Google Summer of Code Ideas
The goal of MSL is to create a toolbox that enables the study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a the distance between two atoms) to complex applications (protein design).
The MSL is not just a program (although some applications are distributed) but a tool for scientists to develop their own methods.
The core of MSL has stabilized over years of development and can be easily extended to create a wide range of applications.
MSL has been extensively used in scientific publications encompassing a variety of applications.
1) Protein structure prediction
4) Modeling algorithms/methods
Ideas
1) Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.
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Knowledge Prerequisite:
2) MSL-light
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3) Convert MSL pointers to using a Smart/Owning pointer system
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4) Create a centralized options mechanism that makes managing options easier.
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5) Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.
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6) Creating a web interface to run MSL programs.
Brief explanation:
There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.
Expected results:
A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.
Knowledge Prerequisite:
Scripting Languages and Web Design
Please email mslib-discussion@lists.sourceforge.net if you would like to work on any of these ideas.
