successful candidate will additionally be responsible for pancreatic cancer literature data curation, release cycles as well as the wider development and extension of the analytical side of this platform.

See the full announcement for details. The new application deadline is January 17.

Dave Clements

GMOD Help Desk

Searchable GMOD Mail Archive

Search Archive

I am pleased to announce that a searchable archive of all GMOD mailing lists is now available at Nabble. This archive has all GMOD Mailing Lists, no matter where they are hosted. You can search all lists at once, or just a particular list.

The archive contains all email posted since May and June of 2010, depending on list. (We are investigating options for loading email from before then as well.)

Happy searching,

Dave Clements

GMOD Help Desk

WebGBrowse Joins GMOD

WebGBrowse, a web interface for setting up GBrowse instances, is now a part of GMOD. WebGBrowse enables biologists and bioinformaticians to

1. upload genome annotation information in GFF3 format,
2. configure display of each genomic feature through simple mouse clicks on a web browser,
3. visualize the configured genome with the integrated GBrowse software.

There is no manual editing of GBrowse configuration files with WebGBrowse. WebGBrowse relieves both the burden of installing GBrowse and the need to learn the configuration semantics. It is also a good way to learn the many GBrowse glyphs and how to configure them.

WebGBrowse is a good match for any organization that has users who want to create their own GBrowse instances, but lack enough computing resources and expertise to do so. WebGBrowse was developed at Indiana University's Center for Genomics and Bioinformatics.

WebGBrowse can be downloaded and installed locally, or you can use the WebGBrowse at CGB. The source is available at SourceForge. WebGBrowse comes with a tutorial, FAQ, and a user and support mailing list.

Ram Podicheti

Center for Genomics and Bioinformatics

New Topic-Based Mailing Lists

Two new GMOD mailing lists have been created as a result of the GMOD Evo Hackathon and subsequent feedback from the community. The two lists are both based on research topics, rather than on specific components:

If you are interested in these topics, please subscribe to the lists and post any comments or questions that you just didn't know where to post before!

Thanks,

Dave Clements

GMOD Help Desk

Sr DB Programmer @ FlyBase

The FlyBase genome database project group at Harvard University is looking for a new software developer to work on Chado related activities. See the job posting for details.

Software Requirements V2.0?

GMOD's procedures and requirements for software to become a part of GMOD were codified in February 2010, following the January 2010 GMOD Meeting. These requirements were in use before February, but were not documented or consistently applied.

These Version 1 requirements are:

• Meets a common need
• Useful over time
• Configurable and Extensible
• Open source license for all users
• Interoperable with existing GMOD Components
• Commitment of support

We'd now like to add two new requirements that probably should have been there in the first version:

1. Component has a support mailing list that is publicly archived
2. Publicly accessible code repository

We discussed these changes at the September 2010 GMOD Meeting , and attendees recommended they be implemented. We are now contacting the community at large (you!) to solicit feedback on the proposal.

If you have any comments, please post them to the membership requirements thread on the gmod-devel list in the next two weeks. If we reach consensus and approval, we'll update the requirements.

Dave Clements

GMOD Help Desk

GMOD Spring Training: Apply Now

Applications are now being accepted for the 2011 GMOD Spring Training course, a five-day hands-on school aimed at teaching new GMOD administrators how to install, configure and integrate popular GMOD Components. The course will be held March 8-12 at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, as part of GMOD Americas 2011.

These components will be covered at the school:

Apply Now

Apollo - genome annotation editor Chado - biological database schema Galaxy - workflow system GBrowse - genome viewer GBrowse_syn - synteny viewer GFF3 - genome annotation file format and tools InterMine - biological data mining system JBrowse - next generation genome browser MAKER - genome annotation pipeline Tripal - web front end to Chado databases

The deadline for applying is the end of Friday, January 7, 2011. Admission is competitive and is based on the strength of the application, especially the statement of interest. The 2010 school had over 60 applicants for the 25 slots. Any application received after deadline will be automatically placed on the waiting list.

The course requires some knowledge of Linux as a prerequisite. The registration fee will be $265 (only $53 per day). There will be a limited number of scholarships available.

This may be the only GMOD School offered in 2011. If you are interested, you are strongly encouraged to apply by January 7.

Thanks,

Dave Clements

GMOD Help Desk

Phenotype RCN Launched

We are pleased to inform you that NSF has recently funded the Phenotype Research Coordination Network (RCN) for researchers who are interested in searching and comparing phenotypes across species and in developing the tools and methods needed in making this possible. The representation of morphology, behavior and other phenotypic features using computational methods such as ontologies and controlled vocabularies is in its infancy. Integrating phenotypes with data across all levels of the biological hierarchy, however, is possible if standards are co-developed and coordinated.

This RCN envisions building a broad base of community knowledge and resources so as to maximize the research potential of web-based data. Funding for participation in meetings, presentations and laboratory exchanges for students, postdocs and faculty from ontology and taxonomic domains (initially plants, arthropods, and vertebrates) is available through the RCN.

We are eager to have you join us! Please sign up for our participant and mailing lists for further information and feel free to contact one of the PIs: Paula Mabee, Andy Deans, Eva Huala, and Suzanna Lewis.

Hope to hear from you soon,

Paula, Andy, Eva, and Suzanna

Help Desk Transition

After three years at the GMOD Help Desk I have decided to take a similar position with the Galaxy project, starting on January 1. I'll still be a part of the GMOD community (and I will still be involved in planning GMOD Americas 2011), but I will no longer be GMOD project staff. I have enormously enjoyed my time on this project and I have learned a lot from working on the project and with the community.

This transition make this an ideal time to reconsider and reconfigure what the GMOD Help Desk does. The Help Desk's current core tasks will continue, including:

• User help
• Web site and documentation
• Training, outreach, and community building
• Developer support

What should the balance be between these tasks? What additional tasks should be added to the mix? If you have any suggestions on how the position should evolve, please send them to the Help Desk. We'll compile your ideas and use them to guide the next incarnation of the help desk.

We are also looking for someone to fill the updated position. If you know of anyone, or are interested yourself, then please contact us as well. It's a great job and there is no better community to work with.

Thanks for everything. It's been a great three years.

Dave Clements

GMOD Help Desk (for one more month)

Virtual Issue in Journal Database

I recently had a chat with one of the editors of the journal Database, an open access journal whose aim for publications lines up very nicely with the goals of GMOD. During this discussion, the idea of a GMOD virtual issue came up, and it is one that I am very excited about. Therefore, I'm reaching out to you (the GMOD community) for ideas as well as commitments to write peer reviewed articles for this publication. Articles can be about theory, tutorial or community. I expect we'll have papers covering many components and for some components we will have multiple papers with different emphases (for example, Chado theory, Chado tutorial, and Chado community papers). Please contact me if you'd like to discuss this further.

The virtual issue approach that Database takes is very appealing, in that the submitted papers do not need to be in by a certain cutoff date, as this is not going to put into a "dead tree" form :-) So, the virtual issue can be created at any point, either when there is just one paper, or when there is a critical mass (which we would have control over), and more papers can be added to it at any time. An example of a Database virtual issue is the one they created for the Biocurator meeting last year.

I look forward to your ideas and commitments!

Scott Cain

GMOD Project Coordinator

December 2010 Calendar

There are almost no submission deadlines in December. (However, to buck the trend, the deadline for applying to the 2011 GMOD Spring Training School will probably be in December.) There are a number of interesting events though:

• BioInfoSummer 2010 and the NETTAB Workshop on Bio-wikis (these both start in November and end in December)
• Automated Imaging and High-Throughput Phenotyping
• International Digital Curation Conference
• Australasian Ontology Workshop
• EMBO Course o Bioinformatics and Comparative Genome Analysis
• International Conference on Genome Informatics

If you know of any upcoming events that are not on the calendar, please send them to me.

Happy holidays,

Dave Clements

GMOD Help Desk

GMOD Americas: March 2011

GMOD Americas 2011 has been scheduled for March 5-12 at the National Evolutionary Synthesis Center (NESCent), in Durham, North Carolina. GMOD Americas 2011 will include:

• March 2011 GMOD Meeting

The next GMOD Community Meeting will be held March 5-6. For the first time, it will be preceded by an Introduction to GMOD session on the evening of March 4. This session will be targeted at GMOD newcomers.

• Satellite Meetings

GMOD community members gather to discuss and work on common topics of interest.

• 2011 GMOD Spring Training

A 5 day GMOD Course covering installation, configuration and integration of GMOD Components.

The details for each of these will be filled in shortly. In particular, we expect to start taking applications for the course in December. Registration for the meetings will likely open in January.

In the meantime, if you have any topics you want to discuss at the Community Meeting or the Satellite Meetings, please add your idea to the meeting page, or contact the GMOD Help Desk.

Mark your calendars!

Dave Clements

GMOD Help Desk

Positions @ JCVI

From the Galaxy mailing list:

We have a few open Bioinformatics/Software Engineers positions at the J.Craig Venter Institute,

one of which involves largely developing further the Galaxy platform for use in-house (writing additional Galaxy wrappers for internal pipelines / tools, integrating Galaxy with existing cluster systems, SGE etc.)

Besides working with Galaxy, these positions involve quite a broad range of software development opportunities (languages ranging from Perl to Java), while at the same time they offer great learning opportunities for working with next-generation sequencing datasets, and learning fundamental techniques related to bioinformatic analysis of these types of data.

Please pass the word, feel free to email me for additional information, or

even go to the careers page to apply.

many thanks !

Konstantinos (Ntino) Krampis, Ph.D.

Bioinformatics Engineer
J.Craig Venter Institute

Comparative Genomics Workshop

The Workshop on Comparative Genomics is being held in Český Krumlov, Czech Republic, 9-21 January 2011. The workshop consists of a series of lectures, demonstrations and computer laboratories that cover various aspects of comparative genomics. Faculty include Anton Nekrutenko leading a session on Galaxy and Sheldon McKay leading a session on GBrowse_syn.

The course is designed for established investigators, postdoctoral scholars, and advanced graduate students. Scientists with strong interests in the uses of short-read sequence data, analytical methods, comparative structure of genomes, SNP detection and analysis, CNV, genome visualization tools and related areas are encouraged to apply for admission. Lectures and computer laboratories total ~90 hours of scheduled instruction. No programming experience is required.

The official application deadline has passed, but there are still a few openings for qualified candidates. There are also some openings in the Workshop on Molecular Evolution, being held immediately after.

Modware Status Update

Good news and update on the current status of Modware development. Modware is getting back on track and is currently being actively developed at dictyBase since last few months. It is being written using Moose and DBIx::Class (more precisely Bio::Chado::Schema or BCS) ORM. This part of development is done in sync with dictyBase's major data migration project which includes literature and gene ontology annotations. So, the first release of this new version is expected to deal with publication and ontology datasets in Chado. Handling of feature module will be added after the first release gets settled down. Like any other standard Perl module Modware's public release will be available from CPAN and the bleeding edge can be grabbed from github.

Relevant documentations and guidelines will also be added to the GMOD wiki. The first CPAN release is expected to be early next year.

Thanks,

Siddhartha Basu

Modware developer, dictyBase

Opening at Cancer Research UK

There is an opening for a bioinformatician at the Centre Barts Cancer Research UK for Molecular Oncology and Imaging working on the Pancreas Expression Database:

... contribute to the development of the pancreatic cancer bioinformatics platform and tools. Working mainly with BioMart, the successful candidate will be expected to address bioinformatics needs related to the update, maintenance and expansion of the pancreatic expression database (www.pancreasexpression.org) to set up the Bioinformatics Infrastructure. The successful candidate will additionally be responsible for pancreatic cancer literature data curation, release cycles as well as the wider development and extension of the analytical side of this platform.

See the full announcement for details. A related position in the same group is also open. Applications close 12 November.

Dave Clements

GMOD Help Desk

Pathway Tools 2010: Virtual, Now

We are offering individuals the ability to attend presentations at the Pathway Tools Workshop remotely. We will be broadcasting the presentation slides via WebEx, and you can hear the voice of the presenter by calling in to a conference call. Please see the workshop teleconference page for information on how to connect via WebEx and how to call into the conference call. See the Workshop agenda, for complete talk titles and times.

Feel free to forward this announcement to interested colleagues.

If you experience any difficulties with connecting, please contact PTools Support <ptools-support@ai.sri.com>

Best regards,

Tomer Altman

Pathway Tools Workshop Coordinator

November 2010 Calendar

November has a number of deadlines and meetings:

Deadlines

• PAG 2011 abstract deadline for posters and demos - November 1
• SWAT4LS: Semantic Web Applications for Life Sciences posters and demos
• Rocky '10 early registration

Conferences, Meetings, and Courses

• ASHG: This include two workshops on Galaxy and is preceded by an OpenHelix workshop that covers BioMart and Galaxy.
• Computational & Comparative Genomics Course at CSHL: This will also include sessions on BioMart and Galaxy.
• GMOD Tools for Evolutionary Biology Hackathon
• InterMine Workshop
• Automated Functional Annotation and Data Mining Course
• BioInfoSummer 2010
• NETTAB Workshop on Bio-wikis

If you know of any upcoming events that are not on the calendar, please send them to me.

Thanks,

Dave Clements

GMOD Help Desk

Pathway Tools 2010 Deadline!

Registration for the Pathway Tools Workshop 2010 closes in two days, on Thursday, October 21. The workshop is being held next week in Menlo Park, CA. This workshop is oriented around SRI's Pathway Tools software and BioCyc Database Collection and will explore pathway bioinformatics and Pathway/Genome Databases.

It will combine presentations by groups outside SRI, tutorials by SRI staff, and a hackathon. See the workshop website for more information and registration link.

Dave Clements

GMOD Help Desk

InterMine 0.94.1 Release

InterMine 0.94.1 is now released, and available as a subversion branch and zip file.

0.94.1 contains fixes for bugs discovered by users when upgrading to 0.94 and a number of minor enhancements.

InterMine 0.94 is a major release with many new features, including:

• a new full text search over the entire database
• template queries with optional constraints
• selection of multiple values in template query constraints
• layout improvements to the template query form
• drag/drop selection of constraint order when creating templates
• better automatic data model generation from the Sequence Ontology
• sequences stored as CLOBs in the database
• major data loading and query/export performance improvements
• export of query results direct to Galaxy

See the full release notes for 0.94 and 0.94.1, and the upgrade instructions if you are migrating from an earlier release.

As always, let us know if you have any problems or questions.

Regards,

The InterMine developers

GMOD Europe 2010 Report

GMOD Europe 2010 was held 13-16 September, 2010 in Cambridge, UK. More than 60 people attended one or more of the events during the week. The September 2010 GMOD Meeting kicked off GMOD Europe 2010. Summaries of all 19 talks are now available on the September 2010 GMOD Meeting page. Talks were given by GMOD users, developers and staff, including:

• The Open Microscopy Environment: Open Informatics for Biological Imaging
• InterMine: new Mines and new features
• BioPivot
• CpG Island and STR Annotator Plugins
• Several web services and distributed resources talks:
  • GMOD RPC API: The almost RESTful GMOD API
  • CRAWL (Chado RESTful Access Web-service Layer)
  • DAS Resource Overview and Update

Plus many other excellent presentations on topics ranging from Cosmic GBrowse to GMOD Sustainability and Organization.

Two Satellite Meetings followed the GMOD meeting. These were lively discussions with ~10 participants on two topics of interest to the GMOD community:

• Post Reference Genome Tools
• Community Annotation

There is also a writeup of the satellites by Mary Mangan on the OpenHelix blog.

The week finished with a BioMart Workshop, which was full, and a InterMine Workshop that was nearly sold out as well.

Finally, I'd like to thank the Cambridge Computational Biology Institute and the School of Biological Sciences Bioinformatics Training Facility for sponsoring and hosting the GMOD Europe 2010 events. I would also like to heap copious gratitude on Gos Micklem, Shelley Lawson, Dave Judge, Xose Fernandez, Syed Haider, and Richard Smith for their work on making this event happen.

Dave Clements

GMOD Help Desk

InterMine Workshop 15-16 Nov

There will be an InterMine workshop in Cambridge, UK on November 15th-16th. You can register for both days or just attend either one.

Day One - InterMine Developers

Building an InterMine data warehouse and deploying the web application. This will use the new MineManager GUI to set up an example InterMine, load data and write a new parser to add custom data, deploy and configure the webapp including the new full text search.

Day Two (morning only) - InterMine Users

Advanced querying. A brief tour of creating custom queries, creating your own templates and using the web service API to build and run queries from Perl or Java code.

InterMine is an open source system for building biological data warehouses with a powerful web interface and query API. See FlyMine or modMine for examples. InterMine can integrate data from many common biological formats and is easy to extend to include your own data. Parsers are included to load data from Chado, Ensembl, UniProt, KEGG, PubMed, TreeFam, GFF3, FASTA, BioPax and many others.

The web application works out of the box for querying any data is easily customisable. It provides a custom query builder, template queries for creating simple 'canned queries', upload and operations on lists, graphical and statistical widgets for analysing lists of data and MyMine accounts for saving user data.

Richard Smith

Community Annotation Satellite

The report from the GMOD Europe 2010 Community Annotation Satellite Meeting is now available. Nine participants from a range of research communities gathered for several hours to discuss their experiences with and thoughts on community annotation. The report covers what has worked and what hasn't, as well as some analysis of why. It also discusses possible models for doing successful community annotation in the future. If you are interested in engaging your community to help you do annotation then I recommend reviewing this.

Many, many thanks to all who participated in this discussion and helped compile the report.

Dave Clements

GMOD Help Desk

October 2010 Calendar

October is calmer than September, but is still relatively full:

Deadlines

• SWAT4LS: Semantic Web Applications for Life Sciences abstracts
• Rocky '10 Bionformatics Conference abstracts
• Plant and Animal Genome (PAG) early registration
• EMBO Global Exchange Lecture Course on Bioinformatics and Comparative Genome Analysis registration

Conferences, Meetings, and Courses

• Biocuration 2010
• Pathway Tools Workshop
• Programming for Biology course
• Next Generation Sequencing Workshop
• RECOMB Comparative Genomics Satellite
• Automated Functional Annotation and Data Mining course
• VisWeek 2010

If you know of any upcoming events that are not on the calendar, please send them to me.

Thanks,

Dave Clements

GMOD Help Desk

InterMine Java / DB Developer

We are looking for a software developer to work with Java and PostgreSQL as part of the Wellcome Trust funded InterMine project here in the Department of Genetics. InterMine is an open source software system for building data warehouses of biological data. It can integrate data from many different formats into a central database and makes the data available to query via a flexible web application and web services. InterMine is used at several high profile genomics databases around the world including databases that we build and maintain in Cambridge. See InterMine.org for more information. Core InterMine development is carried out by a team of developers at Cambridge University. We need a developer to work on all aspects of the server side InterMine code, in particular taking responsibility for the database access and performance of the system.

See the position announcement for full details. The closing date for applications is 24 September 2010.

Richard Smith

BioMart Openings @ OICR

The Ontario Institute for Cancer Research (OICR) has four BioMart or BioMart-related openings:

• Bioinformatician/Data Manager
• Outreach and Training Coordinator ICGC DCC
• Database programmer/Technical Analyst
• Scientific Associate Computational Biology

The BioMart biological data warehouse system is developed at OICR. Please see the job postings for additional details.

Dave Clements

GMOD Help Desk

JBrowse 1.1 Released

JBrowse version 1.1 is released! You can find the code here.

What's new:

• Scalability: JBrowse can now handle very large data tracks, including human EST/SNP tracks, or tracks of next-gen sequence reads. Large datasets are broken into smaller chunks, so there is no loading delay for big tracks.
• Extensibility: A Perl module (ImageTrackRenderer.pm) for creating user-drawn image tracks is now available, based on the CPAN GD.pm module. An example program is provided, draw-basepair-track.pl, that uses this module to draw arcs over a sequence representing the base-pairing interactions of RNA secondary structure.
• Bug fixes: Numerous display glitches have been fixed, including issues with wide-screen monitors and long mostly-offscreen features.

Note: The JSON format used by 1.1 is not backward compatible with previous releases. If you are upgrading from an older version of JBrowse, you will have to regenerate all the JSON files on your server.

See the release notes for full details.

Mitch Skinner

The TopoView Glyph Needs You!

TopoView is a GBrowse glyph created by Victor Strelets at FlyBase to show large amounts of quantitative data in limited screen space. TopoView does this with a 3D plot, showing each new set of data just below and offset from the previous data set. It was developed to display RNA-Seq data.

Josh Goodman presented TopoView at the January 2010 GMOD Meeting, and also discussed it with many attendees at ISMB 2010 (and I'm sure will be willing to discuss it at GMOD Europe 2010 next week). There is a lot of interest in TopoView becoming a standard GBrowse glyph. However, as Victor explains in this posting, TopoView is not yet ready for general release It needs some more work before it is ready for production.

If you are interested in helping get this glyph production ready and in the released glyph set, then please contact Victor. He is looking for folks to help get this out there.

Thanks,

Dave Clements

GMOD Help Desk

InterMine/BioMart Job @ FlyBase

FlyBase is looking for a qualified software engineer to undertake a project to deploy the InterMine and BioMart data management systems. The developer will be responsible for the web and database aspects of these technologies, which will be hosted at the Indiana University FlyBase site in Bloomington, IN. This includes the initial setup and configuration of these two systems, setting up and automating update cycles in sync with the existing FlyBase release cycle, evaluating the capabilities of each, aiding in the integration of these services with existing FlyBase reports and tools, and coordinating these efforts with other model organism databases (MODs). Loading and preprocessing of data for these systems will be performed at the Harvard University FlyBase site so close coordination with developers there will also be required. See the position announcement for details.

GMOD Europe 2010 Update

GMOD Europe 2010 starts in less than two weeks. If you are planning on attending and haven't yet registered, then please do so in the next few days. The BioMart Workshop has only a few slots left, and the registration fee for the GMOD Meeting goes from £50 to £65 on 6 September. We are encouraging people to submit topic suggestions for the GMOD Meeting and the GMOD Satellite Meetings.

We are also pleased to announce that Jason Swedlow of the University of Dundee will be the guest speaker at the GMOD Meeting. Jason will speak on The Open Microscopy Environment: Open Informatics for Biological Imaging, a particularly timely topic as many researchers move into image intensive areas such as phenotypes and gene expression, and as high-throughput imaging platforms become available.

There is still space available at all 4 events, and registration for the GMOD Satellite Meetings, InterMine Workshop and BioMart Workshop are free.

Scott Cain and Dave Clements

Biocuration 2010

I would like to encourage the GMOD community to consider attending Biocuration 2010, being held October 11-14 in Tokyo, Japan. Biocuration is one of the most directly relevant conferences to research communtities working with biological databases. It is sponsored by the International Society for Biocuration (an organization which I strongly encourage GMOD members to join).

Biocuration 2010 "aims to invite all biocurators and their colleagues, providing them with a platform where all the participants including speakers and chairpersons can have intimate discussion and exchange of information under superb environments."

The ISB would particularly like to encourage students and new curators (with less than 5 years of experience) to attend. The ISB is sponsoring the registration fees for 5 students and 5 curators. To apply, please send a request to the ISB before September 6, including the abstract of your presentation. Note that you must be an ISB member to apply for sponsorship. If you are not already a member, you can sign up here. Early bird registration also closes September 6.

Dave Clements
GMOD Help Desk

ISGA Joins GMOD

ISGA, Integrative Services for Genomic Analysis, is now a part of GMOD. ISGA is a biologist-friendly web interface for running and customizing Ergatis bioinformaitics pipelines with integrated tools for visualizing and searching results. ISGA was originally built for prokaryotic genome annotation and we have added a prokaryotic assembly pipeline, and transcriptome annotation and functional genomics pipelines are under development.

A public instance of ISGA is available at http://isga.cgb.indiana.edu. ISGA is also available for download and has a mailing list and development blog. You can read the ISGA manuscript in Bioinformatics

ISGA is currently under active development at the Center for Genomics and Bioinformatics at Indiana University, and developers or other community members interested in contributing should join the mailing list.

Chris Hemmerich

September 2010 Calendar

There's a lot going on in the next 5 weeks that is of interest to the GMOD community. September will be one of our busier months. Upcoming events include:

Deadlines

• Apply to participate in the GMOD Evo Hackathon (August 25)
• Pathway Tools Workshop early registration (September 1)
• Plus deadlines for PAG 2011, RECOMB Comparative Genomics, Automatid Imaging and High-Throughput Phenotyping

GMOD Europe 2010

• 4 days of events in Cambridge UK including the September 2010 GMOD Meeting, GMOD Satellite Meetings, an InterMine Workshop, and a BioMart Workshop (which is almost full)

Lots of relevant conferences

• IWGD, HIBB, Personal Genomes, BioCreative, AMATA, Genome Informatics, BioImage Informatics, Data Sharing International, PRIB, InCoB, ECCB, and Computational Biology

Training

• Bioinformatics Short Course, Ensembl Developers Workshop

If you aren't going to something in September, then you aren't trying!

Thanks,

Dave Clements

GMOD Help Desk

Opening @ Phytozome (JGI)

Phytozome has an opening for a web developer. Phytozome is the public portal to JGI's extensive plant genome data and analysis. The developer in this position will be responsible for creating web interfaces using PHP, CSS, and advanced Javascript. Both the absolute quantity and diversity of plant genomic data produced and integrated by the JGI will be increasing dramatically over the next few years. This is an opportunity to apply your web design and coding skills to an area of biological research undergoing explosive growth and change, working with the JGI's scientists, computational biologists, and developers in a state-of-the-art computational environment.

Phytozome currently incorporates GBrowse and Biomart, as well as Jalview, Lucene, and MView, and will be integrating Galaxy and Chado over the next 12 months.

Please see the job posting for more information on this position.

Chado 1.11 Release

I am pleased to announce the 1.11 release of Chado, the GMOD schema and related tools. The file can be downloaded from SourceForge

In this release, the schema itself has not changed since the 1.1 release in May of this year, but there have been bug fixes (see release notes; thanks to Naama Menda for those fixes) and one added functionality to the materialized view tool. This functionality was required to support full text searching that will be included in the up coming release of the Chado GBrowse adaptor, Bio::DB::Das::Chado.

Also note that the name of the release has changed: previously, releases of the Chado schema were called "gmod" (gmod-0.003, gmod-1.0, and gmod-1.1), but that led to a couple of different kinds of confusion, so with this release going forward, the releases will be called "chado-*".

Since the schema didn't change, if you already have a 1.1 schema and

want the bug fixes and added functionality, all you need to do for installation is to go up to the install step and stop there, i.e.:

perl Makefile.PL
make
sudo make install

Happy GMODing and please direct questions about this release to the schema mailing list,

Scott Cain

GMOD Europe 2010

We are pleased to announce GMOD Europe 2010, four days of GMOD events being held 13-16 September 2010, at the University of Cambridge. GMOD Europe 2010 includes:

Registration is now open for these events. There is a £50 registration fee for the GMOD Meeting to cover catered lunches, coffee/tee breaks, and other expenses. Registration for all other events is free. Please register soon, as space is limited.

See you in Cambridge!

Scott Cain and Dave Clements

PS: If you have topics you want to have covered (or you want to cover) at the GMOD Meeting, or at the Satellite Meetings, please add them to the meeting page, or to the Satellite Meetings list, or contact us. We are also looking for guest speaker nominations for the meeting.

GMOD Evo Hackathon Open Call

We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, being held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC.

This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research:

1. Visualization of comparative genomics data
2. Visualization of phylogenetic data and trees
3. Support for population diversity and phenotype data

If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed!

See the GMOD Evo Hackathon Open Call for details, and for a link to the application form. Applications are due August 25.

The GMOD Evo Hackathon Organizing Committee:

Nicole Washington, Robert Buels, Scott Cain, Dave Clements, Hilmar Lapp, and Sheldon McKay

GMOD Nomination: ISGA

I would like to nominate ISGA for GMOD Membership. ISGA is a bioinformatics pipeline service based on the Ergatis workflow system. ISGA comes with prokaryotic annotation and assembly pipelines and offers an intuitive interface for biologists to run and customize pipelines. ISGA also integrates tools such as GBrowse and BLAST for visualizing and analyzing pipeline results. Since ISGA utilizes Ergatis, ISGA pipelines can be submitted back to the Ergatis community and Ergatis pipelines can be adapted to use ISGA.

ISGA (pronounced "I-S-G-A") was created at Indiana University's Center for Genomics and Bioinformatics (CGB) by Chris Hemmerich, Aaron Buechlein, Ram Podicheti, Kashi Revanna, and Qunfeng Dong. CGB also hosts a public installation of ISGA.

I believe that ISGA meets all of GMOD's membership requirements. The CGB is willing to support ISGA for at least 2 years. ISGA could be useful to anyone working with complex pipelines and is directly applicable to existing and potential Ergatis users. Please see the ISGA page for more information.

If you have any feedback or comments on ISGA becoming a part of GMOD, please send send it to the help desk by August 6.

Thanks,

Dave Clements

GMOD Help Desk

August 2010 Calendar

There's not a lot going on in August but what is going on is significant. First there are submission deadlines for the International Digital Curation Conference (IDCC), and Data Integration in the Life Sciences (DILS 2010). Several noteworthy conferences are also happening:

• ACM International Conference on Bioinformatics and Computational Biology
• YAPC::Europe 2010
• DILS 2010
• International Workshop on Genomics Databases (IWGD)
• High Performance Bioinformatics and Biomedicine (HiBB)

And, sometime in the next month GMOD will

• formally announce GMOD Europe 2010 and
• start taking registrations for the September 2010 GMOD Meeting

If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.

Thanks,

Dave Clements

GMOD Help Desk

GMOD: Spread the Word!

Do you use GMOD tools in your research? If so, then you can help others and GMOD by getting the word out about GMOD and its tools.

There are many ways to do this: cite GMOD in publications, put a Powered by GMOD icon on your web pages, invite a GMOD speaker to your institution or event, include information on GMOD in your presentations. See the GMOD Promotion page for these and other ideas.

Increasing GMOD's visibility has many benefits:

• It introduces biologists to tools that can help them learn from and exploit their data.
• Increased visibility will lead to increased adoption of GMOD tools.
• Increased adoption leads to more people contributing back to the project.
• Increased adoption and development helps GMOD and GMOD components get grant funding.

Finally, GMOD can also help raise the profile of your GMOD-related talk or event by advertising it on GMOD resources.

Please let me know if you have any questions or requests, and please help get the word out.

Thanks,

Dave Clements
GMOD Help Desk

ISMB 2010 Talks & Posters

You can now view most of the GMOD-related presentations and posters from ISMB 2010. This includes

• Deploying Galaxy on the Cloud, Enis Afgan
• Automated Annotation of NGS Transcriptome Data using ISGA and Ergatis, Chris Hemmerich
• GMOD Presents GBrowse 2.0 and JBrowse, Scott Cain
• An Advanced Web Query Interface for Biological Databases (Pathway Tools), Peter Karp
• Galaxy NGS functionality from sample tracking to SNP calling, Ramkrishna Chakrabarty

Plus additional talks and posters on GBrowse, DIYA, Pathway Tools, and Galaxy.

Dave Clements

GMOD Help Desk

Hiring @ Dolan DNALC

There's an opening (Job ID 934) at the Dolan DNA Learning Center (DNALC) of Cold Spring Harbor Laboratory for a programmer to develop cyberinfrastructure to support plant biology research. The programmer will work with a multi-disciplinary team to design, develop, and maintain applications for interfacing public APIs, SQL databases, and large data sets.

The successful candidate should come from a bioinformatics background that includes work with BioPerl, genome databases (such as Chado), browsers, and annotation tools. Expertise in Java, SQL and database schema, and Unix/Linux are essential. Experience developing web user interfaces – templating, Javascript/AJAX, DOM, and CSS – is also desirable.

For more information, go to the CSHL jobs site and search for Job ID 934.

GBrowse 2.13 Release

GBrowse version 2.13 has been released. 2.13 is a maintenance update to 2.12. GBrowse 2.13 and 2.12 include these changes:

New features & enhancements

• The DAS server and client are now functional. You will need Bio::Das version 1.17 and Bio::Graphics version 2.11 for best results.
• The "import track" function now allows you to specify the URL of either a BAM or a BigWig file. The track will be displayed without physically copying the file onto the GBrowse server. You will need Bio::DB::Sam and Bio::DB::BigWig for these features to work.
• Uploading a Wig file now generates a BigWig database for improved performance and scalability. This requires Bio::DB::BigWig to be installed.
• There is now a Get chromosome sizes entry in the File menu.
• Calling GBrowse with the CGI argument action=scan will generate a quick summary of track contents.
• Improved performance when working with truly huge (>1000 track definition) configuration files.
• Fasta, GFF3, SAM and wiggle dumps now include the genome build ID if that information is provided in the data source "metadata" configuration variable.

Bug fixes

• When MySQL is used as the back end for user uploads, it will no longer fail on long filenames.
• Fixed the "eurl" CGI parameter for importing data sets by their URLs.
• Fasta and GFF3 dumps are now working when invoked from the File menu.
• Fixed SAM file processing so as not to die when presented with a SAM @SQ header. This requires Bio::DB::Sam 1.20 to work properly.
• Fixed upload listing table so as not to duplicate track labels.
• Fixed track importation via the eurl parameter so that it works when the user's uploadid is empty (due to clearing cache of cookies).
• Fixed DAS server handling of the link option.

Please use the GMOD bug tracking system to report bugs or feature requests.

Lincoln Stein

Pathway Tools Workshop 2010

Registration is now open for the Pathway Tools Workshop 2010, held October 25th - 29th, 2010 in Menlo Park, CA. Early registration ends September 1.

This workshop is oriented around SRI's Pathway Tools software and BioCyc Database Collection and will explore pathway bioinformatics and Pathway/Genome Databases.

The workshop will combine formal presentations by groups outside SRI International (invited speakers and speakers selected through an abstract-submission process), tutorials by SRI International staff, and a hackathon. Suggested topics include but are not limited to:

• Advances in pathway bioinformatics, model organism databases, genome annotation, and systems biology
• Scientific results achieved with Pathway Tools and BioCyc
• Share expertise on how to develop new organism-specific databases with Pathway Tools
• Share experiences on how to make the most of Pathway Tools
• Presentations by users on extensions they have developed to Pathway Tools
• Presentations by SRI International on recent and planned developments to the software, and on software APIs and the database schema, to educate users on how to compute with PGDBs

Please visit our registration website for details on speakers, fees, travel, and hotels.

Looking forward to seeing you at an upcoming Pathway Tools event.

Best regards,

Tomer Altman

Galaxy Community Tool Sharing

We have introduced a new Galaxy tool sharing community site. The site currently allows you to upload an archive consisting of a single tool, but will soon allow you to upload an archive consisting of a suite of tools. To learn how to use the community site, click on Help → How to upload, download, and install tools.

We hope that you will find this site useful for hosting tools that you would like to contribute and share.

We'll keep you informed as the site's features evolve.

Greg Von Kuster

Logo Program Logos!

Some of the new logos

The Spring 2010 Logo Program was a smashing success and 9 projects now have eye-catching logos that give each resource a strong graphic brand identify. See the Spring 2010 page for a complete list of logos, as well as some of the alternatives that were not chosen.

I would like to thank

• The design students who worked with the participants to understand their projects and produce an excellent set of logos to pick from.
• John Aikman of the Graphic Arts Department at Linn-Benton Community College (LBCC) for being willing to take a chance on this program, and for being willing to work with to hammer out the details.
• And the participants for being willing to work the students to help them gain experience and to understand the projects they were creating logos for.

The GMOD Logo Program might return in the future. Please watch the GMOD News for details, probably later this year. In the mean time, if you would be interested in participating in the next one, please let me know. The more people I hear from, the more likely it is to happen.

Thanks,

Dave Clements

GMOD Help Desk

GMOD @ ISMB 2010

ISMB runs July 9-13 this year and GMOD has a strong presence on the program:

• talks on Galaxy, GBrowse, JBrowse, Pathway Tools, WebGBrowse, ...
• a tutorial on Galaxy,
• many posters, and
• several Special Interest Group (SIG) meetings relevant to GMOD members.

See the GMOD @ ISMB 2010 page for a full listing of GMOD related content, including a session listing you can print in advance. See the ISMB 2010 web site for more on the conference.

Dave Clements

GMOD Help Desk

GMOD Meeting: Sept. 13-14

Thanks to the prep work by Gos Micklem at Cambridge, I am pleased to announce that there will be a two day GMOD community meeting starting on Monday September 13 in Cambridge, England. This meeting occurs immediately prior to the Genome Informatics meeting in Hinxton (for which the abstract deadline is June 25). Registration information for this meeting will be available in a few weeks. In the mean time, you can post topic suggestions to the meeting page.

Please feel free to tell your colleagues and to post to mailing lists that you think would be interested in this meeting.

I look forward to seeing you in England this Fall.

Scott Cain

New GMOD Tutorials

Detailed and hands-on online tutorials are now available for the GMOD Components that were covered at the 2010 GMOD Summer School - Americas. Each tutorial includes a VMware system image to work with, and detailed instructions on how to setup the component on that image. This year we have a Galaxy Tutorial for the first time.

The tutorials are:

• Apollo Tutorial - by Ed Lee
• Chado Tutorial - by Scott Cain, Dave Clements, and Joshua Orvis.
• Galaxy Tutorial - by James Taylor
• GBrowse Tutorial - by Scott Cain
• GBrowse_syn Tutorial - by Sheldon McKay
• JBrowse Tutorial - by Mitch Skinner
• MAKER Tutorial - by Carson Holt
• Tripal Tutorial - by Stephen Ficklin

The 2010 GMOD Summer School - Americas got the best reviews of any course GMOD has ever done. I'd like to thank this year's instructors and participants for making it such a success.

Thanks,

Dave Clements

GMOD Help Desk

ISGA Pipeline Service

Integrated Services for Genomic Analysis (ISGA) is an Ergatis-based bioinformatics pipeline service based at Indiana University's Center for Genomics and Bioinformatics. ISGA is also a free, open-source software package that you can install locally to provide a biologist-friendly web interface to your computational resources. ISGA currently provides prokaryotic annotation and prokaryotic assembly pipelines and offers an intuitive interface for biologists to run and customize pipelines. ISGA also integrates tools such as GBrowse and Blast for visualizing and analyzing pipeline results. Since ISGA utilizes the Ergatis workflow system to execute pipelines, ISGA pipeline can be submitted back to the Ergatis community and other Ergatis pipelines can be adapted to use ISGA. (See Ergatis Update below for what's new with Ergatis.)

For more on ISGA, see the manuscript "An Ergatis-based prokaryotic genome annotation web server" in Bioinformatics, the ISGA pipeline and account tutorials, and the ISGA FAQ page. For help using or installing ISGA, join the isga-users mailing list.

Chris Hemmerich

MAKER 2.0, AGS Workshop

MAKER, the easy to use genome annotation pipeline, is now version 2.0.

Some of the current features and other improvements

• Improved gene model preparation and evidence filtering...
• mRNAseq data in your annotations (use output from programs like TopHat, CuffLinks, and others in MAKER)...
• Annotate eukaryotes and prokayotes...
• Pass through any kind of evidence evidence from any source via GFF3 pass-through...
• Easy single-command-line dump of MAKER output to a Chado database and to JBrowse...
• Same directory parallelization - just start MAKER on top of itself, and it will share the workload with the new process...
• Auto recovery - start, stop, and restart MAKER at any time; MAKER will always just pick up where it left off...
• optional web base GUI for a local MAKER installation

There will also be a workshop on MAKER on June 12 at the 4th Annual Arthropod Genomics Symposium in Kansas City. If you are attending AGS and are interested in genome annotation, please consider attending.

Thanks,
Carson Holt

Load Chado into BioMart

A group at INRA URGI have documented "How to load a Chado database into BioMart". This step by step document details what how to configure BioMart for Chado, and includes some specific use cases useful with Chado. This guide is based on experience at INRA URGI, and was written by Aminah Keliet, Joëlle Amselem, Sandra Derozie, and Delphine Steinbach.

If you are interested in loading your Chado data into a BioMart instance then I recommend starting with this guide.

Thanks,

Dave C.

GMOD Help Desk

June 2010 Calendar

The next 5 weeks includes the a MAKER workshop at the Arthropod Genomics Symposium, and deadlines for ISMB (Boston in July), AMATA (Hobart in September), GIW (Hangzhou in December), ECCB (Ghent in September), InCoB (Tokyo in September), and Genome Informatics (Hinxton in September).

If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.

Thanks,

Dave Clements

GMOD Help Desk

gmod (Chado) 1.1 Released

I am pleased to announce that we released gmod-1.1 today. This release has the GMOD database schema, Chado, and a variety of tools for loading and working with the database. The release can be downloaded from the GMOD SourceForge site.

There have been many people who have helped with getting this release done and I would like to thank all of them. I would like to especially thank Rob Buels and Naama Menda and the rest of the people at the Sol Genomics Network (SGN) for their code contributions, including a pub table loader that works with PubMed and an updated version of the script to calculate cvterm closures.

There have been many changes and bug fixes since the 1.0 release just over two years ago, but the schema itself has changed very little.

For a SQL summary of the changes, see Changes.sql in the release that contains SQL statements that should take a 1.0 release of the Chado schema to the 1.1 schema. See the Changes file for a full list.

If you have been using Chado from a recent svn checkout, you don't need to modify your schema at all, since the last change to the schema was about a year ago.

Now that this release is out, the plan going forward is for frequent, smaller releases, with an eye on the Natural Diversity schema modifications being worked on now.

Thanks for your continued support of the GMOD project,

Scott

GMOD in Boston in July?

From Scott on 2010/05/25:

Scott Cain sent this question about the next GMOD meeting out to several mailing lists on May 17:

Scott hasn't heard back, yea or nay, from very many people so far and we need to make a decision as soon as possible. If you have any thoughts on this, please send them to Scott before 3pm Eastern US time on Monday, May 24. See the GMOD Calendar for a list of what else is going on in July.

Thanks,

Dave C.

GMOD Help Desk

Ergatis Update

The paper "Ergatis: A web interface and scalable software system for bioinformatics workflows" is now available as an advance access manuscript in the journal Bioinformatics. Ergatis "enables users to build, execute, and monitor pipelines for computational analysis of genomics data."

Ergatis now includes pipeline templates for prokaryotic genome annotation and comparative genome analysis, as well as 174 modular 'components' that can be used to create custom pipelines, all of which can be executed either locally or on large compute clusters.

New tools available that use Ergatis include CloVR, which enables bioinformatic pipeline execution in compute clouds and the recently-awarded Data Intensive Academic Grid (DIAG), which will provide a publicly-accessible Ergatis instance as one of its access methods. At the January 2010 GMOD Meeting Chris Hemmerich presented ISGA, which provides a customized, abstract interface to Ergatis designed for biologists with specific pipeline needs.

Joshua Orvis

May 2010 Calendar

The next 5 weeks includes the 2010 GMOD Summer School - Americas and the first Galaxy Developers Conference. Upcoming deadlines include the ISMB technology track (tomorrow), posters at Arthropod Genomics and ECCB10, and papers for GIW 2010.

If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.

Thanks,

Dave Clements

GMOD Help Desk

MaizeGDB: Choosing GBrowse

A paper, "Choosing a genome browser for a Model Organism Database: surveying the Maize community," by the MaizeGDB team has been published in Database. To prepare for the availability of a reference genome, MaizeGDB surveyed their community to assess genome visualization needs. This paper summarizes the survey and MaizeGDB's review of available browsers, and describes why they chose GBrowse. The paper finishes by describing how they implemented GBrowse, including the locus lookup tool (described here), a MaizeGDB extension that uses maize's extensive physical and genetic mapping data to localize genomic regions in GBrowse. This is a great paper for anyone considering which genome browser to use.

I'd also like to highlight the journal the paper appears in: Database: The Journal of Biological Databases and Curation. "Biological Databases and Curation" are what GMOD is about and many of the papers cover issues and resources that are widely applicable in the GMOD community. The current issue also includes papers on community annotation using wikis, and a report on best practices in genome annotation from the ISB 3^rd International Biocuration Conference. Database is an open access publication, making it an even better match for GMOD.

Dave Clements

GMOD Help Desk

YAPC::NA 2010 is Almost Here!

June 21st – 23rd 2010 is quickly approaching and Columbus.PM is getting very excited. Hotel reservation information is available, dorm reservation details are up and ready, the conference is quickly approaching. For everyone still looking for YAPC::NA 2010 (Yet Another Perl Conference North America) details, here is what we have planned. The conference will be held in the brand new beautiful The Ohio State Union.

Larry Wall, Damian Conway, Randal Schwartz, and many others will be in attendance.

The main dorm location is Morrison Tower and the Hotel conference block is in The Blackwell Inn (see Accommodations). Early registration is quickly coming to an end so make sure that you forward this to all of your friends and coworkers and get signed up

today!

I hope to see you all at YAPC::NA 2010 in beautiful Columbus, Ohio.

Heath Bair

YAPC::NA 2010 Conference Chairman

Don Gilbert Nominated for BFA

The Bioinformatics Organization has announced its nominees for the the 2010 Benjamin Franklin Award.

This year's nominees include longtime GMOD contributor Don Gilbert, of Indiana University. Other 2010 nominees are Alex Bateman, David J. Lipman, G.P.S. Raghava, and John Quakenbush. Previous winners of the BFA include Jim Kent, Michael Ashburner, and another long-time GMOD contributor Lincoln Stein.

If you want a say on who should receive the 2010 award, please go to Bioinformatics.org and cast your vote. If you are not already a member you will need to join, but basic membership is free.

Dave Clements

GMOD Help Desk

April 2010 Calendar

There's a lot on the calendar in the next 5 weeks, including (among others) registration deadlines for Arthropod Genomics (early) and the Galaxy Developers Conference, and submission deadlines for ECCB, iEvoBio, BOSC, and ISMB.

If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.

Thanks,

Dave Clements

GMOD Help Desk

Google Summer of Code & OBF

Great news: the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for this summer's Google Summer of Code!

GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see the GSoC 2010 FAQ.

Student applications are due April 9, 2010 at 19:00 UTC. Students who are interested in participating should look at the OBF's GSoC page, which lists project ideas, and who to contact about applying.

For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project's GSoC wiki page.

Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code!

Rob Buels

OBF GSoC 2010 Administrator

InterMine is Hiring

We have four vacancies on InterMine related projects at The University of Cambridge, UK. We are looking for a Web Developer, Bioinformatics Software Developers and a Java Developer. See the position descriptions for more information.

The closing date for applications is 2nd April 2010.

The InterMine Team.

Internships @ Dow AgroSciences

Dow AgroSciences has 7 Bioinformatics summer internship positions open, 2 of which are related to GMOD. We are looking for candidates with experience in installing, configuring, and uploading data into GMOD. Experience with the GBrowse source code and modifying it to create new views (e.g creating new glyphs and modifying existing glyphs as per user needs) is highly preferred. We have started the interview process. Please email your resume ASAP to Navin Elango (nelango@dow.com). For more information about Dow AgroSciences, please visit our website

Navin Elango

Sr. DB Programmer @ FlyBase

FlyBase has a single opening for a developer to join the database team at Harvard University in Cambridge, Mass. The position consists of roles in two model organism database projects, VectorBase and FlyBase, in the development and maintenance of production applications involving Chado, Apollo, Ensembl, and InterMine. For more information, see the job posting.

Dave Emmert

NGS Analyses in Galaxy

The Galaxy team is announcing the launch of the first free public resource for NGS analysis. This service is the beginning of our campaign to provide free web-based utilities for NGS analysis and later in the year will take advantage of the Cloud resources. At present, there are three main groups of tools including:

1. NGS QC and manipulation - contains a variety of tools for dealing with all flavors of fastq datasets as well as outputs of SOLiD and 454 instruments.
2. NGS Mapping - currently includes Bowtie (Illumina & SOLiD), BWA (Illumina), and LASTZ (454) mappers. PerM (SOLiD) is on the way and more will be added in the coming months. Transcriptome tools are also in the final stages of development.
3. NGS SAMTools - includes a variety of utilities for SAM/BAM manipulation. Some are based on SAMtools library, some are written by Galaxy team.

See the announcement page for more information and for links to several Galaxy Quickies (video tutorials) demonstrating the new service.

Anton Nekrutenko

Openings @ SGD

There are 3 openings for Scientific Application Programmers at the Saccharomyces Genome Database (SGD), the model organism database for yeast. These positions will be involved in enhancing databases and data pipelines for the sharing of genomic data. See the job postings for more information.

SGD is both a GMOD contributor (e.g., BLAST Graphic Viewer) and GMOD user.

Logo Program Deadline Extended

The first call to participate in the GMOD Logo Program has been extended to March 19.

We still have some room for additional participants. If you are interested, please submit an application. Participation is limited to non-profits, and costs US$75. Please see the program page for additional details and requirements, and a link to an application form.

Thanks,

Dave Clements

GMOD Help Desk

March 2010 Calendar

There is always a lot going on that is of interest to the GMOD community. Anything that GMOD staff knows about is added to the GMOD Calendar. I'm going to start posting the GMOD calendar here for the upcoming month.

Please let me know if this is useful, and I'll keep doing it. If not, I'll stop and the GMOD News will be a little less cluttered.

Thanks,

Dave Clements

GMOD Help Desk

GMOD Logo Program, Spring 2010

I am pleased to announce the first call for participation in the GMOD Logo Program. This program is for GMOD users and developers that would like a custom designed logo for their web site, database or software. This spring we will be working with students in an advanced design class at Linn-Benton Community College. Interested GMOD users and developers will be paired with students and meet several times (remotely) over a 3 week period this spring, with the end result being a new logo.

Participation is limited to non-profits, and costs US$75. If you are interested, please see the program page for additional details and requirements, and an application form. The program is accepting applications until March 1.

Thanks,

Dave Clements

GMOD Help Desk

GMOD Summer School - Americas

We are now accepting applications for the 2010 GMOD Summer School - Americas. This will be a hands-on multi-day course aimed at teaching new GMOD administrators how to get GMOD Components up and running. The course will introduce participants to the GMOD project and then focus on installation, configuration and integration of popular GMOD Components.

The course will be held May 6-9, at NESCent in Durham, NC. These GMOD Components will be covered:

The deadline for applying is the end of Friday, February 22. Admission is competitive and is based on the strength of the application (especially the statement of interest). In 2009 there were over 50 applications for the 25 slots. Any applications received after the deadline will be automatically placed on the waiting list.

Thanks,

Dave Clements

GMOD Help Desk

GMOD @ February NextGenBUG

If you are anywhere close to Dundee, Scotland on 9 February, consider attending the NextGen Sequencing Bioinformatics User Group (NextGenBUG) meeting being held at the University of Dundee. The program includes two talks with GMOD related content.

• InsectaCentral - assembling and annotating insect transcriptomes, Alexie Papanicolau, Exeter

  InsectaCentral uses GMOD Components (including Chado and GBrowse) extensively in its infrastructure.

• Galaxy: a stairway to NGS heaven, Chris Cole, Dundee

  Chris will be discussing how Dundee uses Galaxy to process their next generation sequencing data.

There will also be talks by Dan Bolser of Dundee and Darrol Baker of CLCBio. If you are interested in attending, please add your name to the participants list.

Dave Clements

GMOD Help Desk

GBrowse 2.0

With thanks to the many people who have worked long and hard on this project, as well as the people who found and reported bugs during the prerelease stage, I am happy I announce that GBrowse 2.00 is now available for downloading from CPAN, and SourceForge.

The following are highlights of the many new features that have been added since the 1.70 release:

• A completely rewritten internal rearchitecture loads tracks asynchronously, providing a more responsive user experience.
• Different database backends can be associated with each track, making backend management much simpler.
• A revamped user interface for a less cluttered and more functional end-user experience.
• A UI theming system with three predefined themes, including a cool "transparent" theme.
• A custom track upload and management system gives users much greater control over custom tracks.
• An optional admin interface allows an authorized user to upload and manage public tracks without editing config files.
• An optional user registration and login system allows users to register stable GBrowse accounts and to keep their settings and custom tracks when they move from one computer to another.
• Support for named subtracks (tracks within tracks) and filtering of those subtracks.
• Support for next generation sequencing data.

There are also a number of features that didn't make it into the 2.00 release, most notably:

• The internal DAS server does not work, although the DAS client (ability to import DAS tracks) does. This will be added in a 2.01 release.
• Internationalization has lagged way behind, and so most of the new features will be presented in English rather than in the user's preferred language (volunteers are needed to help with translations).

Please send help queries to the GBrowse mailing list, and file bug reports at SourceForge.

On behalf of the GMOD team,

Lincoln Stein

WebGBrowse 2.0

WebGBrowse 2.0 is now available at http://webgbrowse.cgb.indiana.edu. Here is some of what's new in WebGBrowse 2.0:

• WebGBrowse 2.0 continues to help the inexperienced users of GBrowse with hosting their GFF3 data without worrying about installation or configuration semantics.
• Users now have a choice of GBrowse display between versions 1.7 and 2.0.
• The display from one version can be migrated to the other by simple button clicks. This helps the users to compare their data display between the two versions without much hassle. It also helps the WebGBrowse users in upgrading/migrating their existing GBrowse displays to version 2.0 seamlessly.
• A few bug fixes from the earlier version.
• For those interested in installing WebGBrowse locally, the current installation package is lot more easier to install and less clumsy than the previous version.

Thanks,

Ram Podicheti

Center for Genomics and Bioinformatics
Indiana University

Tripal v0.2 Released

I’d like to announce the release of the second version of Tripal, v0.2. This version provides new support for controlled vocabularies, databases and several analysis types. This includes better support and visualizations for GO, new KEGG pathways and BRITE hierarchies, InterProScan results and improved BLAST results.

Tripal has been freely and publicly available since May of 2009 and provides a PHP-based Drupal front-end for the Chado database schema. It his highly customizable and is extendable by anyone with Drupal and PHP experience. We encourage end-users to develop new or improved modules that can be shared back with the community. We can offer assistance when needed in the development of new modules.

An updated user’s manual is available, but not quite complete. An update to the manual will be added soon. If you have any questions please feel free to email the Tripal mailing list for assistance.

Tripal can be downloaded from the CUGI website as a compressed package, or developers can retrieve the most up-to-date code from the GMOD SVN.

Best Regards,

Stephen Ficklin

Clemson University Genomics Institute

CMap3D

CMap3D is a 3D visualisation tool for comparative genetic maps that runs on top of a CMap database. CMap, a GMOD component, is a common tool for the storage, comparison and visualisation of genetic maps. However, current map visualisation in CMap is limited to the comparison of adjacent aligned maps. CMap3D overcomes this limitation. Multiple genetic maps can now be compared in three-dimensional space. The CMap3D visualisation tool is based on a client server model ensuring operability with current CMap data repositories.

CMap3D can be applied to any species where genetic map information is available and enables rapid, direct comparison between multiple aligned maps. For more on CMap3D see the CMap3D page at the Australian Centre for Plant Functional Genomics (ACPFG), the PAG 2010 presentation on CMap3D (and other tools), and the CMap3D paper in Bioinformatics.

Chris Duran

DAS Workshop 7-9 April 2010

There will be a Distributed Annotation System (DAS) Workshop at EBI, 7-9 April 2010. In GMOD, DAS is supported by GBrowse, and Chado (and DAS support in Apollo is in the works).

If you don't know about DAS and wish to know how to distribute your latest biological annotation to the world then the upcoming DAS workshop may be for you.

If you know about DAS and are maybe a DAS client developer then the upcoming DAS workshop is for you (as you will need to know about the upcoming DAS 1.6 Specification and how it may affect your software).

See the workshop page for more information and registration details.

Jonathan Warren

GBrowse.org

GBrowse.org

GBrowse.org is a resource for using and setting up GBrowse genome browsers. The site provides one location where biologists and bioinformaticians can find:

1. Genome browser web sites for any organism that has them. If a species has a genome browser anywhere on the web, then we aim to link to it.
2. Links to sequence and annotation files that are available online.
3. Links to genome browser configuration files, when available
4. An FTP site containing genome annotation and configuration files for each annotated genome that does not have its own web site.

GBrowse.org emphasizes the GBrowse genome browser in its organization, but also links to sites that use other browser packages such as UCSC, Ensembl, and JBrowse.

GBrowse.org was first introduced at the August 2009 GMOD Meeting.

Ciao,

Alessandra Bilardi

CRIBI Genomics, University of Padua

Bio::Chado::Schema 0.05 Released

I'd like to announce a new Bio::Chado::Schema release, version 0.05. Changes in this release:

• Got POD generation working, now all classes and methods have POD, including the embedded table and column comments! Thanks to the wonderful DBIx::Class::Schema::Loader folks.
• Turned off DBIC's cascade_delete and cascade_copy on all relations (thanks to Siddhartha Basu for troubleshooting). Deletes break if these are on and you don't have every part of the schema installed.

I uploaded it to CPAN a week ago, so it should have propagated by now to almost all of the CPAN mirrors.

See the Bio::Chado::Schema wiki page for more on what Bio::Chado::Schema is and what it's for.

Rob Buels

SGN

GMOD at PAG 2010

GMOD will once again have a strong presence at the Plant and Animal Genome Conference (PAG 2010), being held January 9-13 in San Diego. There will be over 45 talks, workshops, demonstrations and posters about GMOD Components and projects that use them. See the PAG 2010 page for a full listing and a flier showing highlights. Highlights at PAG 2010 include:

• Animal Genomics with Galaxy, Saturday
• MAKER: An easy to use genome annotation pipeline, Saturday
• Database Resources at the EBI (including BioMart), Sunday
• The Generic Genome Browser: A Hands on Workshop, Sunday
• GBrowse And Next Generation Sequencing Data, Monday
• GMOD Project Update, Monday
• Using the JBrowse Genome Browser with Large Amounts of Data, Monday
• Visualizing And Comparing Genomes (CMap), Monday
• Comparative Genomics Tools In GMOD, Monday
• Using Gramene (including CMap), Tuesday
• Comparative Genomics with GBrowse_syn, Wednesday
• Tripal: a Construction Toolkit for Online Genomic Databases, Wednesday

Many GMOD staff and developers (Scott Cain, Dave Clements, Stephen Ficklin, Carson Holt, Sheldon McKay, Anton Nekrutenko, Mitch Skinner, Ken Youens-Clark) and even more GMOD users will be at PAG. If you are attending please keep an eye open for us.

Finally, the January 2010 GMOD Meeting is being held immediately after PAG. The meeting is full (you are encouraged to add your name to the short waiting list), but there will be several Satellite Meetings, held during PAG, that you can attend even if you don't go to the main GMOD Meeting.

See you in San Diego,

Dave Clements

GMOD Help Desk

Galaxy Developer Conference

The First Galaxy Developer Conference will be held at Cold Spring Harbor Laboratory May 15-17, 2010, immediately after the Biology of Genomes conference. Registration is now open.

This meeting is aimed at developers of analysis tools, bioinformatics staff, and IT managers of sequencing facilities. The meeting will focus on these features of the Galaxy framework:

• tool integration and distributed job management
• deployment of private Galaxy instances on local resources and on the cloud
• management of large datasets with the Galaxy Library System
• using the Galaxy LIMS functionality for managing sample submission at NGS sequencing facilities.

Please register now if you are interested in using and extending Galaxy.

Dave Clements

GMOD Help Desk

Arthropod Genomics Consortium

The Arthropod Genomics Consortium encourages collaboration and information exchange amongst arthropod researchers. The consortium, launched at the 2009 Arthropod Genomics Symposium, has now started a wiki to enable this community to self-organize:

Our goal is to provide a central location for information about arthropod genomics projects, bioinformatics tools, and people interested in arthropod genomics. We think this is a great way to "identify the community"; information from the wiki can be used to support white papers and grant proposals. It will also serve as a central location for links to arthropod genomics resources, news releases and meeting announcements.

Sue Brown, Director, K-State Arthropod Genomics Center

If you are an arthropod researcher, please consider joining this growing consortium.

Dave Clements

GMOD Help Desk

BioPerl Podcast

A podcast on the BioPerl project is available at FLOSS Weekly. It's about an hour long and it's a good introduction to BioPerl, a set of libraries that many popular GMOD Components are built upon. The podcast is an interview with BioPerl heavy hitters Chris Fields and Jason Stajich.

Dave Clements

InterMine 0.92 Released

We have released version 0.92 of InterMine.

The main changes are some improvements to the way integration keys and priorities are configured and validated, a BioPax parser, performance enhancements and some webapp fixes.

Version 0.92 has Release Notes and upgrade information.

Upgrade should be quite straightforward from either 0.9 or 0.91. The

only issue is compatibility of the GO enrichment widget with old databases built before 0.91.

Let us know if you have problems or suggestions for the next releases.

The InterMine team.

CMap Paper in Bioinformatics

A paper describing the CMap comparative map viewer is in the current issue of Bioinformatics:

CMap 1.01: a comparative mapping application for the Internet, by Ken Youens-Clark, Ben Faga, Immanuel V. Yap, Lincoln Stein and Doreen Ware.

CMap is a web-based tool for displaying and comparing maps of any type and from any species. Users can compare an arbitrary number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession.

See the CMap page to learn more. CMap will also be covered in the Gramene workshop and in a poster at PAG 2010.

Dave Clements

GMOD Help Desk

January 2010 GMOD Meeting

I am pleased to announce that the January GMOD meeting will be taking place on January 14 and 15, 2010 in San Diego at the Best Western Seven Seas (the same location as last year). Please see the meeting page for registration information.

Please also take a moment to add suggestions for the agenda. There is no registration fee for this meeting. However, there is limited space, so please register early.

The proprietors of the Best Western have given us an excellent room rate, and extended it to the previous week, so that people attending the GMOD meeting and the Plant and Animal Genome meeting before it may stay at the Best Western the entire time.

Please direct follow up questions to the gmod-devel mailing list (gmod-devel@lists.sourceforge.net).

Thanks and I look forward to seeing you in San Diego!

Scott

Long Term Database Funding

You may have heard about TAIR's funding situation. Basically, their funding is being cut by 25% per year, starting in September 2010, and NSF is encouraging them to find alternative funding sources. This news was sent to the TAIR community (and posted on the Biocurator list) on October 22. A day later the paper "Models for financial sustainability of biological databases and resources" appeared in Database: The Journal of Biological Databases and Curation.

All GMOD users need to give at least some thought to long term funding issues. A discussion thread on long term database funding has now been started on the International Society for Biocuration's (ISB) forum site.

TAIR asked people to do a couple things:

1. Cite TAIR in publications: as a reference, as a source of data in methods sections, and under acknowledgments.
2. Contribute to a discussion on the TAIR web site about
   1. the bioinformatics needs of the Arabidopsis and wider plant biology communities and
   2. how resources like TAIR should be funded.

The discussion at TAIR is now 19 pages long and contains mountains of praise for TAIR, and a few suggestions on alternative funding, including subscriptions, international and industrial support, and advertising. It also contains many statements that none of those options will work. The Database paper discusses similar proposals, plus some others.

If you are interested in long-term funding issues, I encourage you to participate in the discussion at ISB. If you use TAIR and want to see it funded, please post a comment at the TAIR web site. And, if you aren't already doing so, make it easy for your users to cite your database by including an easy to find "Citing this resource" link on your site.

Dave Clements

Two Openings at Bayer CropScience

1. BioAnalyst Scientist:

You will provide support in various activities: Next Generation Sequencing (NGS) data analysis, expression data (microarrays) analysis, genomics and biological networks. The successful applicant should have a PhD or equivalent experience in (plant) genetics and/or genomics. Computer skills are not mandatory but knowledge of bioinformatics applications is required. Excellent communication skills and the ability to support and train researchers with genomics data analysis is essential.

More information: BioAnalyst Scientist

2. BioAnalyst Researcher:

You will support and foster the data management and analysis of Next Generation Sequencing (NGS) data (assembly, processing, development of analysis methods, pipelines, etc.). Candidates must be highly motivated to work on biological questions and flexible to interact with the various groups of the research center. They should have a degree (MSc or PhD) in computational biology, boinformatics, statistics or equivalent level of knowledge and possess some programming skills (e.g. perl and/or python). The candidate should have a good background in (plant) genetics and/or genomics and/or molecular biology.

More information: BioAnalyst Researcher

Operating language in the company is English.

Interested in any of these positions? You can apply here or send your CV to Laurent Viau

Erick Antezana

GBrowse NGS Tutorial & Poster

A tutorial on using GBrowse 2 to visualize next generation sequencing (NGS) data is now available. The tutorial walks through how to configure the GBrowse 2 genome browser to display next generation sequencing (NGS) data using the SAMtools GBrowse adaptor, Bio::DB::Sam. This tutorial was originally taught at the Bioinformatics Australia 2009 (BA2009) GMOD Workshop. The tutorial includes a VMware image to work with and step-by-step instructions for visualizing the example human data that comes with the SAMtools package.

The tutorial includes examples showing read depth coverage, individual reads - including mismatches, using color to show alignment quality, and read-pairs.

A poster (by Scott Cain) demonstrating how to use the adaptor with GBrowse 1 and GBrowse 2 is also available.

Dave Clements

GMOD Help Desk

Galaxy Project Hiring

There are several open software engineer and postdoc positions with the Galaxy project. Galaxy is looking for engineers with with experience in distributed computing, visualization, and usability. The positions will initially focus on making next generation sequencing (NGS) data analysis more widely accessible, transparent, and reproducible, as well as development of bioinformatic tools in areas enabled by NGS: re-sequencing, de novo assembly, metagenomics, transcriptome analysis and epigenetics. Postdoc positions will address biological questions (e.g., mutagenesis and sex chromosome evolution from NGS data) using Galaxy tools.

See the official posting for full details and contact information.

Visualizing Biological Data Workshop

The first EMBO Workshop on Visualizing Biological Data (VizBi) will be held 3-5 March 2010, at the EMBL Advanced Training Centre in Heidelberg, Germany.

The goal of the workshop is to bring together researchers developing and using visualization systems across all areas of biology, including genomics, sequence analysis, macromolecular structures, systems biology, and imaging (including microscopy and magnetic resonance imaging). The primary focus will be on visualizing processed and annotated data in their biological context, rather than on processing of raw data.

The workshop is limited in the total number participants, and each participant is normally required to present a poster and to give a fastforward presentation about their work (limited to 30 seconds and 1 slide). To apply to join the workshop, please submit an abstract and image related to your work. Submissions close on 16 November 2009.

Openings at Syngenta

There are two openings at Syngenta, recently named one of the top biotechnology employers by Science, in Research Triangle Park, NC.

Genomic Database Specialist (#1435): We are currently using the Chado schema, and this individual will be responsible for maintaining and optimizing database systems for genome annotation and related information. Experience overseeing database systems is required and experience with Oracle and PostgreSQL is desirable. The ideal candidate will have a solid understanding of genomics and a background in a life sciences setting. Strong competency with Unix and Perl is required.

Genome Annotation Specialist (#1434): This individual will be responsible for implementing automated annotation pipelines for genome, transcript, and proteins sequences. Advanced knowledge of sequence analysis tools is required. Experience with modern high throughput sequencing analytics is desirable. A strong competency with Unix and scripting in a language such as Perl is required.

Both positions will work with Chado and GBrowse, and will help evaluate the adoption of additional GMOD tools. See the links for more details.

Eric Ganko

Opening at SGD

There is an opening for a Bioinformatics Analyst at the Saccharomyces Genome Database (SGD), the model organism database for yeast.

The position includes interacting with international research laboratories, working with genomic data, evaluating new technologies, analysis via computational methods created by others but integrated at SGD, knowledge of new experimental methodology, large genomic datasets and their computational analysis, and bioinformatic analysis of data types such as RNA transcription and second-generation sequencing. Experience with comparative genomics is also desirable.

SGD is both a GMOD contributor (e.g., BLAST Graphic Viewer) and GMOD user, and this position will work with the GBrowse genome viewer as well as other GMOD tools.

See the Stanford jobs site (search for posting 36125) for more.

Apollo 1.11.2 Released

I've just cut a new Apollo release that fixes some GFF3 and Chado writeback issues. As usual, you can get the most current version of Apollo at:

http://apollo.berkeleybop.org/current/

Cheers,

Ed Lee

2009 GMOD Survey Results

The results of the 2009 GMOD Community Survey are now available online. This year's survey focused on genomic and comparative genomics visualization was taken by 45 respondents. The survey includes:

• Use Cases - what people would like visualization software to do.
• Feature Ranking - what features are the most (and least) important to users.
• Plus general feedback on visualization tools, documentation, and the project.

The survey results will be used to improve GMOD and guide its future direction. This year's survey complements the 2008 GMOD Community Survey, which covered all of GMOD.

And, finally, we have our 3 winners of GMOD Gear:

• James Estill of the University of Georgia
• Philippe Lamesch of TAIR
• Sandra Lövenich of ETH Zürich

Thanks to everyone who took the time to participate in the survey.

Dave Clements

GMOD Help Desk

GMOD Tutorials! GMOD Training!

Detailed and hands-on online tutorials are now available for the GMOD Components that were covered at the 2009 GMOD Summer Schools. Each tutorial includes a VMware system image to work with, and detailed instructions on how to setup the component on that image.

The tutorials are:

• Apollo Tutorial - by Ed Lee
• Artemis-Chado Integration Tutorial - by Robin Houston, Tim Carver and Giles Velarde
• BioMart Tutorial - by Junjun Zhang and Syed Haider
• Chado Tutorial - by Scott Cain, Joshua Orvis, and Dave Clements
• GBrowse Tutorial - by Scott Cain and Sheldon McKay
• GBrowse_syn Tutorial - by Sheldon McKay
• JBrowse Tutorial - by Mitch Skinner and Ian Holmes
• MAKER Tutorial - by Carson Holt
• Tripal Tutorial - by Stephen Ficklin

There is also a plethora of GMOD related training and outreach going on in the next few months. Here's what I know about:

Dave Clements
GMOD Help Desk

modENCODE & Gramene Openings

The modENCODE and Gramene projects are both hiring.

modENCODE

modENCODE is looking for a few consultants. The project's aim is to discover and explore the genomes of C. elegans and D. melanogaster, using new scientific strategies and new technologies for discovery.

Consultants will be responsible for interacting with several external research labs, as well as with internal software developers, to collect and collate experimental data

of many different types. In addition to a strong background in biology, candidates must be knowledgeable in programming and/or software development. Candidates must also possess verbal and written communication skills, particularly for understanding requirements from biologists, and to productively work in a collaborative environment.

Please see the complete job description for details.

modENCODE is a power GMOD user. The project uses GBrowse, Chado, InterMine, JBrowse, and GBrowse_syn. (See Nicole Washington's talk at the January 2009 GMOD Meeting for some details on how they are used.)

Gramene

Gramene has several bioinformatics openings in the Jaiswal lab at Oregon State University.

The positions involve development and maintenance of the databases, software and analysis pipelines necessary for development of the Plant Gene Expression, biochemical and regulatory pathway networks, comparative genomics, text mining (Textpresso) and biological ontology projects. Gramene is a long-time GMOD user and is the home of the CMap comparative map viewer.

See the position announcement for full details.

GMOD @ Bioinformatics Australia

There will be a half-day pre-conference GMOD workshop on 28 October, 2009, at Bioinformatics Australia (BA2009). The workshop will introduce GMOD Components for visualization, annotation, and data management, and the GMOD project as a whole. The workshop will also include a GBrowse demonstration with a worked example that includes next generation sequencing data.

Thanks to sponsorship from Bioplatforms Australia admission to the workshop is included in the conference registration fee.

Please see the workshop page or contact the GMOD Help Desk for more information.

Dave Clements

GMOD Help Desk

InterMine Data Warehouse Workshop

We are running another InterMine workshop in Cambridge, UK on November 16th-17th.

This is intended for software developers to learn the InterMine system. The two day course will step through creating a new Mine, integrating real data and deploying and customising the web application.

The course is free to attend, more details and sign up information

are available on the workshop page.

Please get in touch if you have any questions.

Regards,

Richard Smith

Tripal: A Web Front End for Chado

Tripal is a new web front end for Chado databases and is now a part of GMOD. Tripal is a collection of Drupal modules initially developed by the Clemson University Genomics Institute (CUGI). Tripal is already powering several web sites, including the Marine Genomics Project and Fagaceae Genomics Web.

Tripal supports Drupal themes, page content and look and feel customization, materialized views, searching, and job management out of the box.

Tripal can be downloaded from the GMOD SVN repository. Tripal (already!) has an extensive User's Guide and a tutorial to help users install, configure and extend Tripal.

If you use or are considering using Chado, please take a look at Tripal.

Dave Clements

GMOD Help Desk

Reactome User Survey

Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools. With this in mind, we are actively soliciting comments from the research community in order to assess community needs. We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools.

You can access the survey at SurveyMonkey

Thank you for taking part.

Robin Haw

Manager of Reactome Outreach Outreach [at] reactome.org http://www.reactome.org

Posted by Scott Cain

DIYA: Do It Yourself Annotator

DIYA, the Do It Yourself Annotator is now officially a part of GMOD. DIYA is a modular and configurable open source pipeline framework, written in Perl, used (initially) for the rapid annotation of microbial genome sequences. The software is currently used to take nucleotide sequence contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in GFF format. Current development seeks to integrate DIYA with the AMOS collection of assembly tools.

DIYA resides in Sourceforge, where it has mailing lists and a blog, and uses Trac for development tracking. DIYA is stable and version 1.0 has been released.

DIYA is part of the Do It Yourself Genomics (DIYG) Project. Developers of DIYA (and DIYG) include Andrew Stewart and Brian Osborne (formerly of the GMOD Help Desk). The DIYA community is looking for interested developers to contribute to DIYA. See the DIYA page for more.

Dave Clements

GMOD Help Desk

Chado in RDF: OpenFlyData

The OpenFlyData project has ported the FlyBase Chado database and several other Drosophila gene expression databases to the Resource Description Framework (RDF). Each source database has a separate RDF store, and OpenFlyData provides both a browser and a programmatic SPARQL-based interface to each. Source databases include the Chado database from FlyBase, BDGP, FlyAtlas and FlyTED.

Transforming databases into RDF can be an effective way to merge these data, and does not require mapping everything to a central relational schema. The common graph-based data model facilitates the reuse of RDF data published by other projects, with fewer constraints on the kind of questions you can ask.

For more on OpenFlyData, see the Linked Data for GMOD Databases presentation from the August 2009 GMOD Meeting, and the OpenFlyData web site.

Jun Zhou and Dave Clements

Bioinformatics Position at SpBase

The Sea Urchin Model Organism database (SpBase) has an opening for a Bioinformatician. From the position announcement:

See the job posting for more on the position. Please contact Andy Cameron if you have questions about the position.

SpBase uses several GMOD Components, including GBrowse, Apollo, BioMart, and Chado.

Dave C.

GMOD Help Desk

2009 GMOD Community Survey

Please take a few minutes to fill out the 2009 GMOD Community Survey and your name will be entered to win a free GMOD T-shirt or mug! This year's survey focuses on genome and comparative genomics visualization (and is much shorter than the 2008 survey). We are asking all GMOD users and developers to provide your feedback.

Three randomly selected survey participants will receive the GMOD T-shirt or mug of their choice. Names will be drawn from the first 100 responses, so get your response in early. The survey closes at the end of the day on September 25.

Please contact the GMOD Help Desk if you have any questions.

Thank you,

Dave Clements

GMOD Help Desk

CVS to SVN Conversion: Done

⇒

GMOD's CVS source code repository was converted to Subversion (SVN) on September 15, 2009. Directions on how to use SVN are explained at Version Control System Access. Details of the conversion itself are at CVS to Subversion Conversion.

Inactive projects were moved out of the main directory and placed in the Inactive directory. The CVS repository is still there and accessible, but it is now read-only. The GMOD web site has been updated to reflect the move to Subversion.

We have identified a few outstanding issues and these are listed on the conversion page. If you come across any additional issues, please either update that list or email the GMOD Help Desk.

Finally, many thanks to Rob Buels of Cornell / SGN for doing the work.

Dave Clements

FlyBase Bioinformatics Engineer

Please see the official advert for full details and application procedure.

The Indiana University division of FlyBase in Bloomington, Indiana is currently looking for a qualified software engineer to help with deploying the InterMine and BioMart data management systems. The developer will be responsible for the web accessible aspect of these technologies. This includes the initial setup and configuration of these two systems, setting up and automating update cycles in sync with the existing FlyBase release cycle, evaluating the capabilities of each, aiding in the integration of these services with existing FlyBase reports and tools, and coordinating these efforts with other model organism databases (MODs). Loading and preprocessing of data for these systems will be performed at the Harvard University FlyBase site so close coordination with developers there will also be required.

Josh Goodman

Server Maintenance: Sept 9

  The GMOD website and server will be down for maintenance on Wednesday, September 9, 2009 for up to 90 minutes, sometime between 1pm and 5pm Eastern US time. The server is being moved to a new a data center. We apologize for any inconvenience this may cause you.

Please let us know if you have any questions.

Dave Clements

GMOD Help Desk

BioMart Ruby API

Daz Oakley of the Wellcome Trust Sanger Institute has released a Ruby library/API for BioMart. Daz says "It's quite basic for the moment and only does single dataset queries, but it will be quite easy to build upon the base from here."

The source is available from GitHub, and the documentation is at rdoc.info.

The Ruby API is the latest addition to a growing list of third party software that supports BioMart. This list includes Galaxy, Bioclipse, biomaRt-BioConductor, Cytoscape, Taverna, and

WebLab

Dave Clements

GMOD Help Desk

JBrowse paper

A paper on the JBrowse genome browser is in this month's issue of Genome Research. If you haven't looked at JBrowse before, it feels both very familiar and radically different at the same time.

JBrowse is a Web 2.0 genome browser that features:

• Client side rendering, and very fast rendering at that.
• As a consequence it has very low server disk space, server CPU, security and network bandwidth requirements.
• An interface that is entirely AJAX based. Everything is done with AJAX.
• GFF3, Chado and/or Wiggle track compatibility
• JSON based configuration files (very similar to GBrowse config files in their content)
• Easy embedding in other web applications (an example of embedding a genome browser in a wiki is provided)

JBrowse features smooth panning, zooming, navigation, and track selection and sets a new standard for the genome browser interface.

Dave Clements

GMOD Help Desk

Aug 2009 GMOD Meeting Report

The August 2009 GMOD Meeting was held 6-7 August, 2009 in Oxford, UK, immediately following the 2009 GMOD Summer School - Europe. It was the first GMOD meeting outside North America and it was an excellent way to finish GMOD Europe 2009. The meeting was attended by ~45 people representing almost 30 different organizations. The meeting report and links to presentations are now available on the August 2009 GMOD Meeting page. There were 17 presentations by GMOD users, developers, and project staff.

Some highlights:

• SAM and SAMtools: file formats and programs for compact representation of Next Generation Sequencing data, and a talk on using SAM/SAMtools in GBrowse.
• An RDF implementation of data from a Chado database.
• Reports from 2 power GBrowse users, the CBRG at Oxford, and Bayer CropScience
• New Perl and Java middleware packages for Chado.

Plus many other excellent presentations on topics ranging from DAS to GBrowse.org.

Please take a look at the meeting report for an update on what's going on in the GMOD community.

Finally, I'd like to thank the Computational Biology Research Group (CBRG) at the University of Oxford for hosting and financially supporting GMOD Europe 2009. We could not have done this without you.

Dave Clements

GMOD Help Desk

Bio::Chado::Schema 0.03 Released

The first official release of Bio::Chado::Schema is now on the CPAN. This project establishes a standard set of base modules for building Chado middleware in Perl. The project is looking for development help, and discussion is on the GMOD Schema mailing list.

--RobertBuels 22:10, 29 August 2009 (UTC)

InterMine 0.91 Released

We've released InterMine 0.91 and there is a new subversion branch and tar.gz for download. The main changes are fixes to some QueryBuilder features, occasional export issues and improved password security. There is a new TreeFam parser and an improvement to ontology querying.

This update shouldn't require any changes to Mines and sources you have created. See details on upgrading and the release notes.

Please let us know if you have any bug reports or feature requests.

The InterMine team

CVS to SVN Conversion: Sept 15

⇒

GMOD's CVS source code repository will be converted to Subversion (SVN) on September 15, 2009. Rob Buels of Cornell / SGN has generously offered to to do this. Notes on the conversion are described on the CVS to Subversion Conversion page. The discussion leading up to this decision on the GMOD Developers mailing list.

If you are not a GMOD developer then this will, at most, change how you get pre-release copies of GMOD components. In the future you will do SVN checkouts instead of CVS checkouts. The doc on this web site will be updated to describe how to do this.

See SourceForge for a complete list of projects in GMOD CVS. This list is reproduced on the CVS to Subversion Conversion page. Between now and September 15, we will contact project developers to confirm what projects are still active. All projects will be moved to SVN, but any projects that are no longer active will be placed in a separate archive directory. This will significantly clean up the repository. See the CVS to Subversion Conversion page for the current status of each project.

Rob has created a preview version of the repository. Feel free to poke around. This version does not have any projects archived.

Rob will move the projects on September 15. Before then everyone with uncommitted code changes should commit them to CVS. After September 15, all CVS checkouts you have should be removed and new checkouts made with SVN. We'll provide doc on how to do this. We will send out exact details on the move a few days before it happens.

Please let Rob and Dave know if you have any questions. We'll send out a reminder and additional info a few days before the conversion.

Thanks,

Dave Clements and Rob Buels

GBrowse 1.70 Released

Hello,

I am pleased to announce the official release of GBrowse 1.70. This is a bug fix release for GBrowse 1.69. It introduces no new functionality to the GBrowse portion of the application, however, GBrowse_syn is considerably improved along with documentation and a tutorial.

There will likely be one more release in the GBrowse 1 development path, which will introduce improved support for circular genomes. After that, development on this path will end and further development will focus on GBrowse 2.

GBrowse can be installed with the GBrowse netinstaller.

GBrowse 1.70 can be downloaded directly from SourceForge.

A big thanks to Lincoln Stein, the lead developer of GBrowse, Sheldon McKay, the developer of GBrowse_syn, and all of the GBrowse users who debug and provide help on the GBrowse mailing list.

Changes from 1.69 to 1.70:

• Bug fixes for the Chado adapter, including improving wildcard searching and fixing a bug that caused ALL features on a reference sequence to be returned when the segment was at the beginning of the reference sequence.
• Fixed Galaxy support bug which caused prevented features from multiple tracks being selected.
• Fixed problem with feature highlighting which caused highlighting to get "stuck"on beige.
• Removed annoying debugging statements from log files
• Fixed character encoding issues for onClick popup balloons
• Killed annoying "missing path" warning on windows systems
• Fixed issue in which the selected region shown in the overview is offset from true region.
• Silenced log file warnings when inkscape isn't present.
• Added "merge searches" option to turn merging of similarly-named features on and off.
• Moved Bio::DB::Das::Chado and Bio::DB::BioSQL to their own packages and out of the GBrowse distribution so they can be updated independently via CPAN
• Fixed encoding of version number at the bottom of the page.
• Made the DAS script compatible with DAS Registry

Scott

Lepidoptera Bioinformatics

A session on data analysis, mining, general bioinformatics support, and related topics will be held on Friday, August 28th 2009, at the International Workshop on Molecular Biology and Genetics of Lepidoptera in Crete. The aim is to find solutions to common problems of annotation, curation and comparative analysis of the growing body of transcript and genomic sequences for lepidopteran species. Several databases, including InsectaCentral and LepidoDB, both of which use GMOD Components, will be discussed in the workshop.

The session is held during the last conference day and is one hour long; we encourage Crete participants to talk to us during the week and point out related problems you are facing in your own work. We will then produce a list to be discussed during the session and focus on soliciting ideas on how to organize collaborative and centralized efforts to everyone's benefit. We would especially like to identify potential funding sources, groups willing to help write consultation papers and grant proposals and individuals willing to contribute to realistic solutions.

We would like to encourage those of you who are not planning to attend the Crete workshop to contact us with your thoughts and ideas on these and related subjects.

Marian Goldsmith, Alexie Papanicolaou, and Fabrice Legeai.

Ant Genomics Bioinformatician

The deadline for this position has now passed.

The Swiss Institute of Bioinformatics and the Keller lab in Lausanne have an opening for a full-time bioinformatician.

In brief, this position will focus on the assembly and annotation of genomic sequence from ants, as well as sharing the results with molecular myrmecologists via a GMOD database.

Closing date: 15 September 2009

See the official ad for full details and application procedure

Informal enquiries to yannick.wurm \at\ unil.ch or laurent.falquet \at\ isb-sib.ch

FlyBase Sys Admin/Developer

The Cambridge (UK) division of FlyBase currently seeks a Systems Administrator/Software Developer, working either full or part-time to support its team of genetic literature curators.

The core tasks of this role include systems administration and the maintenance of Perl scripts and files required by the curators in their work. These tasks will occupy approximately 50% of a full-time position, and we are happy to consider applicants who only wish to work part-time (50%) to perform these essential tasks. However, we would like to enhance the current scripts/files and develop additional software to aid curators, and the remaining 50% of the full-time position would be spent on these areas.

Closing date: 24 August 2009.

See the official advert for full details and application procedure.

Informal enquiries to Steven Marygold (sjm41@gen.cam.ac.uk).

Insect Pest Workshop, 16-17 Nov

Given the development of cheaper high throughput sequencing technologies, it is easy to predict that in the very near future, new genomes of insects relevant to agriculture will be available. This opens several other challenges such as the bioinformatics treatment of the raw data (handling of billions of sequences, assembly of short reads…) and the development of databases opened to biologists for an easy, friendly and efficient extraction of information. With access to several insect species genomes, one will not only work on their favourite insect, but will take advantage of the increasing knowledge from genomic comparison analyses. This compels the community to develop standards for different tasks towards the exploitation of genome sequences: annotation, cross-species comparisons, interoperability between databases, ... Several tools and databases already exist and are used for genome browsing and annotation.

In that context, the purpose of this workshop will be:

• To exchange within an international panel of attendants our views on the present and future of insect genome databases
• To settle an international community that will form a functional network for insect genome and database development
• To discuss strategies to meet the demand of increasing number of new insect genomes
• To prepare a new road map for integration of genomes databases for insects relevant to agriculture

The perimeter of that discussion encompasses insect species related to agriculture, either harmful (pests) or beneficial as controllers of pest populations or as producers of plant by-products (such as silk, honey, ...).

Registration for the meeting is free and has to be done online on this website and will be limited to 40 participants. A statement of interest is needed. A 10 minute presentation may be asked.

August 2009 GMOD Meeting

The next GMOD meeting will be held 6-7 August, at the University of Oxford, in Oxford, United Kingdom. Registration is now open. Space is available on a first come, first served basis and there is room for 55 attendees. The meeting cost is £50.

As with previous GMOD meetings, the meeting will have a mixture of project talks, component talks, and user talks. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now. For examples of what happens at a GMOD meeting, see the writeups of the January 2009, July 2008, or any other previous meeting. GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project.

Details on transportation, suggested lodging, and other logistics are on the August 2009 GMOD Meeting page.

Please join us in Oxford this August,

Dave Clements

GMOD Help Desk

Join ISB

The International Society for Biocuration (ISB) is now accepting member registrations. I strongly encourage GMOD community members to think about joining ISB. GMOD and ISB have many shared and complementary interests.

Membership rates start at less than US$20 for students to a little over US$100 for principal investigators from industry.

Please consider this investment,

Dave Clements

GMOD Help Desk

Apollo 1.11.0 Released

A new version of Apollo has been released. Highlights for this release include:

• The "Sequence Aligner" ("Exon Detail Editor" with alignment viewing) is now public
• Brought back the "Types panel" which works in conjunction with the the "Preferences editor"
• Various bug fixes

As always, you can download the current version at:

http://apollo.berkeleybop.org/current/install.html

Ed Lee

NextGen Sequence in GBrowse

There will be a talk on visualizing next generation sequence data in GBrowse at Next Generation Genome Analysis in Non-Model Organisms, an American Genetic Association Special Event held June 11-13, 2009 at the University of Connecticut. The talk will demonstrate how GBrowse can visualize both individual reads and summary and derived data. This talk will become a wiki page after the meeting.

June will be a busy month for GMOD outreach. If you can't make it to this meeting, there will also be GMOD workshops at SMBE and the Arthropod Genomics Symposium.

Dave Clements

GMOD Help Desk

WebGBrowse Has Arrived

WebGBrowse - A Web Server for GBrowse Configuration Made Easy

WebGBrowse is a web site that guides users through the process of creating a GBrowse configuration file and then shows them how their data renders with that configuration. Users can configure GBrowse, either from scratch, or by uploading a preexisting GBrowse configuration file. Tracks are defined using a graphical user interface where users first select the glyph to use (over 40 glyphs are currently supported), and are then prompted for that glyph's settings. Data is provided by uploading a GFF3 file.

WebGBrowse has an extensive tutorial and FAQ, and was just published in Bioinformatics. WebGBrowse is open source and can also be installed locally.

WebGBrowse was created by Ram Podicheti, Rajesh Gollapudi, and Qunfeng Dong, all of the The Center for Genomics and Bioinformatics (CGB) at Indiana University - Bloomington. WebGBrowse was first presented by Ram Podicheti at the January 2009 GMOD Meeting.

WebGBrowse is an excellent way to get started with GBrowse, and to learn what glyphs are available, and what options each glyph supports. Please contact the CGB if you have any questions.

Dave Clements

GMOD Help Desk

GMOD Workshops at SMBE, AGS

There will be GMOD workshops at two major conferences in June 2009:

	Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2009) June 3-7, 2009 Iowa City, Iowa	Database Tools for Evolutionary Genomics: An introduction to GMOD software for managing, annotating and visualizing genomic data Saturday, June 6, 2:30-5:00pm This workshop will cover some of the most widely used GMOD software components, including the Chado database, the GBrowse genome browser, the CMap comparative map browser, and the Apollo genome curation tool. The workshop will also cover, in some depth, the GBrowse_syn comparative genomics viewer, and the MAKER genome annotation pipeline for eukaryotes. Speakers (Ben Faga, Sheldon McKay, Mark Yandell, and Dave Clements) will address both existing functionality and ongoing developments specifically targeted at better supporting evolutionary data and research. No knowledge of programming is necessary.
	3rd Annual Arthropod Genomics Symposium June 11 - 14, 2009 Kansas City, Missouri	Chado Databases and Integration with GMOD Tools Pre-Symposium Workshop - Thursday, June 11, 4:30-6:30 p.m. Scott Cain, Ontario Institute for Cancer Research, will provide training on Chado database design, data loading and exporting, and integration with other GMOD tools such as Apollo and GBrowse. Particular emphasis will be given to comparative genomics tools. There is no cost to attend this optional workshop, but registration is requested.

Please let Dave (SMBE) or Scott (AGS) know if you have any questions about the workshops.

Thanks,

Dave Clements

GMOD Help Desk

Pathway Tools Workshop, August

There will be a Pathway Tools Workshop, August 19-28, 2009 at SRI International. This two-part workshop covers Pathway Tools and the BioCyc Database Collection.

Part 1: Tutorial, August 19-21

This introductory tutorial will educate the new user on aspects of Pathway Tools including basic use of the Pathway/Genome Navigator, Editors, and PathoLogic. Students can bring a genome and leave with a draft Pathway/Genome Database.

Tutorial space is limited.

Part 2: Workshop August 24-28

The workshop will combine formal presentations by groups outside SRI International (invited speakers and speakers selected through an abstract-submission process), tutorials by SRI International staff, and a hackathon. Suggested topics include but are not limited to:

• Share expertise on how to develop new organism-specific databases with Pathway Tools
• Present new scientific results achieved with Pathway Tools and BioCyc
• Share experiences on how to make the most of Pathway Tools
• Presentations by users on extensions they have developed to Pathway Tools
• Presentations by SRI International on recent and planned developments to the software, and on software APIs and the database schema, to educate users on how to compute with PGDBs
• Discussions of requested future enhancements to Pathway Tools and BioCyc
• Ideas for other software tools to integrate with Pathway Tools
• Group development of new Pathway Tools enhancements

Should you wish to make a presentation at the meeting, please submit a proposed title and abstract to ptools-info@ai.sri.com.

Please check the following website for updates.

2009 GMOD Summer Schools

Template:2009SummerSchoolApplicationBlurb

We are now accepting applications for the 2009 GMOD Summer Schools. GMOD Summer Schools are hands-on multi-day courses aimed at teaching new GMOD users how to get up and running with GMOD. Summer schools introduce participants to the GMOD project and focus on installation, configuration and integration of popular GMOD Components. In 2009 we are proud to offer two schools, one on each side of the Atlantic:

	Americas 16-19 July NESCent Durham NC		The courses include sessions on these popular GMOD components: GBrowse - the Generic Genome Browser Chado - a modular and extensible database schema Apollo - genome annotation editor BioMart - biological data warehouse system GBrowse_syn - a GBrowse based synteny viewer JBrowse - a brand new Web 2.0 genome browser Artemis - Chado Integration (Europe only) MAKER - Genome annotation pipeline (Americas only) Tripal - Web front end for Chado (Americas only)
	Europe 3-6 August Oxford University Oxford UK

The European summer school is part of GMOD Europe 2009, a week long event which also includes the August 2009 GMOD Meeting. This is the first time a GMOD Summer School or GMOD meeting will be held outside of North America.

Thanks,

Dave Clements

GMOD Help Desk

Apollo 1.10 Released

A new version of Apollo has been released. Highlights for this release include:

• Support for remote NCBI BLAST (blastn, blastx, tblastx)
• Support for remote NCBI Primer BLAST (primer identification tool)
• Numerous bug fixes

The nice thing about the remote analysis support is that now users do not have to install those tools locally (which can be a pain) and don't need to download the very large NCBI databases. These requests are handled in the background, so you can keep on working as usual and once the analysis is complete, the results will be automatically incorporated into the results track.

We're very interested in getting feedback from users who may use the primer identification functionality. If you could provide information on how you'd use such a tool and possibly what kind of filtering criteria you might need, it would be great so that we may incorporate these changes in future releases.

As always, you can download the current version at:

http://apollo.berkeleybop.org/current/install.html

Ed Lee

Biocuration Conference, April

The 3rd International Biocuration Conference will be held in Berlin, Germany, April 16-19, 2009. This conference is a forum for curators and developers of biological databases to discuss their work, promote collaboration, and foster a sense of community in this active and growing area of research. I don't think GMOD community members will find a higher concentration of people working on biological databases at any other conference. Anyone interested in the methods and tools employed in biocuration is encouraged to attend.

Early registration ends in two days (on 20 February, 2009).

Dave Clements

GMOD Help Desk

Biomedical Ontology Conference

The International Conference on Biomedical Ontologies (ICBO), will be held in Buffalo, New York from July 23-26, 2009. Ontologies are widely used in GMOD for annotation, controlled vocabularies, reasoning, and data sharing. Paper submissions are due March 1, and posters are due April 10. ICBO will be held in conjunction with four days of tutorials and classes from July 20-23, 2009.

See the ICBO conference web site for details.

Dave Clements

GMOD Help Desk

January 2009 Meeting Report

The January 2009 GMOD Meeting was held January 15-16, 2009 in San Diego, immediately following the Plant and Animal Genome (PAG) conference. The meeting was attended by over 50 people representing about 35 different organizations. The meeting report and links to presentations are now available on the January 2009 GMOD Meeting page. There were 19 presentations by GMOD users and developers.

Some highlights:

• How best to share data?
• BioMart integration with other GMOD Components.
• JBroswe update
• WebGBrowse - GBrowse configuration on the web.
• A Drupal interface to Chado.

Plus 14 other excellent user and developer presentations.

Please take a look at the meeting report for an update on what's going on in the GMOD community.

We hope to see you at the upcoming August 2009 GMOD Meeting, in Oxford UK (and our first meeting in Europe).

Dave Clements

GMOD Help Desk

GBrowse User Tutorial

A comprehensive GBrowse User Tutorial was released by OpenHelix this week. The narrated tutorial covers:

• the basic layout and search methods in GBrowse
• how to access detailed annotation data tied to genomic sequences
• how to select and customize annotations using tracks
• how to upload and incorporate your own data or other external data sources
• take a tour of different GBrowse installations at model organism databases

The tutorial also includes PowerPoint slides, handouts, and exercises that can be used for reference or for training others. The narration is reproduced in the notes area on the slides.

The GBrowse User Tutorial is part of a set of model organism resource tutorials funded in a large part by NHGRI. The set includes tutorials on how to navigate and use RGD, MGI, and WormBase, and in the future for ZFIN, FlyBase, and SGD (all of which are GMOD users and/or contributors).

This tutorial focuses on using GBrowse and complements the GBrowse2 Admin Tutorial. It is an excellent resource for any organization that wants to help its users use GBrowse better.

Dave Clements

GMOD Help Desk

Opening at Dow AgroSciences

Dow AgroSciences has a short term contract position available for someone with GMOD experience. The candidate proposed here will be responsible for three main tasks and several secondary ones:

1. Install the open source software components for the Chado database, data loaders, and genome browser.
2. Deploy the GBrowse genome browser in a centralized location in our intranet, which can be used by Dow AgroSciences scientists across functions.
3. Test the system by performing preprocess (e.g annotate, perform alignments) and upload whole-genome data from Arabidopsis.
4. Link the genome browser to Dow AgroSciences major internal databases, such as Variety, markerDB, QTL locate, and microarray database.
5. Provide integration tests to ensure the transparency of the data among the different systems.
6. Present to other Dow AgroSciences scientists to raise awareness of capability.
7. Complete written documentation of project development, implementation, and continued maintenance.

Interested candidates please send a resume to Mindi Dippold at mdippold@dow.com.

New Ergatis Release

A new version of Ergatis, a web-based utility for creating, running and reusing computational analysis pipelines, is now available for download.

This version includes

• Interface improvements
• New components, notably:
  • RNAmmer - RNA identification on genomic sequence
  • p_func - Derives gene function assertions based on tiers of provided evidence, such as BLAST, HMM, etc..
  • 454_mplex_seq_bin_trim - A binning and trimming script for multiplex 454 sequence data
  • phylip_dnadist - A wrapper for a parallelized version of PHYLIP's dnadist
• New pipeline templates
• Bug fixes

A new version of the automated Prokaryotic Annotation Pipeline is also included, as well as a pipeline creation tutorial. For a full list of the changes, see the CHANGELOG file.

As always, installation instructions can be found within each package and in web form.

Job Openings at Georgetown

Two Positions Immediately Available at Georgetown University in Washington, DC

Bioinformatics Engineer

This position is part of the USDA-funded Hymenoptera Genome Database project, which includes BeeBase (honey bee genome) and NasoniaBase (wasp genome). This person will implement GMOD software and develop new query interfaces; develop scripts for automated data retrieval and database loading; develop computational pipelines for updating homology, functional annotation data and GBrowse tracks. Requires MS degree in bioinformatics or related field, and demonstration of programming experience. Experience with Perl, HTML, CGI, Java, MySQL and PostgreSQL is preferred.

Bioinformatics Systems Analyst

Duties include system administration, bioinformatics database maintenance, system backup management, problem diagnosis, and creation of system documentation. Must have experience in Linux system administration Perl, Java, Apache PostgreSQL, and MySQL. Experience with GMOD and BioPerl is highly desired.

Contact Chris Elsik: chris.elsik@gmail.com

BioGraphics now at gmod.org

The Bio::Graphics modules which have long been a core part of BioPerl have been separated out and the code base is now housed in the cvs repository at SourceForge. This action has been taken to give the authors more flexibility over releases, particularly so that frequent updates can occur as needed around new GBrowse releases. Releases of Bio::Graphics are already on CPAN, so it can be installed in the cpan shell. Additionally, the gbrowse_netinstall.pl script for installing GBrowse automatically has been updated to install Bio::Graphics before installing GBrowse.

GMOD at PAG 2009

GMOD will once again have a strong presence at the Plant and Animal Genome Conference (PAG 2009). There will be over 35 talks, workshops, demonstrations and posters about GMOD Components and projects that use them. See the PAG 2009 page for a printable listing of GMOD related events.

The January 2009 GMOD Meeting is immediately after PAG, and many GMOD developers and users will likely attend both meetings.

If you haven't registered yet for either or the GMOD meeting, you are encouraged to do so.

GMOD Meeting Registration Open

January 2009 GMOD Meeting

Registration is now open for the January 2009 GMOD Meeting. The meeting will be held January 15-16, 2009 in sunny San Diego, immediately following the 2009 Plant and Animal Genome Conference (PAG 2009).

Registration is free.

If you haven't attended a GMOD Meeting before then you are encouraged to find out why the overwhelming majority of past attendees have found meetings to be useful and well organized. See the July 2008 GMOD Meeting report (or any of the other previous report) for an idea of what goes on at GMOD Meetings.

Finally, if you have items that you would like on the agenda, please add them to the meeting page.

As always, please let the GMOD Help Desk know if you have any questions.

Thanks,

Dave Clements

GMOD Help Desk

GMOD Community Survey Results

The results of the 2008 GMOD Community Survey are now available online. The survey was taken by 89 respondents. The survey includes questions on:

• What GMOD Components they use
• Feedback on the specific components they use.
• The servers that GMOD runs on.
• GMOD Meetings
• GMOD Project overall (What is being done well, what needs improvement, what should be our focus for the next 12-18 months)
• GMOD Help Desk
• GMOD course in Europe and Asia/Pacific
• Organisms studied
• Biological areas of interest

Your responses will be used to improve GMOD and guide its future direction.

And finally, we have our 3 winners of GMOD Gear:

• Randall Svancara of Washington State University
• Victor Jun M. Ulat of the International Rice Research Institute
• Pinglei Zhou of FlyBase.

Please let the GMOD Help Desk know if you have any questions about the survey.

Thanks,

Dave C

GMOD Help Desk

January 2009 GMOD Meeting

Note: Registration is now open for the January 2009 GMOD Meeting. 2008/11/20

The next GMOD community meeting will be held January 15-16, 2009 in sunny San Diego, immediately following the 2009 Plant and Animal Genome Conference (PAG 2009). Early details on the GMOD meeting are now available on the January 2009 GMOD Meeting page. We'll update that page as we have more. If you want to know what happens at a GMOD meeting see the notes from the July 2008 GMOD Meeting or any of the other previous meetings.

It's also worth noting that GMOD will again have a strong presence at the PAG 2009 meeting itself. If you are interested in attending PAG 2009, early registration closes November 1.

And, just in case it slipped your mind, it is still not too late to fill out the GMOD Community Survey and be entered to win GMOD gear!

Thanks,

Dave Clements

GMOD Help Desk

2008 GMOD Community Survey

Please take a few minutes to fill out the 2008 GMOD Community Survey and your name will be entered to win a free GMOD T-shirt or mug!

We are asking all GMOD users and developers to provide input on how GMOD is doing, and how it can be improved. All questions are optional, but please provide as much information as you can. The survey covers GMOD in general, and any GMOD components that you use (and it only asks about components that you indicate you use).

Three randomly selected survey participants will receive the GMOD T-shirt or mug of their choice. Names will be drawn from the first 100 responses we receive, so get your response in early.

Please contact the GMOD Help Desk at <help@gmod.org> if you have any questions.

Thank you,

The GMOD Team

Get GMOD Gear!

Note: Want to win a shirt of mug for free? Then participate in the 2008 GMOD Community Survey. Three participants will be randomly selected to receive the GMOD item of their choice.

GMOD has a store at CafePress where you can buy GMOD gear. Currently there are two T-shirt styles and a coffee mug. (We also take requests if you want to see additional gear - for example, a long sleeved T shirt or even a GMOD Pet Bowl).

Please note:

• GMOD gear is offered at cost. GMOD does not make any money from the sale of these items.
• The GMOD News will return to its usual, somewhat more sedate, style with the next posting.

Dave Clements
GMOD Help Desk

InterMine Workshop

An InterMine Workshop is being offered at the University of Cambridge, 30th-31st October 2008. This workshop is intended for software developers aspiring to build a database and web interface with the InterMine software. An example of such a database is FlyMine but InterMine imposes no restriction on the sort of data it can be used to manage. A reasonable grasp of programming in either Java or PERL is essential. Some experience with relational database would also be very useful.

The workshop will be hands-on, taking you through all the steps of setting up an InterMine data warehouse. We will integrate some real data using existing InterMine parsers then extend the data model and write parsers in Java/Perl to include some custom data. This will include loading data from Chado. On the second day we will deploy and configure the web application, add a new widget for analysing lists and learn how to query with web services and the API. This should provide you with the necessary experience to set up your own InterMine system.

See the workshop announcement for details and registration information. The workshop is free to attend.

Richard Smith

Pathway Tools Tutorial in London

A Pathway Tools and BioCyc tutorial well be held September 22-23, 2008 at Kings College London. This tutorial is kindly hosted by the Centre for Bioinformatics at King's College London (KCBI).

Day 1 is intended to teach users of Pathway Tools databases such as BioCyc, YeastCyc, MouseCyc, and AraCyc how to make the most of these resources.

Day 2 will address creation of new Pathway/Genome Databases (PGDBs) with Pathway Tools,

and how to query PGDBs programmatically.

Pathway Tools includes a unique combination of bioinformatics algorithms including a

predictor of metabolic pathways, an operon predictor, and an algorithm for predicting which genes in a genome code for missing enzymes in predicted metabolic pathways ("pathway holes"). It also contains tools for painting omics data onto genome-scale visualizations of metabolic networks and regulatory networks.

The tutorial is free of charge.

For more information see the tutorial page at SRI.

Peter Karp

GBrowse 1.69 Released

I am very happy to announce that GBrowse 1.69 was released today. This release of GBrowse comes with a variety of user interface enhancements, performance improvements, bug fixes and a security fix. This release come courtesy of considerable work from the GBrowse developers, most notably Lincoln Stein, the lead developer and Sheldon McKay who did much of the JavaScript work. The release can be obtained from SourceForge, or, you can use the GBrowse net installer.

More information about GBrowse, including platform specific installation instructions, can be found on the GBrowse page.

You can try out the new version on the GMOD website as well.

Finally, here is a list of the major changes since the 1.68 release:

• Draggable tracks; use "drag and drop" option to activate.
• Collapsible tracks - comes for free with "drag and drop"
• Popup balloons w/ Ajax content; use "balloon tips" option to activate.
• Caching of individual tracks for better performance; use "cache time" option to control.
• Changed licensing model to dual license under Perl Artistic 2.0 and GPL.
• Fix duplicated tracks during dragging.
• Features with same name are now found, not merged.
• Galaxy support, courtesy Greg Von Kuster
• Can change fill and outline color of selected regions on overview & regionview.
• Various bugs squashed.
• When updating settings or searching, the browser scrolls to the top of the overview section as a convenience.
• Fixed cross-site scripting vulnerability.

Thank you and happy GBrowsing,

Scott Cain

GMOD Project Coordinator

Web Site Changes

The GMOD web site doesn't look very different, but it was updated on Monday, August 11,2008. Here's what changed:

• The site was upgraded from Mediawiki 1.9.3 to MediaWiki 1.12.0.
• Replaced the default MediaWiki site search mechanism with Google.
• URLs have been rationalized. Previously, there were many different URL to get to each wiki page. Now all URLs are redirected to http://gmod.org/wiki/Page_Name

We have done our best to make this upgrade as smooth and transparent as possible. However, if you do notice anything unusual, please notify the GMOD Help Desk.

Thanks,

Dave Clements

GMOD Help Desk

Website Down: Aug 11 2008

  The GMOD website will be down for maintenance on Monday, August 11, 2008 starting at 8pm Eastern / 5pm Pacific (both US). We expect it to be down for about an hour. We apologize for any inconvenience this may cause you.

Please let us know if you have any questions.

Dave Clements

GMOD Help Desk

Upcoming Pathway Tools Tutorial

SRI's Bioinformatics Research Group will hold a Pathway Tools tutorial session from September 2-5, 2008, at SRI International in Menlo Park, CA. Each day will combine lectures with lab sessions in which students apply the software to a sample genome. No programming experience is required.

Pathway Tools includes a unique combination of bioinformatics algorithms including a predictor of metabolic pathways, an operon predictor, and an algorithm for predicting which genes in a genome code for missing enzymes in predicted metabolic pathways ("pathway holes").

Please see the Pathway Tools Tutorial page for a detailed schedule, registration information, and other details.

Peter Karp

July 2008 GMOD Meeting Report

The July 2008 GMOD Meeting was held on July 16-17, 2008 at the University of Toronto. The meeting was attended by over 30 people representing more than 20 different organizations. The meeting report and links to presentations are now available on the July 2008 GMOD Meeting page. Several GMOD Components were covered, including Chado, the Community Annotation System, and Table Editor (plus several more). We also heard reports from many GMOD users, including SGN, WikiMods, and Xenbase (plus several more).

Dave Clements

GMOD Help Desk

cas-utils-0.1 Released

In the wake of the GMOD Summer School a little over a week ago, I decided that I should create a release that has the tools that I used to tie together GBrowse, Apollo and Chado. It can be downloaded at:

http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=284978

These utilities consist of 4 main tools:

• A CGI for selecting a region in GBrowse, extracting the data for

that region from Apollo and creating an XML file and a Java Webstart (.jnlp) file for Apollo.

• A CGI for accepting uploads of edited XML files to either be

immediately loaded into Chado or to be held for validation.

• A configuration perl module to make modifying the CGI's behavior easy.
• A Module::Build based installer that queries the user for needed setup data.

While this release of cas-utils assumes that the port for connecting to the database is blocked for outside users, future releases of these tools could be configured to assume the reverse. Another item planned for a future release is tools for integrating Chado with a MediaWiki site for more text-based annotation. Of course, because of the nature of these tools, it is assumed that several things are already in place and working:

• Chado with computational analysis and annotation data already loaded.
• GBrowse (either 1.69 (to be released soon) or from the stable cvs branch).
• Apollo, both as an installed application (like in /usr/bin), and as

source that has been built into a webstart application and installed for the web server to use.

If you have questions about either cas-utils or any of the

prerequisites, please send questions to the most appropriate mailing list:

• Chado: gmod-schema@lists.sourceforge.net
• GBrowse: gmod-gbrowse@lists.sourceforge.net
• Apollo: apollo@fruitfly.org

I've only tested this application on CentOS 4.6 and Ubuntu 8.04, though there is no reason to believe that this wouldn't work on any Linux and probably on MacOS as well. I am considerably less sure that this would work out of the box on Windows, but support for that could probably be in a future release if the demand is there.

Thanks and happy curating!

Scott Cain

Job Openings with GnpAnnot

GnpAnnot, an INRA project, is offering 2 positions for programmers to implement and/or improve GMOD interfaces for Chado databases.

18 month position for a Java programmer

Environment:

The job opportunity will be located at IRISA, in Rennes France.

Description:

The engineer will write specifications, design, develop, test and deploy diverse applications and web interfaces dedicated to genomics analyses and comparative genomics.

The applications will use a 3-tiered architecture based on J2EE technology.

Skills:

• experience in Java development
• good knowledge of J2EE technologies (Hibernate, Spring, Struts et JSP) - experience with BioPerl or Perl objects

The job should start on the first of September 2008

Contact:

Fabrice Legeai fabrice.legeai@rennes.inra.fr

One year object-oriented programmer (Java, Perl Object)

Environment:

The job opportunity will be located at INRA-URGI in Versailles (Near Paris), France.

Description:

The applicant will write specifications and develop/improve, databases and interfaces from the GMOD project (Chado, Apollo, GBrowse).

Skills

• Good experience in Java and Perl programming
• Knowledge of GMOD tools will be appreciated

Answers expected before September the 5th. The job should start on the 1st of October.

Contacts:

• Joelle Amselem: joelle.amselem((at))versailles.inra.fr
• Michael Alaux: michael.alaux((at))versailles.inra.fr

update october 2008: position for the first year now assigned.

Stéphanie Sidibe-Bocs, the PI of GnpAnnot, will be at BOSC and ISMB this week and is available to discuss the project and these openings. You can e-mail Stéphanie at stephanie.sidibe-bocs@cirad.fr, or just introduce yourself when you see her.

GMOD @ ISMB and BOSC

GMOD has a strong presence at the ISMB 2008 and BOSC 2008 meetings, getting under way this week in Toronto. There are over a dozen talks and posters at the BOSC and ISMB conferences about GMOD Components, or that feature research that using GMOD components. See ISMB 2008 for a complete list and for a flier we'll be distributing at the conference.

Dave Clements

GMOD Help Desk

2008 Summer School Report

Or, what 29 people did with their summer vacation.

The first annual GMOD Summer Schoolsummer was held July 11-13, 2008 at NESCent in Durham, NC. It was attended by 25 students and 4 instructors from 19 different states plus France and The Netherlands. Researchers came from the arthropod, vertebrate, prokaryote, plant, fungus, and virus communities. The questions and discussions were lively and participants were fully involved in the hands-on class. Students started the class with a minimal install of Linux and finished 2 1/2 (sometimes bumpy) days later with a system that was running Chado, GBrowse, Apollo, and CMap.

I would like to thank the participants, the instructors (Scott, Ben and Ed) and the folks at NESCent for getting the GMOD Summer School off to a fabulous start.

We will be having a Second Annual Summer School in 2009 at NESCent. We will use what we learned at this year's course to make next year's even better. Watch this space for information on that course as next summer gets closer.

There has also been some discussion of holding the course in Europe. If you would be interested in attending a several day course on GMOD in Europe please send me an e-mail. If we get enough interest, we might try and pull it off.

Thanks,

Dave Clements

GMOD Help Desk

CMap 1.01 Released

Version 1.01 of CMap has been released.

I'm quite excited about using GFF3 for data import/export which is possible with this release.

You can get the new version from SourceForge, http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129

Highlights of this release are:

• Added a GFF3 parser and producer for easier and more complete data import and export (requires latest version of bioperl-live to import GFF).
• Added a module to serve data to CMap3D, a 3D viewer being developed by Chris Duran and Dave Edwards.

If you have any questions, please let me know.

This is only an incremental update. For anyone who installed version 1.0, simply download the new release and run

perl Build.PL; ./Build; sudo ./Build install

No updates to the database or config files are needed.

If you are updating from an older version, see the documentation in the upgrade/ directory included in the package.

Ben

GMOD Meeting Registration

Registration is now open for the July 2008 GMOD Meeting. The meeting is scheduled for July 16-17, 2008 at the University of Toronto, immediately before ISMB 2008 (also in Toronto), and just a few days after the 2008 GMOD Summer School.

Watch the July 2008 GMOD Meeting page for more information as the meeting draws nearer. If you have any questions or requests about the July 2008 meeting, please contact the GMOD Help Desk at help@gmod.org. See the notes from previous meetings for an idea of what is discussed at GMOD meetings.

MAKER Joins GMOD

MAKER is a portable and easy to configure genome annotation pipeline that has just become a part of GMOD. It's purpose is to allow smaller eukaryotic genome projects to annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal. It outputs are in GFF3 or FASTA format, and can be directly loaded into Chado, GBrowse, and Apollo.

MAKER was created and is maintained by the Mark Yandell Lab at the University of Utah.

See MAKER for more on how you can use it to automatically annotate your genomic data.

Apollo 1.9 Released

Apollo 1.9.0 has been released. This release includes a number of bug fixes and some additions. The biggest new feature for this release is the Preferences Editor, which gives a graphical way to edit style/tiers files. This is aimed towards the non-power users and as such, it only supports a small subset (the ones we figured would be most useful) of the many options for those files. Power users might still want to manually edit the style/tiers files if they want to change something not supported through the GUI. Note that with this addition, the old Types Panel and Style Editor (which was basically just a text editor) have been retired.

You can get the new release of Apollo at:

http://apollo.berkeleybop.org

Ed Lee

GMOD Summer School Update

July 11-13, 2008
National Evolutionary Synthesis Center (NESCent)
Durham, North Carolina, USA

The 2008 GMOD Summer School is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. The summer school was announced on March 7, 2008.

The 2008 GMOD Summer School is now full. However, the waiting list is still small and if you are interested then you are encouraged to submit an application.

If you have already applied for the GMOD Summer School you should have received an e-mail from the Help Desk informing you of your admission status.

Apollo 1.8 Released

I'm excited to let everyone know that we're releasing a new version of Apollo (1.8.0) today. There are many additions/bug fixes with this release. Most notably, due to popular demand, an 'undo' system. You can now access the 'undo' function through 'Edit→Undo' (or ctrl-u). For more information on the changes, check out the release doc.

On another note, the official Apollo URL has changed. It's no longer:

http://www.fruitfly.org/annot/apollo

but rather:

http://apollo.berkeleybop.org

Please update your bookmarks accordingly.

Ed Lee

Sea Urchin Genome Database

Today, Tuesday April 4th, the Sea Urchin Genome Database went public. Based on the GMOD tools and applications the site organizes and displays the genome sequence and annotations produced by the Baylor College of Medicine Human Genome Sequencing Center and the sea urchin research community. This site housed at the Center for Computational Regulatory Genomics, the Beckman Institute at California Institute of Technology plans to enrich and extend the sea urchin sequence and annotations.

Visit us at SpBase.

Andy Cameron

Chado Doc Reorganization

Chado is the database schema of GMOD and it has quite a bit of documentation in this web site. However, this documentation could be better organized and integrated. We are launching the Chado Documentation Reorganization effort to do just that.

During this effort the existing Chado documentation may be unstable. We will do our best to make this reorganization be as painless as possible.

The Chado Documentation Reorganization page summarizes our existing documentation and then proposes a plan for restructuring it. If you have any suggestions or comments on this then please send us your feedback.

Thanks,

Dave Clements

GMOD Help Desk

iPlant Collaborative Job Openings

Cold Spring Harbor Laboratory is seeking experienced software developers/bioinformaticians to join the iPlant Collaborative, a new NSF-funded initiative which seeks to develop a comprehensive national cyberinfrastructure which will unite researchers in every plant biology discipline.

See the iPlant job board for job descriptions.

GMOD 1.0 Released

I am very pleased to announce the release of GMOD 1.0. The file can be downloaded from SourceForge at:

http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=19511

This release comes at a time when both the Chado schema and its

associated tools have matured and are now quite stable. The plan going forward is to have more frequent releases with schema changes between versions clearly delineated.

In addition to the Chado schema, this release includes:

• Tools for creating a new database.
• Tools for populating it with ontology data (using go-perl).
• A fairly new tool for updating ontologies contributed by the developers of SGN, the Sol Genomics Network.
• Tools for loading sequence feature (i.e. GFF3) data.
• GMODTools for creating bulk download files like GFF and Fasta (See GMODTools for more information).

Other data can be loaded using XORT. This release of Chado works well with the upcoming release of GBrowse, as well as with the current versions of Apollo and CMap. It should also work well with GMODWeb/Turnkey.

With this release, there are so many people in the GMOD community that I

would like to thank that I couldn't possibly list them all, but at a bare minimum, I would like to thank the developers at FlyBase and the Berkeley Drosophila Genome Project, especially Chris Mungall and Dave Emmert, as well as others who have contributed code to the GMOD project over the past several years.

Please direct any questions about using this release to the GMOD schema mailing list, gmod-schema@lists.sourceforge.net.

Scott Cain

CMap 1.0 Released

Version 1.0 of CMap has been released.

You can get the new version from SourceForge, http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129

Highlights of this release are:

• Ribbon option for correspondences
• New Feature Glyphs
• A dot-plot view
• An image_only URL parameter allowing a CMap image to be embedded in another page
• Easier install with directory guessing
• API better documented for writing custom scripts to load data

If you have any questions, please email the CMap mailing list.

Ben

July 2008 GMOD Meeting

The next GMOD community meeting has been scheduled for July 16-17, 2008 at the University of Toronto, immediately before ISMB 2008 (also in Toronto), and just a few days after the 2008 GMOD Summer School.

Watch the July 2008 GMOD Meeting page for more information as the meeting gets nearer. If you have any questions or requests about the July 2008 meeting, please contact the GMOD Help Desk at help@gmod.org. See the notes from previous meetings for an idea of what is discussed at GMOD meetings.

Thanks,

Dave Clements
GMOD Help Desk

SynBrowse Developers Needed

The SynBrowse synteny viewer, a GMOD component, is moving towards its second major release. Xiaokang Pan, the project's lead developer, is looking for volunteer developers to help get this release out sooner.

SynBrowse2 is written in Perl, and is built on several open source components, including parts of GBrowse. SynBrowse2 need particular improvements in run-time performance and its alignment parsing tools. Ideally, programmers will develop SynBrowse2 using a set of animal or microbial genomes (Xiaokang is already working with several plant genomes). Programmers can improve the alignment parsing tools, fix potential bugs and hopefully improve other parts of SynBrowse as well.

If you have any interest in and/or experience with multiple alignment or synteny visualization tools please considering contributing to the SynBrowse project. Xiaokang can be reached at xiaokangpan@gmail.com.

Thanks,

Dave Clements

GMOD Help Desk

GMOD at ParameciumDB

Curious to know what is involved in becoming a GMOD user and creating a GMOD based web site? You can now read the GMOD User Story, an article about ParameciumDB's experience with implementing GMOD. The article describes what GMOD components ParameciumDB uses and how they connect them together. ParameciumDB uses several GMOD components, including Chado, GMODWeb, Apollo, and GBrowse. Please contact Linda Sperling <linda.sperling@cgm.cnrs-gif.fr> if you have questions about GMOD at ParameciumDB.

This is the first of a series of articles on how different organizations use GMOD components to achieve their goals. User stories will give readers a feel for what implementation choices are involved and which ones each organization made. If you are interested in describing your experience with GMOD, please consider creating a user story page for your project. You can just start writing (this is a wiki!) or contact the GMOD Help Desk for assistance. If we aren't swamped with volunteers, then I will be asking (cajoling?) several not-so-randomly picked projects to write user stories describing their experiences. I'm hoping to have a new story every other month or so.

Thanks,

Dave Clements

GMOD Help Desk

Beta Test CMap: Win a T-Shirt!

UPDATE: We have our winners. Even still, please feel free to give the release candidate a try and let us know how it goes.

We need beta testers for the CMap 1.0 release candidate.

Win this shirt!

If I get four (or more) people who let me know that they will try out the release candidate, I will draw two of their names (or email addresses) and buy them each a GMOD T-shirt (based on random drawing, void where prohibited, etc). Testers from around the world are welcome (and eligible for the shirts as long as Cafe Press ships there and it isn't prohibited by law).

You can get the release candidate from SourceForge.

To view the T-shirt or get one for yourself visit

Cafe Press. Note: There is no price markup for GMOD. The only one making money on the shirts is Cafe Press.

If the threshold is broken, I will hold the drawing on Friday the 15th at 1pm CST (2pm Eastern) and email the winners for their addresses and shirt sizes. If you don't want to be entered in the drawing just let me know. There is already one beta tester, so only three to go.

Remember: If no one beta tests, everyone beta tests.

Thanks,

Ben Faga,
faga.cshl@gmail.com

GMOD Summer School

July 11-13, 2008
National Evolutionary Synthesis Center (NESCent)
Durham, North Carolina, USA

The first annual GMOD Summer School will be held July 11-13, 2008 at the National Evolutionary Synthesis Center (NESCent), in Durham, North Carolina, USA. This is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. There will also be a concurrent 1 day session aimed at principal investigators that will give decision makers an overview of what GMOD can do, how the project operates, and what level of resources are needed to get a GMOD installation up and running. If you are interested in attending please submit a Statement of Interest before April 15, 2008. The course is free but class size is limited. See the GMOD Summer School page for more information and a tentative program.

Ten Recent Web Site Changes

This entry summarizes several recent changes in the GMOD web site. These changes are designed to make the site more useful, and hopefully will make your GMOD web site experience more pleasant.

Ten Recent Web Site Changes to Make Your GMOD Life Easier:

1. Categories - Most of the pages in the GMOD web site have now been tagged, and those tags can be used as an alternative way to navigate the site. We have also added tools that make it easier to assign tags when creating content. (Note: The category hierarchy is still work in progress. Suggestions are welcome.)
2. GMOD News - News items of interest to the GMOD community. This is also available as an RSS feed.
3. Main Page - Items from the GMOD News page and recently edited pages (non-minor edits) now show up in the right sidebar.
4. Calendar - Calendar of events of interest to the GMOD project.
5. Glossary - Short definitions of non-biological terms used in GMOD.
6. GMOD Mailing Lists - Shows more lists, and sorts them into Overview, Component, and Inactive lists. If your list isn't here, please add it.
7. Site Guidelines - Guidelines for creating and editing content on the GMOD web site.
8. GMOD Help Desk - Explains services offered by the help desk.
9. Computing Requirements - Description of expertise and computing systems you'll need to set up a GMOD installation.
10. Databases and GMOD - An overview of database concepts and how databases are used in GMOD.

Note that several of these pages need continuing contributions from the community. That means you! We particularly encourage you to get in the habit of submitting new Calendar, Glossary, and News items.

Our next big goal for the web site is to reorganize the Chado documentation. Watch the web site for details on this.

As always, please let us know if you have any questions or comments.

Thanks,

Dave Clements, GMOD Help Desk

help@gmod.org

Pathway Tools Workshop

A session at the Cambridge Healthtech Pathway Analysis conference, March 26-28, 2008 in San Francisco, will describe Pathway Tools, a GMOD component for modeling metabolic pathways and regulatory networks. There will also be presentations by these GMOD member databases that use Pathway Tools in their databases:

• Mouse
• dictyBase
• SGD
• Solanaceae Genomics Network

Early registration is available until February 22, 2008

GMOD at Arthropod Genomics

There will be two GMOD related workshops at the Arthropod Genomics Symposium, April 10-13, 2008, in Kansas City.

• Community Contributions to Genome Annotation - Christine Elsik of BeeBase will discuss how to install and use the Apollo genome annotation tool.
• Chado: A Database Schema for Integrating Biological Data - Scott Cain and Dave Clements will cover Chado's logical concepts, the types of data it can represent, how to import and export data, and how Chado integrates with other GMOD components such as Apollo and GBrowse.

GMOD has a particularly strong presence in the arthropod community (e.g., BeetleBase, BeeBase, FlyBase, wFleaBase, ...). If you are an arthropod researcher interested in using GMOD Components then this meeting will be time well spent.

Early registration and poster abstract submissions are both open until February 29.

Apollo 1.7.0 Released

Version 1.7.0 of Apollo has just been released. You can access the updated Apollo page at http://www.fruitfly.org/annot/apollo

Changes in this version include

• Added GFF3 support
• Added program source filtering for reading off Chado databases
• Lots of work on the ensj adapter to allow it to work better with recent ensembl schemas, handle ditags, give finer control of gene loading, increase speed of gene loading, bug fixes to history, cigar parsing in ensj layer, loading of contig features
• Allow layout of display to be saved to / loaded from a file. Most useful for synteny where initial display set up can take time. The saved layout also includes the current base position and zoom factor, and on loading you can choose to use those.
• Ability to edit settings for a type (new popup menu item in feature popup). The settings which can be edited are the glyph used for drawing the feature and the columns in the table displayed in the evidence panel.
• New drawing glyph which shades exons darker or lighter depending on their phase (DrawablePhaseHighlightGeneFeatureSet). Also a version of that which uses straight lines to join exons rather than 'hats' (DrawablePhaseHighlightNoHatGeneFeatureSet)
• Work on ensembl synteny adapter so it works with latest ensembl compara db schema, and basic support for allowing different alignment sets to be selected.
• PureJDBCTransactionWriter added. This entailed some changes to other classes, but in almost every case the changes are 1. reverse compatible and 2. invisible to the end user.
• Uses of Log4J for generating log files.

Plus many other changes. See the release notes for more.

We are hoping to cut releases on a more regular basis (after the year and a half long hiatus). So please let us know if you find any bugs and they will be addressed and put into a new release as soon as possible.

GBrowse Tutorial at PAG XVI

Scott Cain will present a GBrowse tutorial at the Plant and Animal Genome XVI Conference (PAG-XVI), January 12-16, 2008, in San Diego. This will be a hands-on tutorial on how to install and use the GBrowse genome browser. If you are attending PAG and you are interested in GBrowse then please consider attending.

See the PAG tutorial page for additional information.

Modware Feedback Wanted

Modware provides an object-oriented Perl API for Chado suitable for use by any application based on GMOD. This Chado API supports creating, retrieving and updating objects in a Chado database. Modware makes heavy use of BioPerl to provide a familiar and intuitive interface for objects stored inside of a Chado database.

Recently, a VMware Virutal Machine was released to make download and

testing of a fully configured and installed version of Modware available. Modware developers continue to add new features, including representation of BLAST hits (currently on CVS HEAD).

One critical piece of the project that is missing is feedback from the

community. If you are interested in a Chado API, please download the Modware Virtual Machine found on the Modware home page and give it a try. Email all feature requests, questions, and comments to gmod-ware-users@sourceforge.net.

November 2007 GMOD Meeting

The November 2007 GMOD Meeting was attended by nearly 40 people from across the GMOD community. Community annotation and comparative genomics were two popular topics at this meeting. See November 2007 GMOD Meeting for a list of presentations and a summary of the meeting.

GMODTools 1.1 Released

Version 1.1 of GMODTools has been released. Version 1.1 adds these features and corrections:

• No chromosome/scaffold/golden_path files. This change is needed to handle partially assembled genomes with many (1000s to 100,000s) of scaffolds. Flag no_csomesplit=1 to use this (should become default).
• Gene Ontology association file, see go_association tags in configurations
• Validate main variables in chado database: ${golden_path}, ${seq_ontology}. This step, on now by default, checks that database contains configured values. If failed, db is inspected for real values.
• Miscellany bugs cured and configuration updates, e.g., tables/overview now again active.

GMODTools is a Perl package that generates Fasta, GFF, DNA and other bulk genome annotation files from Chado databases.

GMOD Help Desk is Back

After a several month hiatus, the GMOD Help Desk is back. Dave Clements has taken the role created by Brian Osborne earlier this year. Dave will work on the same sorts of things that Brian did: Maintaining and improving the GMOD web site and documentation, and supporting the GMOD user community. See GMOD Help Desk for more.

FlyBase Converts to Chado

This summer, FlyBase finished its reimplementation using Chado, the modular GMOD database schema which FlyBase originated and continues to develop in collaboration with GMOD and several GMOD-affiliated database projects. The FlyBase implementation of Chado integrates over 100 years of Drosophila genetic and genomic research data. In addition to supporting the ongoing genome annotation and scientific literature curation for D. melanogaster, the main Drosophilid model organism, FlyBase is currently working to incorporate the new genome sequences, annotations, and cross-species comparative data for eleven additional Drosophila species into the single production instance of Chado.

PostgreSQL dumps of FlyBase-chado are available at ftp://ftp.flybase.net/releases/current/psql/

Pathway Tools 11.5 Released

Version 11.5 of Pathway Tools has been released. Version 11.5 includes

• Support for cellular regulation.
• Electron transport information
• Zooming in genome view
• Stricter pruning to eliminate pathway predictions that are likely to be false-positive predictions

See the Pathway Tools release notes for details.

Pathway Tools is a comprehensive symbolic systems biology software package that supports several use cases in bioinformatics and systems biology.

ISMB/Bioinformatics Chado Paper

The paper 'A Chado case study: an ontology-based modular schema for representing genome-associated biological information' by Chris Mungall, Dave Emmert, and The FlyBase Consortium, was presented at ISMB/ECCB 2007, and is now available in the journal Bioinformatics.

The paper describes the overall Chado philosophy and the 5 core Chado modules.

BioMart 0.6 Released

Version 0.6 of the BioMart has been released. Version 0.6 includes support for a 1.5 DAS server, and improvements to MartView and MartBuilder. See BioMart News for more.

BioMart is a query oriented database management system for biological data.

GBrowse 1.68 Released

Version 1.68 of GBrowse is a stability release which improves the documentation and installation process. It includes a new script called gbrowse_netinstall.pl, which will semi-automatically install GBrowse across the Internet on Windows, Mac OSX and Linux platforms.