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