Biopython Project Update
www.biopython.org
Peter J. A. Cock
James Hutton Institute (formerly Scottish Crop Research Institute),
Invergowrie, Dundee, DD2 5DA, Scotland, UK
Saturday 16th July 2011,
Bioinformatics Open Source Conference (BOSC),
ISMB/ECCB, Vienna, Austria

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
Talk Outline
1 Introduction
2 Biopython Releases
3 Biopython Releases
4 Google Summer of Code
5 Integrated Testing
6 Acknowledgements

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
What is Biopython?
Free, open source library for bioinformatics
Supported by Open Bioinformatics Foundation
Runs on Windows, Linux, Mac OS X, etc
International team of volunteer developers
Currently about three releases per year
Extensive Biopython Tutorial Cookbook
See www.biopython.org for more details

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
Why Biopython?
Python Perl Ruby Java
Biopython BioPerl BioRuby BioJava
All the Bio* OBF projects are now mature and capable. . .
Which programming language are you most comfortable in?
Which language/library do your group/colleagues use?
Do you have any specic needs to narrow the choice?

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
Why Biopython?
Python Perl Ruby Java
Biopython BioPerl BioRuby BioJava
All the Bio* OBF projects are now mature and capable. . .
Which programming language are you most comfortable in?
Which language/library do your group/colleagues use?
Do you have any specic needs to narrow the choice?
Which logo do you like best?

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
Biopython Releases
So, what have we done since BOSC 2010?

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
Biopython 1.55 (August 2010)
Lots of work on Python 3 support
Made our command line tool wrappers directly executable
12 contributors, 6 new

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
Biopython 1.56 (Nov 2010)
UniProt XML parser
IMGT parser and writer (variant of EMBL le format)
13 contributors, 6 new

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
Biopython 1.57 (April 2011)
Index sequence at les with SQLite backend
15 contributors, 6 new

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
Biopython 1.58 (August 2011?)
Support for PAML (Phylogenetic Analysis by Maximum
Likelihood) package
SeqXML parser, see http://seqxml.org
Explicit initial probabilities in HMM Viterbi algorithm
So far 9 contributors, 5 new

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
Google Summer of Code (GSoC)
Last summer (2010)
Joao Rodrigues PDB code
This summer (2011)
Mikael Trellet biomolecular interface analysis
Michele Silva Python bridge for Mocapy++
Justinas Daugmaudis Plugin system for Mocapy++

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
Buildbot
Setup about 6 months ago
Using Buildbot, http://buildbot.org
Runs on Amazon cloud server http://testing.open-bio.org
Slave machine get latest code, build test
Running nightly builds
Cover Linux, Mac OS X and Windows
Cover Python 2.x, 3.1, 3.2 and Jython
Spot regressions early!

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
Personal Acknowledgements
Society for General Microbiology (SGM)
Travel grant to attend BOSC/ISMB/ECCB
James Hutton Institute
(formerly Scottish Crop Research Institute), UK
My supportive employers

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle
Project Acknowledgements
Open Bioinformatics Foundation (OBF)
(Non-prot which looks after Bio* projects)
BioTeam Inc.
(Company that hosts the OBF servers)
GitHub Inc.
(Repository hosting)
Google Summer of Code
(Six students funded so far)
The many individuals who have
contributed over the years