What is Pygr?

News

• June 2008: stable production release Pygr v.0.7.1 is available.
  
• May 2008: 25 minute video of a talk on Pygr and pygr.Data available.
  
• April 2008: We've switched over to Google Code from Sourceforge, and we've also created a new Pygr Developer discussion group / mailing list.
  
• April 2008: Pygr has been selected by Google and the Python Software Foundation for not one but two Google Summer of Code projects.  We're very excited to congratulate Jenny Qian and Rachel McCreary on their projects being selected, and look forward to participating in their projects!
  
• April 2008: We have switched over from our internal CVS source code repository, to a public git repository for the Pygr source code.  You can now get the very latest code, and start your own experimental branches...
  
• September 2007: Version 0.7b3 code available in Sourceforge with updated documentation. use_virtual_lpo option has been changed into pairwiseMode. Now, pygr can create NLMSA from UCSC axtNet format (use axtFiles instead of mafFiles, Pygr Cookbook). Text <-> Binary conversion function for NLMSA has been changed (not compatible with previous versions) due to seqDict saving feature. 32-bit Windows and Mac versions are available, too. You can checkout latest developmental version of pygr in SourceForge CVS (updated everyday from our CVS). $ cvs -z3 -d:pserver:anonymous@pygr.cvs.sourceforge.net:/cvsroot/pygr co -P pygr
  
• August 2007: SciPy07 presentation slides.
  
• August 2007: version 0.7beta2 code available in SourceForge with updated documentation. 32-bit Windows Versions (Python2.4 and Python2.5) are also available (tests modules are not included in Windows Versions). It includes additional several automated tests (megatest for large scale testing). These test modules will give ample amount of pygr example codes.
  
• July 2007: version 0.7beta1 code available in SourceForge.  This is the first public beta of v0.7.  It includes a new set of automated tests of pygr's new functionality.
  
• June 2007: version 0.7alpha0 code available in CVS, with updated documentation.  This is the functionally complete release, but it is still alpha code, in testing.
  
• April 2007: version 0.7 release plan is now available.
• April 2007: new pygr-developer forum created for all pygr development discussions.
  
• March 2007: documentation for the upcoming version 0.7 release is now available.  Many new features, including annotation databases, XMLRPC sharing of multigenome alignment databases, and much more.
  
• August 2006. Pygr was presented in a software demo at ISMB2006, Brazil. Click to download presentation slides.
  
• July 2006: Pygr 0.5 release on SourceForge. Genome alignment database system and other features improved.
  
• March 2006: Pygr 0.3alpha release on SourceForge.  New highly scalable genome alignment database system.
  
• September 2005: Pygr 0.2 released on SourceForge.  A new installer, lots of improvements...
  
• July 2005: Zach Fierstadt has joined the developer team to produce a genuine release package for Pygr (yes!  An installer!  Just think...)
• June 2005: Pygr was presented in a software demo at ISMB2005.  We've posted some tutorials covering the material from that demonstration.
• April 2005: v.0.1 available for download.
• November 2004: UCLA's Center for Computational Biology established as one of four NIH centers nationwide for the NIH Roadmap Initiative for Bioinformatics and Computational Biology.  The Pygr project is supported by NIH-CCB.
  
• June 2004: Apple Bioinformatics Cluster Award to C. Lee.  The Pygr project has been generously supported by Apple Computer.