Modware

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Modware is an object-oriented Perl API for Chado. It allows object-oriented querying and loading of a Chado database and returns data structures that a programmer can readily use without knowing the details of how the object is stored in the relational schema.

Many bioinformatics programmers are familiar with the Bio::SeqFeature object system for representing biological features in BioPerl. Modware utilizes this framework for easy programmatic access and manipulation of biological features directly from Chado.

Please use our bug tracker on SourceForge to report bugs and feature reqeusts.

• For a wiki-ized version of a presentation done at the GMOD meeting in January 2007: Modware Presentation
• For a VERY quick tour of the kinds of things you can do with Modware, check out the Examples Page
• For detailed documentation on the API, check out the API docs.
• To download Modware and CVS access, go to the Project page.
• For a general discussion of GMOD Middleware: GMOD Middleware

Status

Modware is being rewritten at dictyBase, replacing the Class::DBI backend ORM to use Schema instead. This upgrade is expected be done around the end of September 2010. The new Modware will handle both ontology and publications (pub module) in addition to handling various bio features.

Getting Started

• Install Chado
• Install Modware, and there is an option to make install_sample that will install the Dictyostelium Genome
• Explore the API documentation and ask questions to gmod-ware-users@lists.sourceforge.net.

Feedback Wanted

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.

Acknowledgments

This software was developed for dictyBase at the Center for Genetic Medicine at Northwestern University, which is funded by NIH Grants GM64426 and HG0022.

Support

	Mailing List Link	Description	Archive(s)
Modware	gmod-ware-users	Modware support and developer mailing list.	Nabble (2010/05+), Sourceforge