It’s been a long time coming but it’s finally PyCogent 1.9 release time. I thank all contributors to the library. The developers, documenters and bug reporters. Your efforts are greatly appreciated!
This is a landmark release for a number of reasons. First, it’s been a very long time since the release of 1.5.3. Second, Python 3 is firmly established and the main PyCogent dependencies are now available for it. Third, there have been major changes in the Python and bioinformatics landscape. One of these with direct relevance to PyCogent has been development of scikit-bio. This exciting new project is substantively derived from PyCogent. This and other developments mean we have an excellent opportunity to refocus PyCogent. While more detailed announcements will be made later, I can say that it will become more focussed on statistical comparative molecular evolutionary analyses. It will be ported to Python 3, and there will be at least one other derivative project for the Ensembl querying code.
So stay tuned, exciting developments ahead!
This is a quick maintenance release to fix an error in the documentation build and a bug in an application controller.
Many thanks to all the contributors, but a special thanks to Jai Rideout for driving the release through to completion! Check the ChangeLog for details. For users of the Ensembl code, note that while we now support Ensembl release 68 (the latest version at time of writing) Ensembl’s habit of changing their API means this compatibility is quickly broken. In which case, you can obtain the most up-to-date version of the Ensembl code in the svn repository (see instructions here).
A Postdoctoral position is available in the Huttley lab to work on the development and application of improved models of sequence divergence. The work will build on the PyCogent toolkit for statistical modelling of molecular evolution. Position description and contact details for more information are available here.
Full applications must be submitted before January 22nd 2012.
Many thanks to all the contributors! Despite the minor point release, this version has many new additions. Check the ChangeLog for a summary. Of particular note is we have removed code authored by Ziheng Yang (without loss of functionality) as it is not available under an open source license.
This is our first release of a standalone PyCogent application (requires OSX 10.6 and can be downloaded from here). Our aims are to remove barriers to using the PyCogent library and to reduce the effort required for Bioinformaticians to make their work accessible for Biologists. The app is a multi-tabbed python interpreter that includes the PyCogent (bleeding edge version) library and its dependencies. In addition to supporting statistical plus graphical analyses of genomic data, the app implements a novel Script Form system. Script Forms are designed to reduce the burden on Bioinformaticians for making scripts readily useable to Biologists. So download the app and give it a try!
Many thanks to all the contributors for the new features, bug-fixes and performance enhancements. Major additions to the documentation too! As usual, check the ChangeLog for a summary what has gone into this point release. Of particular note are: the inclusion of some parsers for handling next-generatiuon sequencing data; progress display code employed by the cogent.evolve module; and some enhancements to the Ensembl querying code.