Google Summer of Code 2013
BioJava at GSoC Introduction
BioJava is applying to take part in this year’s Google Summer of Code again as part of the OBF - the Open Bioinformatics Foundation. See this year’s GSoC page of the OBF.
If you want to propose a project, have a look at the
Please read the GSoC page at the Open Bioinformatics Foundation and the main Google Summer of Code page for more details about the program.
Mentor List
The following developers are possible Mentors for 2013:
- Peter Troshin
- Spencer Bliven
- Michael Heuer
- Andreas Prlic
Project Proposals
Port the BioJava 1 or 2 functionality to BioJava 3
As you might have noticed some functionality present in BioJava 1/2 is missing from the BioJava 3. This is not because this functionality is obsolete or not needed; this is because nobody had time to refactor it to work in the BioJava 3.
So your challenge is to identify such functionality and write a proposal where you specify
- What functionality you are going to port
- How you are going to do that (e.g. what needs changing)
This project is be suitable to a confident Java developer.
Please send your proposals to the BioJava dev mailing list early, so we can discuss them in details.
P.S. Actually you are not limited to the old versions of BioJava, there are plenty of small little known Java projects in the Bioinformatics field which can be of interest to a wider user community. You can integrate them as a whole or cannibalize them and extract something useful on its own. You are more than welcome to optimize and improve the code while porting it to BioJava as you see fit.
Possible Mentors
Peter Troshin 2nd mentor : not yet assigned
Improve structural alignment datastructures to support topology-independent alignments
Rationale
BioJava contains a number of algorithms for aligning protein structures. In the most general case, an alignment consists of a mapping between residues of two (or more) proteins. However, for historical and performance reasons alignments are stored as linear, sorted arrays. This makes it difficult to express cases where the order of aligned residues differs between the two proteins. For instance, storing the following alignment requires some creative work-arounds:
123456
456123
Additionally, the class to store structural alignments (AFPChain) contains a number of unneccessary, poorly documented, or algorithm-specific parameters which should be removed or refactored.
Approach & Goals
Your challenge is to propose and implement a data structure for storing structure alignments which
- Is flexible enough to store topology-independent alignments
- Efficiently utilizes memory
- Has good performance for common tasks
Difficulty and needed skills
Moderate technical difficulty, but requires strong planning and abstract thinking.
This project requires an understanding of basic data structures and performance considerations. A successful proposal should consider not only the new data structure, but also suggest a plan for integrating it into existing methods, particularly in the biojava3-structure and biojava3-structure-gui modules.
Possible Mentors
Spencer Bliven 2nd mentor: not yet assigned
Topology Diagrams of Protein Structures
Rationale
Topology diagrams are useful for visualising the arrangement and connectivity of secondary structure elements of proteins. We are currently not aware of an easy to use Java implementation of software for drawing such diagrams.
Approach & Goals
The goal of this project would be to use the available tools from biojava (load structures, define secondary structure) and implement a layout algorithm that would arrange a representation of secondary structure elements in a way so it can be easily used for various visualisation libraries. Depending on the speed of progress a visualisation layer could be added on top of this (e.g HTML5 vector graphics, JPanel, etc.).
Difficulty and needed skills
This project requires some algorithmic knowledge for developing the layout-algorithm for the secondary structure elements.
Possible Mentors
Andreas Prlic 2nd mentor: not yet assigned
Sequence Variation
Rationale
Several similar file specifications exist for dealing with sequence variation, including:
VCF (Variant Call Format) is a text file format used by the 1000 Genomes project and others for representing variation against a reference sequence.
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
The Genome Variation Format (GVF) is a text file format for describing sequence variants at nucleotide resolution relative to a reference genome. GVF is a type of GFF3 file with additional pragmas and attributes specified.
http://www.sequenceontology.org/resources/gvf_1.02.html http://www.sequenceontology.org/resources/gff3.html
Some support for these file specifications is already present in various bioinformatics libraries (and in fact biojava3 already provides GFF3 support); it would be desireable to pull these together behind a set of common APIs in biojava3.
Approach & Goals
- Consider existing open source VCF and GVF implementations (Genotype Analysis Toolkit, GATK, VCFTools, Picard, GVF-Parser, etc.)
- Design APIs for common entities (Allele, Genotype, Haplotype, etc.)
- Create adaptors to third party implementations or implement support directly in Biojava3
Difficulty and needed skills
Moderate difficulty.
Strength in API design, the ability to learn from existing codebases, and experience with Java and other languages (i.e. Perl and Python) will be necessary.
Possible Mentors
Michael Heuer 2nd mentor: not yet assigned