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Community           Integration        Democratization




            Biopython: challenges

                 Brad Chapman
                   Peter Cock
              Biopython contributors
             http://biopython.org


                  10 July 2010
Community               Integration           Democratization




    3 challenges for successful open source
    projects

            Community
            Integration
            Democratization
Community     Integration   Democratization



Distributed code access
Community             Integration          Democratization



Recruiting and training
    Google Summer of Code

            2009   Eric Talevich
                   phyloXML; Bio.Phylo
                   Nick Matzke
                   Biogeographical Phylogenetics
            2010   Jo˜o Rodrigues
                     a
                   Structural biology; Bio.PDB
Community     Integration    Democratization



Answering questions better
Community     Integration   Democratization



Recognizing contributions
Community     Integration    Democratization



Diversity of Python bioinformatics
Community               Integration           Democratization



Interoperability


            Avoid re-implementation
            Convert core objects
            Document workflows with multiple
            libraries
            Communicate better
Community               Integration            Democratization



Wrapping external tools


    import subprocess
    from Bio.Blast.Applications import (
            NcbiblastxCommandline)
    cl = NcbiblastxCommandline(query="opuntia.fasta",
            db="nr", evalue=0.001, outfmt=5,
            out="opuntia.xml")
    subprocess.call(str(cl))
Community    Integration   Democratization



Documenting standards
Community               Integration            Democratization



Making code easier to use

    >>> from Bio import SeqIO
    >>> memory_dict = SeqIO.index("in.gb", "genbank")
    >>> memory_dict.keys()
    [’Z78484.1’, ... ’Z78471.1’]
    >>> seq_record = memory_dict["Z78475.1"]
    >>> print seq_record.description
    P.supardii 5.8S rRNA gene and ITS1 and ITS2 DNA
    >>> seq_record.seq
    Seq(’CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGG...GGT’,
            IUPACAmbiguousDNA())
Community     Integration   Democratization



Challenges of big data
Community                  Integration                 Democratization



Cloud: easier to distribute

            On-demand computational resources like
            Amazon EC2
            Provide ready-to-go images
            Biopython and many associated
            bioinformatics libraries
            Biological data
    http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
Community          Integration      Democratization



Following up


       Home http://biopython.org
        Code http://github.com/biopython
       BOSC Talk to Eric, Tiago or myself

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Biopython at BOSC 2010

  • 1. Community Integration Democratization Biopython: challenges Brad Chapman Peter Cock Biopython contributors http://biopython.org 10 July 2010
  • 2. Community Integration Democratization 3 challenges for successful open source projects Community Integration Democratization
  • 3. Community Integration Democratization Distributed code access
  • 4. Community Integration Democratization Recruiting and training Google Summer of Code 2009 Eric Talevich phyloXML; Bio.Phylo Nick Matzke Biogeographical Phylogenetics 2010 Jo˜o Rodrigues a Structural biology; Bio.PDB
  • 5. Community Integration Democratization Answering questions better
  • 6. Community Integration Democratization Recognizing contributions
  • 7. Community Integration Democratization Diversity of Python bioinformatics
  • 8. Community Integration Democratization Interoperability Avoid re-implementation Convert core objects Document workflows with multiple libraries Communicate better
  • 9. Community Integration Democratization Wrapping external tools import subprocess from Bio.Blast.Applications import ( NcbiblastxCommandline) cl = NcbiblastxCommandline(query="opuntia.fasta", db="nr", evalue=0.001, outfmt=5, out="opuntia.xml") subprocess.call(str(cl))
  • 10. Community Integration Democratization Documenting standards
  • 11. Community Integration Democratization Making code easier to use >>> from Bio import SeqIO >>> memory_dict = SeqIO.index("in.gb", "genbank") >>> memory_dict.keys() [’Z78484.1’, ... ’Z78471.1’] >>> seq_record = memory_dict["Z78475.1"] >>> print seq_record.description P.supardii 5.8S rRNA gene and ITS1 and ITS2 DNA >>> seq_record.seq Seq(’CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGG...GGT’, IUPACAmbiguousDNA())
  • 12. Community Integration Democratization Challenges of big data
  • 13. Community Integration Democratization Cloud: easier to distribute On-demand computational resources like Amazon EC2 Provide ready-to-go images Biopython and many associated bioinformatics libraries Biological data http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
  • 14. Community Integration Democratization Following up Home http://biopython.org Code http://github.com/biopython BOSC Talk to Eric, Tiago or myself