Difference between revisions of "Google Summer of Code Ideas"

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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).
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'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.
  
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The MSL is not just a program (although some applications are distributed) but a tool for scientists to develop their own methods.
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'''Goal'''
  
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The core of MSL has stabilized over years of development and can be easily extended to create a wide range of applications.
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The goal of MSL is to create a toolbox to enable a programmer to design powerful and advanced applications for molecular analysis, modeling, prediction and design.  At the same time, MSL should also allow the rapid creation of applications that perform simple tasks (for example, measuring the distance between two atoms).
  
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MSL has been extensively used in scientific publications encompassing a variety of applications.
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'''History'''
  
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MSL has been developed in the past 5 year (9 years if we include its early predecessor).  It has an extensive code base (over 150 objects and 100,000 lines of code).  After years in beta, the first stable version (1.0) released was released in 2012.
  
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1) [http://senes.biochem.wisc.edu/pdf/FtsBdimer-preprint.pdf Protein structure prediction]
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The MSL primary citation and description is the following:
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* Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A "Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)", ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 [http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF]
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MSL has been extensively used in scientific publications encompassing a variety of applications. For example,  [http://senes.biochem.wisc.edu/pdf/FtsBdimer-preprint.pdf protein structure prediction], [http://www.ncbi.nlm.nih.gov/pubmed/23422424 protein design], [http://www.ncbi.nlm.nih.gov/pubmed/23089864 protein engineering] and [http://senes.biochem.wisc.edu/pdf/EBL-2012-Proteins.pdf modeling algorithms/methods].
  
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2) [http://www.ncbi.nlm.nih.gov/pubmed/23422424 Protein design]
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'''Current development'''
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3) [http://www.ncbi.nlm.nih.gov/pubmed/23089864 Protein Engineering]
 
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4) [http://senes.biochem.wisc.edu/pdf/EBL-2012-Proteins.pdf Modeling algorithms/methods]
 
  
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Write a paragraph linking to the following ideas...
  
  

Revision as of 19:34, 28 March 2013

MSL (Molecular Software Libraries) is an open source C++ library of objects related to macromolecular modeling.

Goal

The goal of MSL is to create a toolbox to enable a programmer to design powerful and advanced applications for molecular analysis, modeling, prediction and design. At the same time, MSL should also allow the rapid creation of applications that perform simple tasks (for example, measuring the distance between two atoms).

History

MSL has been developed in the past 5 year (9 years if we include its early predecessor). It has an extensive code base (over 150 objects and 100,000 lines of code). After years in beta, the first stable version (1.0) released was released in 2012.

The MSL primary citation and description is the following:

  • Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A "Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)", J Comput. Chem. 2012 33(20), 1645-61 Download PDF

MSL has been extensively used in scientific publications encompassing a variety of applications. For example, protein structure prediction, protein design, protein engineering and modeling algorithms/methods.

Current development

Write a paragraph linking to the following ideas...


Ideas

1) Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.

Brief explanation:

Expected results:

Knowledge Prerequisite:



2) MSL-light

Brief explanation:

Expected results:

Knowledge Prerequisite:



3) Convert MSL pointers to using a Smart/Owning pointer system

Brief explanation:

Expected results:

Knowledge Prerequisite:



4) Create a centralized options mechanism that makes managing options easier.

Brief explanation:

Expected results:

Knowledge Prerequisite:



5) Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.

Brief explanation:

Expected results:

Knowledge Prerequisite:


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.

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