[Biopython-dev] Proposal for GSoC 2017

[Sourav Singh]

Hello Everyone,

I am looking to propose a project for GSoC 2017 under BioPython.

I have written my project proposal below. If anyone would be interested in
mentoring me on the project, it would be great.

*Project Title*- Add support for LLVM/ CUDA kernels to BioPython using
Numba.



*About Project-*
Currently Biopython has support for PyPy compiler, but the support for PyPy
is not proper since Biopython depends on NumPy for certain functionalities,
and NumPy has been ported to PyPy compiler. The aim of this project is to
add support for LLVM compiler and if needed, support for GPUs through Numba.

*Approach-*

I am currently trying to undertake some pilot tests on kNN module of
Biopython and benchmark the results accordingly. The project would involve
adding support for LLVM using Numba for certain specific modules in
Biopython which can benefit highly with the speedup. If needed, Support for
CUDA kernels can also be added to Biopython.

*Knowledge required-*

1) Programming skills in Python
2) Knowledge of BioPython internals.
3) Knowledge of LLVM workings
4) Knowledge of CUDA.



*Difficulty-*
Medium to Hard depending on the kind of module being worked on.

Regards,

Sourav
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