The Open Bioinformatics foundation successfully applied to participate in the Google Summer of Code.
Usually, each BioPython proposal has one or more mentors assigned to it. Nevertheless, we encourage potential students to contact the mailing list with their own ideas for proposals. There is therefore not a set list of 'available' mentors, since it highly depends on which projects are proposed every year.
Past mentors include:
The BioPython proposals for 2013 will be published here once discussed. We encourage potential students to join the mailing lists and actively participate in these discussions, either by submitting their own ideas or contributing to improving existing ones.
- 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.
- Difficulty and needed skills
- Medium/Hard depending on how many objectives are attempted. The student needs to be fluent in Python and have knowledge of the BioPython codebase. 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 & 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
- 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.
- Reece Hart (Locus Development, San Francisco); Brad Chapman; James Casbon