Celebrating 50,000 Publications: Physical Review E Milestones

Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences
Gavin E. Crooks Phys. Rev. E 60, 2721 (2000)

Physical Review E published its 50,000th paper in September 2015. To celebrate this, the journal presents a series of milestone papers that were published since its inception in 1993. This is an eclectic collection of papers that made significant contributions to their field, chosen by the editors. A new milestone will be added each week.

WebLogo 3.3 Released

WebLogo 3.3 web-sever

WebLogo 3.3 code

3.3 (2012-07-02)
[Gavin Crooks, David Sivak]
* Improved the algorithm that guesses the sequence type (DNA, RNA or protein) (Kudos: Bug report, Roland Pache )
* Fixed an issue with reading transfac matrices with alternative alphabets(Kudos: Bug report, Nima Emami )
* Fixed Motif.reindex()
* Implemented Motif.reverse() and Motif.complement() (Can now reverse complement transfac matrix input on the command
line.) (Kudos: Feature request, Seth P Boudreaux )
* Command line interface now automagically recognizes transfac files.
* Add command line option “–reverse-stacks NO” which inverts the logo stacks so that the most conserved monomers are at the bottom of the stack, rather than the top. This ordering is consistent with the standard ordering for histograms, and is arguably a better representation. (Kudos: Luke Hutchison )
* Fixed an issue so that the correct color scheme is chosen for the specified sequence type.
* Miscellaneous minor bug fixes and refactoring.

WebLogo 3.1 released

WebLogo 3.1 web-sever

WebLogo 3.1 code

This release contains mostly code improvement, minor bug fixes, small user enhancements and other miscellanies maintenance.

* Command line: Add parsing of transfac PWM files
* Command line: Add reverse and complement transformations
* Improve clustal file parsing
* Currently compatible with python 2.5, 2.6 and 2.7
* Deprecate support for python 2.3 and 2.4
* Migrate corebio library into weblogo for easier maintenance and development.
* Add new annotate option for custom annotation line
* Miscellaneous minor bug fixes and refactoring.

* Incorporates bug fixes and feedback from Gavin Crooks, John Gilman, Kevin Schutz and Perry Evan.