biopython at bosc 2010
TRANSCRIPT
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Community Integration Democratization
Biopython: challenges
Brad Chapman
Peter Cock
Biopython contributors
http://biopython.org
10 July 2010
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Community Integration Democratization
3 challenges for successful open source
projects
Community
Integration
Democratization
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Community Integration Democratization
Distributed code access
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Community Integration Democratization
Recruiting and training
Google Summer of Code
2009 Eric Talevich
phyloXML; Bio.Phylo
Nick Matzke
Biogeographical Phylogenetics
2010 Joao Rodrigues
Structural biology; Bio.PDB
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Community Integration Democratization
Answering questions better
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Community Integration Democratization
Recognizing contributions
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Community Integration Democratization
Diversity of Python bioinformatics
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Community Integration Democratization
Interoperability
Avoid re-implementation
Convert core objects
Document workflows with multiple
libraries
Communicate better
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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))
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Community Integration Democratization
Documenting standards
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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())
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Community Integration Democratization
Challenges of big data
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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/
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Community Integration Democratization
Following up
Home http://biopython.org
Code http://github.com/biopython
BOSC Talk to Eric, Tiago or myself