GSoC/GCI Archive
Google Summer of Code 2014

Open Bioinformatics Foundation

License: Artistic license 2.0

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The Open Bioinformatics Foundation (OBF) is a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. It acts as an umbrella organization for the BioPerl, Biopython, BioRuby, BioJava, BioSQL and EMBOSS projects, among others, and organizes conferences and workshops to promote and support open-source bioinformatics.


  • [JSBML GSoC Idea#4] Redesign the implementation of mathematical formulas Make the JSBML library more modular by redesigning how mathematical formulas are implemented. End product should be functionally identical to the current library and should be more efficient.
  • Addition of a Lazy Loading Sequence Parser to Biopython’s SeqIO Package Biopython’s SeqIO package is used to parse sequence files such as the popular FASTA format and heavily annotated formats like GenBank flat file format. Currently the module will completely parse a sequence prior to returning a sequence record object. By implementing an indexing and lazy loading sequence parser, Biopython can enable more efficient use of large sequence files such as chromosomes or entire genomes.
  • An ultra-fast scalable RESTful API to query large numbers of VCF datapoints To run arbitrarily complex queries against dense datasets such as VCF genomic mutations one must have a proper data model and a sensible approach towards query composability in order to be able to "take shortcuts" even when the DBMS' query planner wouldn't be able to. "Composability" is a sharp edge but with proper tooling one can evade the most common pitfalls while still being able to abstract-away implementation details.
  • Dynamic Modeling of Cellular Populations within JSBML The goal of the project is to help the JSBML community standardize the dynamic modeling of cellular population. The proposed project is intended to assist the JSBML community in the development of potential packages required for dynamic modeling of cellular population. Namely, the goal is to help the community with the arrays, dynamic structure, and hierarchical model composition packages.
  • Improving the Plug-in interface for CellDesigner This proposal attempts to allow a program written in JSBML to map CellDesigner’s plug-in data structure to a JSMBL data structure, among other goals. First, the SMBL Layout Extension and Render Extension will be used to clone the CellDesigner network layout. Second, JSBML-based plugins will pull data from CellDesigner so the CellDesigner model will be fully represented in JSBML. Finally, a plug-in will be developed that will randomly generate a biochemical network and will be written in JSBML.
  • Open Source high-performance Biohaskell Providing Open Source programs as it is done by the Open Bioinformatics Foundation (OBF) is helpful and time-saving for many researchers. I would like to support this idea by contributing to the OBF. I bring experience in a bio-computational research project, a mathematical background and desire to deepen my knowledge of functional programming. I am particularly interested in the transitive alignment project mentored by Ketil Malde (Biohaskell) since the idea seems to be new and challenging.