Difference between revisions of "Google Summer of Code Ideas"

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The main goal of MSL is to create a set of tools that enable the computational study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a distance or edit a dihedral) to complex applications (protein modeling or design).
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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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The MSL library is not a program (although some applications are distributed) but a tool for scientist to code their own methods.
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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.
 +
 
 +
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.  
 
MSL has been extensively used in scientific publications encompassing a variety of applications.  
 +
  
 
1) [http://senes.biochem.wisc.edu/pdf/FtsBdimer-preprint.pdf Protein structure prediction]
 
1) [http://senes.biochem.wisc.edu/pdf/FtsBdimer-preprint.pdf Protein structure prediction]
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4) [http://senes.biochem.wisc.edu/pdf/EBL-2012-Proteins.pdf Modeling algorithms/methods]
 
4) [http://senes.biochem.wisc.edu/pdf/EBL-2012-Proteins.pdf Modeling algorithms/methods]
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1) Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.
 
1) Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.
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 +
Brief explanation:
 +
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Expected results:
 +
 +
Knowledge Prerequisite:
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 +
 +
  
 
2) MSL-light
 
2) MSL-light
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 +
Brief explanation:
 +
 +
Expected results:
 +
 +
Knowledge Prerequisite:
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 +
 +
  
 
3) Convert MSL pointers to using a Smart/Owning pointer system
 
3) Convert MSL pointers to using a Smart/Owning pointer system
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 +
Brief explanation:
 +
 +
Expected results:
 +
 +
Knowledge Prerequisite:
 +
 +
 +
  
 
4) Create a centralized options mechanism that makes managing options easier.
 
4) Create a centralized options mechanism that makes managing options easier.
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Brief explanation:
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 +
Expected results:
 +
 +
Knowledge Prerequisite:
 +
 +
 +
  
 
5) Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.  
 
5) Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.  
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Brief explanation:
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Expected results:
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Knowledge Prerequisite:
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6) Creating a web interface to run MSL programs.
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Brief explanation:
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    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 knowledge of MSL.
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 +
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.
 +
 +
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Knowledge Prerequisite:
 +
    Scripting Languages and Web Design
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Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.
 
Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.

Revision as of 19:02, 28 March 2013

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

2) Protein design

3) Protein Engineering

4) Modeling algorithms/methods



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 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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