Introductions to Pygr

• a two minute intro to Worldbase and Pygr
• an overview paper about Pygr

Pygr-0.8 (latest) Docs

On-line version:

• Overview.
• Tutorials.
• Module Documentation etc.
• API reference.
• Pygr Developer's Guide.
• Intervaldb C Library.

Alternatively, an off-line version can downloaded here: HTML PDF.

Pygr Papers

• Pygr: A Python graph framework for highly scalable comparative genomics and annotation database analysis: this new Manuscript is intended to be an overview of the basic functionality of Pygr. Please send feedback to Chris Lee!
• Code Examples for the Pygr manuscript
• for other papers see this page

Pygr Cookbook

• Pygr recipes: this is currently being moved to the wiki, but for the moment look at this existing version

Pygr 0.7 (old) Docs

• Tutorial.
• Module Documentation.
• Testing.
• Intervaldb C Library.

Pygr Forum and Other Information

• DevelopmentRoadmap: plans for the next three releases of Pygr
• Pygr Developer Forum: use this group to ask your questions about Pygr
• Pygr Versions, Publications, Presentations

Talks

• Tutorial on Pygr and Worldbase for comparative genomics and easy access / sharing of complex, large-scale datasets: Demonstrates basic capabilities for easy access and data mining of large scale comparative genomics resources using Python.
• Exploring the future of bioinformatics data sharing and mining with Pygr and Worldbase: talk given to a scientific computing audience at SciPy 2009, Caltech, Aug. 2009. This talk focuses almost entirely on Worldbase, and emphasizes CS aspects more than the DAM-SIG talk below, shows real code examples etc.
• A full software stack for visualizing next-generation sequence information: Talk by Titus Brown, Michigan State University. Presented at SciPy 2009 Conference held August 18-23, 2009 at CalTech in Pasadena CA
• Exploring the future of bioinformatics data sharing and mining with Pygr and Worldbase: talk given to a bioinformatics audience at the Data Analysis and Management SIG, ISMB 2009, Stockholm, June 2009.
• Pygr and pygr.Data talk at UCLA Bioinformatics retreat (slides in PDF): May 2008
• a short talk about Pygr
• SciPy 2007 presentation: August 2007.
• ISMB 2006 Software Demo: includes working examples from pygr tutorials.
• ISMB 2005 tutorial: a quick intro to the goals of the Pygr project; this was followed by running various code examples, more or less following the tutorial examples in the docs.