Google Summer of Code
As part of the Open Bioinformatics Foundation, Biopython is participating in Google Summer of Code (GSoC) again in 2012. This page contains a list of project ideas for the upcoming summer; potential GSoC students can base an application on any of these ideas, or propose something new.
In 2009, Biopython was involved with GSoC in collaboration with our friends at NESCent, and had two projects funded:
- Nick Matzke worked on Biogeographical Phylogenetics.
- Eric Talevich added support for parsing and writing phyloXML.
In 2010, another project was funded:
- João Rodrigues worked on the Structural Biology module Bio.PDB, adding several features used in everyday structural bioinformatics. These features are now gradually being merged into the mainline with João's help.
In 2011, three projects were funded in Biopython via the OBF:
- Mikael Trellet added support for biomolecular interface analysis to the Bio.PDB module.
- Michele Silva wrote a Python bridge for Mocapy++ and linked it to Bio.PDB to enable statistical analysis of protein structures.
- Justinas Daugmaudis also enhanced Mocapy++ in a complementary way, developing a plugin system for Mocapy++ allowing users to easily write new nodes (probability distribution functions) in Python.
In 2012, two projects were funded in Biopython via the OBF:
- Wibowo Arindrarto: SearchIO Implementation in Biopython (blog)
- Lenna Peterson: Diff My DNA: Development of a Genomic Variant Toolkit for Biopython (blog)
Please read the GSoC page at the Open Bioinformatics Foundation and the main Google Summer of Code page for more details about the program. If you are interested in contributing as a mentor or student next year, please introduce yourself on the mailing list.
2012 Project ideas
- Biopython has general APIs for parsing and writing assorted sequence file formats (SeqIO), multiple sequence alignments (AlignIO), phylogenetic trees (Phylo) and motifs (Bio.Motif). An obvious omission is something equivalent to BioPerl's SearchIO. The goal of this proposal is to develop an easy-to-use Python interface in the same style as SeqIO, AlignIO, etc but for pairwise search results. This would aim to cover EMBOSS muscle & water, BLAST XML, BLAST tabular, HMMER, Bill Pearson's FASTA alignments, and so on.
Much of the low level parsing code to handle these file formats already exists in Biopython, and much as the SeqIO and AlignIO modules are linked and share code, similar links apply to the proposed SearchIO module when using pairwise alignment file formats. However, SearchIO will also support pairwise search results where the pairwise sequence alignment itself is not available (e.g. the default BLAST tabular output). A crucial aspect of this work will be to design a pairwise-search-result object heirachy that reflects this, probably with a subclass inheriting from both the pairwise-search-result and the existing MultipleSequenceAlignment object.
Beyond the initial challenge of an iterator based parsing and writing framework, random access akin to the Bio.SeqIO.index and index_db functionality would be most desirable for working with large datasets.
- The project will cover a range of important file formats from major Bioinformatics tools, thus will require familiarity with running these tools, and understanding their output and its meaning. Inter-converting file formats is part of this.
- Involved toolkits or projects
- Degree of difficulty and needed skills
- Medium/Hard depending on how many objectives are attempted. The student needs to be fluent in Python. Experience with all of the command line tools listed would be clear advantages, as would first hand experience using BioPerl's SearchIO. You will also need to know or learn the git version control system.
- Peter Cock
Representation and manipulation of genomic variants
- Computational analysis of genomic variation requires the ability to reliably communicate and manipulate variants. The goal of this project is to provide facilities within BioPython to represent sequence variation objects, convert them to and from common human and file representations, and provide common manipulations on them.
- Approach and Goals
- Object representation
- identify variation types to be represented (SNV, CNV, repeats, inversions, etc)
- develop internal machine representation for variation types
- ensure coverage of essential standards, including HGVS, GFF, VCF
- External representations
- write parser and generators between objects and external string and file formats
- canonicalize variations with more than one valid representation (e.g., ins versus dup and left shifting repeats).
- develop coordinate mapping between genomic, cDNA, and protein sequences (HGVS)
- release code to appropriate community efforts and write short manuscript
- implement web service for HGVS conversion
- The major challenge in this project is to design an API that separates internal representations of variation from the multiple external representations. Ideally, the libraries developed in this project will provide low-level functionality of coordinate conversion and parsing, and high-level functionality for the most common use cases. This aim requires analyzing the proposals to determine which aspects may be impossible or difficult to represent with a simple grammar.
- pysam VCF support
- Biopython GFF support
- HGVS "nomenclature"
- VCF, [VCFtools http://vcftools.sourceforge.net/]
- GFF3, GVF
- Degree of difficulty and needed skills
- Easy-to-Medium depending on how many objectives are attempted. The student will need have skills in most or all of: basic molecular biology (genomes, transcripts, proteins), genomic variation, Python, BioPython, Perl, BioPerl, NCBI Eutilities and/or Ensembl API. Experience with computer grammars is highly desirable. You will also need to know or learn the git version control system.