Modware is an object oriented API for the Chado database schema. Chado is a public-domain genomics schema distributed by the Generic Model Organism Database Project (GMOD). Modware builds a powerful link between Chado and Bioperl by creating classes and a framework for creating Bioperl objects from records in a Chado instance. This brings a familiar, object-oriented interface to the complex data inside of a genome database.
It is recommended that you download The Modware VMWare appliance to test-drive Modware. It has Modware preinstalled on a fully populated Chado Database in a Ubuntu Linux environment. To run it, you need to download VMware Player (for Linux and Windows), or VMWare Fusion (for Mac). See the Getting Started with Modware Using VMware Appliance. The VMware appliance has a sample database containing the Dictyostelium genome installed and is accessible through a Modware installation.
- Modware was presented at BOSC 2007 in Vienna, Austria. Slides from the talk at BOSC are here.
- 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.
- Download Modware, explore the API documentation and ask questions to gmod-ware-users@lists.sourceforge.net!
COMING SOON
Modware has begun development on the CVS HEAD to work with the impending GMOD 0.1 release. Also coming soon:- DONE!
Iterators for Modware::Search results. Iterators provide much better performance when the results list is big. - DONE!
Use of contigs as reference features (as opposed to only using chromosomes). - DONE!
Non-coding RNA support (ncRNAS). - Support for polypeptide features for all mRNAs
- Support UTRs
- DONE!
Generic features for features that do not have explicit support. - Phenotype Annotations.
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This software was developed for dictyBase at the Center for Genetic Medicine at Northwestern University, which is funded by NIH Grants GM64426 and HG0022. |
For more information contact: e-just at northwestern.edu |
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Copyright © 2007, Northwestern University All rights reserved. |
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