Biopython Project Updatewww.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 Acknowledgements

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 Acknowledgements

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 Acknowledgements

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 speci�c needs to narrow the choice?

Which logo do you like best?

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowledgements

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 speci�c needs to narrow the choice?

Which logo do you like best?

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowledgements

Biopython Releases

So, what have we done since BOSC 2010?

Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowledgements

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 Acknowledgements

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 Acknowledgements

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 Acknowledgements

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 Acknowledgements

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 Acknowledgements

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 Acknowledgements

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 Acknowledgements

Project Acknowledgements

Open Bioinformatics Foundation (OBF)

(Non-pro�t 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