[Biopython-dev] Report from the Python & Friends workshop

[Kristian Rother]

Hi,

I'd like share a report from a recent bioinformatics Python meeting
(basically because we did Biopython work there). Sorry for crossposting.

At the Python & Friends Workshop 2010 in Karpacz, 20 Python
bioinformaticians spent three busy days programming and learning about
newest technologies. The Polish & German ISCB Student Council members
brought together an equal number of people from both countries.

Some highlights of the workshop were:

   * A keynote on Biopython and subsequent tutorial were given by Peter
Cock. During the session, the brand new GSOC code branch for analyzing
PDB structures was tested. We found the center of mass, coarse-grained
models, and renumbering features working well, but the hydrogenation
and SS-bond calculation require further testing.

   * The K-means clustering algorithm implemented in numpy was explained
in detail, and an intense numpy tutorial prepared by Bartosz Telenczuk.

   * A live demonstration on how to search & cluster ligands with the
Schroedinger software package was given by Ewa Bielska.

   * The Galaxy tool integration workbench was in the focus of interest of
many participants, and Sebastian Schultheiss gave a hands-on tutorial.
A closer interaction of the Galaxy platform with Biopython would
probably be useful for many people.

   * In a hackathon session, a memory leak in the KDTree code of Biopython
was closed.

   * And of course, there was a hike into the mountains near the Czech
border.

The workshop took place in an informal setting bringing together groups
with a variety of backgrounds. According to participants, it made sense to
find out what tools are there, and to plan strategic issues like py3k
migration.

The workshop has been organized by Teresa Szczepinska (ISCB Student
Council, regional group Poland), Sebastian Schultheiss (ISCB Student
Council, regional group Germany), Stefan Günther (Freiburg) and Kristian
Rother (Poznan).

Best Regards,
    Kristian