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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

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Talk6 biopython bosc2011

  • 1. 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
  • 2. 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
  • 3. 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
  • 4. 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?
  • 5. 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?
  • 6. Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing Acknowle Biopython Releases So, what have we done since BOSC 2010?
  • 7. 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
  • 8. 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
  • 9. 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
  • 10. 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
  • 11. 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++
  • 12. 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!
  • 13. 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
  • 14. 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