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E Talevich - Biopython project-update

  1. 1. Project Update Bioinformatics Open Source Conference (BOSC) July 14, 2012 Long Beach, California, USA Eric Talevich, Peter Cock, Brad Chapman, João Rodrigues, and Biopython contributors
  2. 2. Hello, BOSC Biopython is a freely available Python library for biological computation, and a long-running, distributed collaboration to produce and maintain it [1]. ● Supported by the Open Bioinformatics Foundation (OBF) ● "This is Python's Bio* library. There are several Bio* libraries like it, but this one is ours." ● http://biopython.org/ _____ [1] Cock, P.J.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., de Hoon, M.J. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. doi:10.1093 /bioinformatics/btp163
  3. 3. Bio.Graphics (Biopython 1.59, February 2012) New features in... BasicChromosome: ● Draw simple sub-features on chromosome segments ● Show the position of genes, SNPs or other loci GenomeDiagram [2]: ● Cross-links between tracks ● Track-specific start/end positions for showing regions _____ [2] Pritchard, L., White, J.A., Birch, P.R., Toth, I. (2010) GenomeDiagram: a python package for the visualization of large-scale genomic data. Bioinformatics 2(5) 616-7. doi:10.1093/bioinformatics/btk021
  4. 4. BasicChromosome: Potato NB-LRRs Jupe et al. (2012) BMC Genomics
  5. 5. GenomeDiagram: A tale of three phages Swanson et al. (2012) PLoS One (to appear)
  6. 6. GenomeDiagram imitates Artemis Comparison Tool (ACT)
  7. 7. SeqIO and AlignIO (Biopython 1.58, August 2011) ● SeqXML format [3] ● Read support for ABI chromatogram files (Wibowo A.) ● "phylip-relaxed" format (Connor McCoy, Brandon I.) ○ Relaxes the 10-character limit on taxon names ○ Space-delimited instead ○ Used in RAxML, PhyML, PAML, etc. _____ [3] Schmitt et al. (2011) SeqXML and OrthoXML: standards for sequence and orthology information. Briefings in Bioinformatics 12(5): 485-488. doi:10.1093 /bib/bbr025
  8. 8. Bio.Phylo & pypaml ● PAML interop: wrappers, I/O, glue ○ Merged Brandon Invergo’s pypaml as Bio.Phylo.PAML (Biopython 1.58, August 2011) ● Phylo.draw improvements ● RAxML wrapper (Biopython 1.60, June 2012) ● Paper in review [4] _____ [4] Talevich, E., Invergo, B.M., Cock, P.J.A., Chapman, B.A. (2012) Bio.Phylo: a unified toolkit for processing, analysis and visualization of phylogenetic data in Biopython. BMC Bioinformatics, in review
  9. 9. Phylo.draw and matplotlib
  10. 10. Bio.bgzf (Blocked GNU Zip Format) ● BGZF is a GZIP variant that compresses blocks of a fixed, known size ● Used in Next Generation Sequencing for efficient random access to compressed files ○ SAM + BGZF = BAM Bio.SeqIO can now index BGZF compressed sequence files. (Biopython 1.60, June 2012)
  11. 11. TogoWS (Biopython 1.59, February 2012) ● TogoWS is an integrated web resource for bioinformatics databases and services ● Provided by the Database Center for Life Science in Japan ● Usage is similar to NCBI Entrez _____ http://togows.dbcls.jp/
  12. 12. PyPy and Python 3 Biopython: ● works well on PyPy 1.9 (excluding NumPy & C extensions) ● works on Python 3 (excluding some C extensions), but concerns remain about performance in default unicode mode. ○ Currently 'beta' level support.
  13. 13. Bio.PDB ● mmCIF parser restored (Biopython 1.60, June 2012) ○ Lenna Peterson fixed a 4-year-old lex/yacc-related compilation issue ○ That was awesome ○ Now she's a GSoC student ○ Py3/PyPy/Jython compatibility in progress ● Merging GSoC results incrementally ○ Atom element names & weights (João Rodrigues, GSoC 2010) ○ Lots of feature branches remaining...
  14. 14. Bio.PDB feature branches PDBParser Bio.Struct Mocapy++ Generic Features InterfaceAnalysis mmCIF Parser GSOC '10 '11 '12 ...
  15. 15. Google Summer of Code (GSoC) In 2011, Biopython had three projects funded via the OBF: ● Mikael Trellet (Bio.PDB) ● Michele Silva (Bio.PDB, Mocapy++) ● Justinas Daugmaudis (Mocapy++) In 2012, we have two projects via the OBF: ● Wibowo Arindrarto: (SearchIO) ● Lenna Peterson: (Variants) _____ http://biopython.org/wiki/Google_Summer_of_Code http://www.open-bio.org/wiki/Google_Summer_of_Code https://www.google-melange.com/
  16. 16. GSoC 2011: Mikael Trellet Biomolecular interfaces in Bio.PDB Mentor: João Rodrigues ● Representation of protein-protein interfaces: SM(I)CRA ● Determining interfaces from PDB coordinates ● Analyses of these objects _____ http://biopython.org/wiki/GSoC2011_mtrellet
  17. 17. GSoC 2011: Michele Silva Python/Biopython bindings for Mocapy++ Mentor: Thomas Hamelryck Michele Silva wrote a Python bridge for Mocapy++ and linked it to Bio.PDB to enable statistical analysis of protein structures. More-or-less ready to merge after the next Mocapy++ release. _____ http://biopython.org/wiki/GSOC2011_Mocapy
  18. 18. GSoC 2011: Justinas Daugmaudis Mocapy extensions in Python Mentor: Thomas Hamelryck Enhance Mocapy++ in a complementary way, developing a plugin system for Mocapy++ allowing users to easily write new nodes (probability distribution functions) in Python. He's finishing this as part of his master's thesis project with Thomas Hamelryck. _____ http://biopython.org/wiki/GSOC2011_MocapyExt
  19. 19. GSoC 2012: Lenna Peterson Diff My DNA: Development of a Genomic Variant Toolkit for Biopython Mentors: Brad Chapman, James Casbon ● I/O for VCF, GVF formats ● internal schema for variant data _____ http://arklenna.tumblr.com/tagged/gsoc2012
  20. 20. GSoC 2012: Wibowo Arindrarto SearchIO implementation in Biopython Mentor: Peter Cock Unified, BioPerl-like API for search results from BLAST, HMMer, FASTA, etc. _____ http://biopython.org/wiki/SearchIO http://bow.web.id/blog/tag/gsoc/
  21. 21. Thanks ● OBF ● BOSC organizers ● Biopython contributors ● Scientists like you Check us out: ● Website: http://biopython.org ● Code: https://github.com/biopython/biopython

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