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
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
Biopython at BOSC 2010