GMOD
Modware
Contents
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
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%253A%253AChado%253A%253ASchema 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 this wiki. The first CPAN release is expected to be early next year.
Siddhartha Basu, Modware developer, dictyBase, 2010/10/28
Getting Started
- Install Chado
- Install Modware, and there is an option to
make install_samplethat 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 |