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Biopython at BOSC 2010
Biopython at BOSC 2010
Biopython at BOSC 2010
Biopython at BOSC 2010
Biopython at BOSC 2010
Biopython at BOSC 2010
Biopython at BOSC 2010
Biopython at BOSC 2010
Biopython at BOSC 2010
Biopython at BOSC 2010
Biopython at BOSC 2010
Biopython at BOSC 2010
Biopython at BOSC 2010
Biopython at BOSC 2010
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Biopython at BOSC 2010

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  • 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

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