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Chapman bosc2010 biopython

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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