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Talk6 biopython bosc2011
 

Talk6 biopython bosc2011

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    Talk6 biopython bosc2011 Talk6 biopython bosc2011 Presentation Transcript

    • Biopython Project Update www.biopython.org Peter J. A. CockJames 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 AcknowleTalk 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 AcknowleWhat 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 AcknowleWhy 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 AcknowleWhy 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 AcknowleBiopython Releases So, what have we done since BOSC 2010?
    • Introduction Biopython Releases Biopython Releases Google Summer of Code Integrated Testing AcknowleBiopython 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 AcknowleBiopython 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 AcknowleBiopython 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 AcknowleBiopython 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 AcknowleGoogle 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 AcknowleBuildbot 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 AcknowlePersonal 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 AcknowleProject 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