Note: Each slide has a '.' at the bottom left corner which
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Presentations by Andrew Dalke
Dalke Scientific Software, LLC
O'Reilly Bioinformatics Conference
January 28-31, 2002
is an international collaboration to collect and produce open source
bioinformatics tools written in the Python programming
language. Founded in 1999 it now has users and developers from four
different continents. Biopython is one of the projects developed under
the umbrella of the Open Bioinformatics Foundation (www.open-bio.org).
This is an exciting time in the Biopython. We are approaching the 1.0
release. The distribution includes interfaces to query local and
distributed bioinformatics tools and databases, data structures for
manipulating biological resources, a generalized parsing framework
which unifies the many flat-file formats, libraries for working with
different database systems, and servers to provide remote access to
The presentation will start with an overview of the Biopython project
then show how the different aspects can be used to build a
bioinformatics platform for a research group. It will end with
pointers to other Python projects in the life sciences, including
projects in structural biology and chemical informatics.
Martel, Parsing, and Bioformats
One of the tedious problems in bioinformatics is dealing with legacy
flat-file formats. In this talk Andrew will present Martel, the
Biopython parser generator which lets us handle existing files as if
they are already in XML.
A Plea for Paranoia
Code, documentation, and databases all have errors. All too often they
are silent and hidden. Just because something seems to work and has
been used for years doesn't mean it's right. I'll show problems taken
from bio software and suggestions for how to write and test code to
make errors noisy and visible.