MSL-Libraries - User contributions [en]

Main Page

2018-10-29T19:39:22Z

Senes:

=MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.=

[[Image:MSL-logo.png|right|400px]]

'''MSL''' is a open source C++ software library for molecular modeling produced in the [http://seneslab.org '''Senes Lab'''] at the University of Wisconsin-Madison, in collaboration with a team or researchers from a number of Universities and companies.

===Philosophy===
The main goal 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).

The MSL library is '''not''' a program (although some applications are distributed) but a tool for scientist to code their own methods.

===Features===
Some of the features supported by the library are:

* Support for reading and writing PDB and CRD files.
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
* Support for rotamer libraries.
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other energy funtions.
* Support for CHARMM topology and parameter files.
* Structure building from scratch (using internal coordinates)
* Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
* Local backbone sampling.
* Crystal lattice generation.
* A '''[[PyMOL Python Interface]]''' for calling MSL code from within PyMOL.
* A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
* And more...

===Documentation===
The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]'''. A step by step '''[[Tutorial|tutorial]]''' is being assembled.

===Status===
Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.

===Source===

The source code can be downloaded on SourceForge. Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page. ([[ToDo|"To do" list]]).

===Main development team:===

* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* Dan Kulp, Vaccine & Immunotherapy Center, The Wistar Institute and The University of Pennsylvania, PA [https://wistar.org/our-scientists/daniel-kulp, '''Kulp Lab''']
* Jason Donald, Manus Biosynthesis, Cambridge MA
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
* Gevorg Grigoryan, James Zhang, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']

=== Reference ===
Article published using MSL should cite:
<pubmed>22565567</pubmed>

'''MSL (including early versions) has been used in the following work:'''
<pubmed>29301955 29233891 29028318 28076776 26702098 26184105 25216398 25212195 24828077 24569864 24003111 23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>

Main Page

2014-05-24T21:00:01Z

Senes: /* Reference */

=MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.=

[[Image:MSL-logo.png|right|400px]]

'''MSL''' is a open source C++ software library for molecular modeling produced in the [http://seneslab.org '''Senes Lab'''] at the University of Wisconsin-Madison, in collaboration with a team or researchers from a number of Universities and companies.

===Philosophy===
The main goal 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).

The MSL library is '''not''' a program (although some applications are distributed) but a tool for scientist to code their own methods.

===Features===
Some of the features supported by the library are:

* Support for reading and writing PDB and CRD files.
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
* Support for rotamer libraries.
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other energy funtions.
* Support for CHARMM topology and parameter files.
* Structure building from scratch (using internal coordinates)
* Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
* Local backbone sampling.
* Crystal lattice generation.
* A '''[[PyMOL Python Interface]]''' for calling MSL code from within PyMOL.
* A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
* And more...

===Documentation===
The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]'''. A step by step '''[[Tutorial|tutorial]]''' is being assembled.

===Status===
Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.

===Source===

The source code can be downloaded on SourceForge. Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page. ([[ToDo|"To do" list]]).

===Main development team:===

* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA
* Jason Donald, Manus Biosynthesis, Cambridge MA
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
* Gevorg Grigoryan, James Zhang, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']

=== Reference ===
Article published using MSL should cite:
<pubmed>22565567</pubmed>

'''MSL (including early versions) has been used in the following work:'''
<pubmed>24828077 24569864 24003111 23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>

Tutorial:Getting started: Downloading MSL

2014-02-19T00:22:30Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

===Download links===
* '''v.1.1, stable release, created Apr 3, 2013, last update (v.1.1.0.9) Feb 11, 2014'''
** Download a tar ball (.tgz file) from the SourceForge MSL web site '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.0.0.9.tgz/download mslib-1.1.0.9.tgz]'''

* '''v.1.0, old release (bug fixes back-ported), created Jul 8, 2012, last update (v.1.0.0.14) Feb 11, 2014'''
** Download a tar ball (.tgz file) from the SourceForge MSL web site '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.14.tgz/download mslib-1.0.0.14.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----

===History===

==== Version 1.1, released 3 April, 2013 ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

==== Version 1.0,released 8 July, 2013 ====
'''First release'''

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Password-less submit to SVN

2014-02-11T18:19:40Z

Senes: Created page with "=== On your linux computer === * Create a private/public key. '''NOTE:''' set the passphrase to blank. ssh-keygen -t rsa * Print the content of the newly created public key ..."

=== On your linux computer ===
* Create a private/public key. '''NOTE:''' set the passphrase to blank.
ssh-keygen -t rsa

* Print the content of the newly created public key
cat .ssh/id_rsa.pub

* Copy the public key (without line breaks)

=== On SourceForge ===
* Go to https://sourceforge.net/account/ssh
* Log in if prompted
* Paste the public key in the box

Committing code to MSL

2014-02-11T18:14:18Z

Senes: /* Automated checkin */

==Automated checkin==
In the MSL repository exists a "scripts" directory. Inside should be 3 files:
''' submit.py miscUtils.py mslBuildTools.py''' . The primary driver of svn submission is '''submit.py'''

* MUST SUBMIT FROM MSLDIR
> cd $MSLDIR

* To add new files, or to submit modified files, run:
>python ./scripts/submit.py --f <list of files> --m <description of changes,additions>

Note, you can submit multiple files, each with different descriptions if you wish. For instance, you can run:

>python ./scripts/submit.py --f file1.cpp --m "This is a message for file 1."
>python ./scripts/submit.py --f file2.cpp file2.h file3.cpp file3.h Makefile --m "This is a message for files 2 and 3, plus the Makefile."

When you run submit in this way, the files are not yet submitted. The script simply keeps track of the files that you intend to submit.

* Once you are ready to submit all of your files, run:
>python ./scripts/submit.py --now
This will then pull a fresh tree, copy over the files you have indicated previously when running submit.py -f, and then build the tree. Provided the build
completes successfully, the files will then be submitted to the repository. If the build fails, you'll see an error message. You can correct the error and then run submit.py -now again.

Use multiple cores (example 8):
>python ./scripts/submit.py --now 8

* Click here for instructions on how to enable [[Password-less submit to SVN]]

Main Page

2013-11-21T20:06:57Z

Senes:

=MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.=

[[Image:MSL-logo.png|right|400px]]

'''MSL''' is a open source C++ software library for molecular modeling produced in the [http://seneslab.org '''Senes Lab'''] at the University of Wisconsin-Madison, in collaboration with a team or researchers from a number of Universities and companies.

===Philosophy===
The main goal 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).

The MSL library is '''not''' a program (although some applications are distributed) but a tool for scientist to code their own methods.

===Features===
Some of the features supported by the library are:

* Support for reading and writing PDB and CRD files.
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
* Support for rotamer libraries.
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other energy funtions.
* Support for CHARMM topology and parameter files.
* Structure building from scratch (using internal coordinates)
* Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
* Local backbone sampling.
* Crystal lattice generation.
* A '''[[PyMOL Python Interface]]''' for calling MSL code from within PyMOL.
* A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
* And more...

===Documentation===
The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]'''. A step by step '''[[Tutorial|tutorial]]''' is being assembled.

===Status===
Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.

===Source===

The source code can be downloaded on SourceForge. Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page. ([[ToDo|"To do" list]]).

===Main development team:===

* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA
* Jason Donald, Agrivida, Inc., Medford MA
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
* Gevorg Grigoryan, James Zhang, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']

=== Reference ===
Article published using MSL should cite:
<pubmed>22565567</pubmed>

'''MSL (including early versions) has been used in the following work:'''
<pubmed>24003111 23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>

Main Page

2013-11-21T17:40:29Z

Senes: /* MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules. */

=MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.=

[[Image:MSL-logo.png|right|400px]]

'''MSL''' is a open source C++ software library for molecular modeling produced in the [http://seneslab.org '''Senes Lab'''] at the University of Wisconsin-Madison in collaboration with a team or researchers from a number of Universities and companies.

===Philosophy===
The main goal 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).

The MSL library is '''not''' a program (although some applications are distributed) but a tool for scientist to code their own methods.

===Features===
Some of the features supported by the library are:

* Support for reading and writing PDB and CRD files.
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
* Support for rotamer libraries.
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other energy funtions.
* Support for CHARMM topology and parameter files.
* Structure building from scratch (using internal coordinates)
* Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
* Local backbone sampling.
* Crystal lattice generation.
* A '''[[PyMOL Python Interface]]''' for calling MSL code from within PyMOL.
* A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
* And more...

===Documentation===
The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]'''. A step by step '''[[Tutorial|tutorial]]''' is being assembled.

===Status===
Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.

===Source===

The source code can be downloaded on SourceForge. Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page. ([[ToDo|"To do" list]]).

===Main development team:===

* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA
* Jason Donald, Agrivida, Inc., Medford MA
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
* Gevorg Grigoryan, James Zhang, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']

=== Reference ===
Article published using MSL should cite:
<pubmed>22565567</pubmed>

'''MSL (including early versions) has been used in the following work:'''
<pubmed>24003111 23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>

Main Page

2013-11-21T17:40:18Z

Senes: /* MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules. */

=MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.=

[[Image:MSL-logo.png|right|400px]]

MSL is a open source C++ software library for molecular modeling produced in the [http://seneslab.org '''Senes Lab'''] at the University of Wisconsin-Madison in collaboration with a team or researchers from a number of Universities and companies.

===Philosophy===
The main goal 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).

The MSL library is '''not''' a program (although some applications are distributed) but a tool for scientist to code their own methods.

===Features===
Some of the features supported by the library are:

* Support for reading and writing PDB and CRD files.
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
* Support for rotamer libraries.
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other energy funtions.
* Support for CHARMM topology and parameter files.
* Structure building from scratch (using internal coordinates)
* Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
* Local backbone sampling.
* Crystal lattice generation.
* A '''[[PyMOL Python Interface]]''' for calling MSL code from within PyMOL.
* A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
* And more...

===Documentation===
The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]'''. A step by step '''[[Tutorial|tutorial]]''' is being assembled.

===Status===
Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.

===Source===

The source code can be downloaded on SourceForge. Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page. ([[ToDo|"To do" list]]).

===Main development team:===

* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA
* Jason Donald, Agrivida, Inc., Medford MA
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
* Gevorg Grigoryan, James Zhang, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']

=== Reference ===
Article published using MSL should cite:
<pubmed>22565567</pubmed>

'''MSL (including early versions) has been used in the following work:'''
<pubmed>24003111 23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>

Main Page

2013-11-21T17:39:33Z

Senes: /* MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules. */

=MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.=

[[Image:MSL-logo.png|right|400px]]

MSL is a open source C++ software library for molecular modeling produced in the [http://seneslab.org Senes Lab] at the University of Wisconsin-Madison in collaboration with a team or researchers from a number of Universities and companies.

===Philosophy===
The main goal 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).

The MSL library is '''not''' a program (although some applications are distributed) but a tool for scientist to code their own methods.

===Features===
Some of the features supported by the library are:

* Support for reading and writing PDB and CRD files.
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
* Support for rotamer libraries.
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other energy funtions.
* Support for CHARMM topology and parameter files.
* Structure building from scratch (using internal coordinates)
* Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
* Local backbone sampling.
* Crystal lattice generation.
* A '''[[PyMOL Python Interface]]''' for calling MSL code from within PyMOL.
* A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
* And more...

===Documentation===
The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]'''. A step by step '''[[Tutorial|tutorial]]''' is being assembled.

===Status===
Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.

===Source===

The source code can be downloaded on SourceForge. Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page. ([[ToDo|"To do" list]]).

===Main development team:===

* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA
* Jason Donald, Agrivida, Inc., Medford MA
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
* Gevorg Grigoryan, James Zhang, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']

=== Reference ===
Article published using MSL should cite:
<pubmed>22565567</pubmed>

'''MSL (including early versions) has been used in the following work:'''
<pubmed>24003111 23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>

Tutorial:Getting started: Downloading MSL

2013-09-27T19:12:15Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

===Download links===
* '''v.1.1, stable release, created Apr 3, 2013, last update (v.1.1.0.8) Sep 27, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL web site '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.0.0.8.tgz/download mslib-1.1.0.8.tgz]'''

* '''v.1.0, old release (bug fixes back-ported), created Jul 8, 2012, last update (v.1.0.0.13) Sep 18, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL web site '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz/download mslib-1.0.0.13.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----

===History===

==== Version 1.1, released 3 April, 2013 ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

==== Version 1.0,released 8 July, 2013 ====
'''First release'''

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-09-27T19:11:31Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

===Download links===
* '''v.1.1, stable release, created Apr 3, 2013, last update (v.1.1.0.8) Sep 27, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.0.0.8.tgz/download mslib-1.1.0.8.tgz]'''

* '''v.1.0, old release (bug fixes back-ported), created Jul 8, 2012, last update (v.1.0.0.13) Sep 18, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz/download mslib-1.0.0.13.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----

===History===

==== Version 1.1, released 3 April, 2013 ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

==== Version 1.0,released 8 July, 2013 ====
'''First release'''

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-09-26T16:37:37Z

Senes:

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

===Download links===
* '''v.1.1, stable release, created Apr 3, 2013, last update (v.1.1.0.7) Sep 25, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.0.0.7.tgz/download mslib-1.1.0.7.tgz]'''

* '''v.1.0, old release (bug fixes back-ported), created Jul 8, 2012, last update (v.1.0.0.13) Sep 18, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz/download mslib-1.0.0.13.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----

===History===

==== Version 1.1, released 3 April, 2013 ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

==== Version 1.0,released 8 July, 2013 ====
'''First release'''

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-09-26T15:11:34Z

Senes: /* History */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

===Download links===
* '''v.1.1, stable release, created Apr 3, 2013, last update (v.1.1.0.7) Sep 25, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.7.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.7.tgz]'''

* '''v.1.0, old release (bug fixes back-ported), created Jul 8, 2012, last update (v.1.0.0.13) Sep 18, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----

===History===

==== Version 1.1, released 3 April, 2013 ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

==== Version 1.0,released 8 July, 2013 ====
'''First release'''

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-09-26T15:10:54Z

Senes: /* History */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

===Download links===
* '''v.1.1, stable release, created Apr 3, 2013, last update (v.1.1.0.7) Sep 25, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.7.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.7.tgz]'''

* '''v.1.0, old release (bug fixes back-ported), created Jul 8, 2012, last update (v.1.0.0.13) Sep 18, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----

===History===

==== Version 1.1, released 3 April, 2013 ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

==== Version 1.0 first release 8 July, 2013 ====

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-09-26T15:10:01Z

Senes:

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

===Download links===
* '''v.1.1, stable release, created Apr 3, 2013, last update (v.1.1.0.7) Sep 25, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.7.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.7.tgz]'''

* '''v.1.0, old release (bug fixes back-ported), created Jul 8, 2012, last update (v.1.0.0.13) Sep 18, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----

===History===

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

==== Version 1.0 first release (07/08/2012) ====

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-09-26T15:09:32Z

Senes:

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

===Download links===
* '''v.1.1, stable release, created Apr 3, 2013, last update (v.1.1.0.7) Sep 25, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.7.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.7.tgz]'''

* '''v.1.0, old release (bug fixes back-ported), created Jul 8, 2012, last update (v.1.0.0.13) Sep 18, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

===History===

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

==== Version 1.0 first release (07/08/2012) ====

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-09-26T15:07:13Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

===Download links===
* '''v.1.1, stable release, created Apr 3, 2013, last update (v.1.1.0.7) Sep 25, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.7.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.7.tgz]'''

* '''v.1.0, old release (bug fixes back-ported), created Jul 8, 2012, last update (v.1.0.0.13) Sep 18, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Creating branches

2013-09-26T01:26:13Z

Senes: Created page with "Quick memo svn copy svn+ssh://svn.code.sf.net/p/mslib/code/trunk svn+ssh://svn.code.sf.net/p/mslib/code/branches/v.1.2 -m "Creating v.1.2. branch""

Quick memo

svn copy svn+ssh://svn.code.sf.net/p/mslib/code/trunk svn+ssh://svn.code.sf.net/p/mslib/code/branches/v.1.2 -m "Creating v.1.2. branch"

Documentation

2013-09-26T01:25:56Z

Senes: /* Developers of MSL */

==MSL Documentation==

=== Getting started ===
An introduction for first users and some simple programs that illustrate how to use different features of the library are provided in the '''[[Tutorial]]'''.

=== MSL Objects ===
A description of the objects and link to the source code on SourceForge is provided in the '''[[MSL Objects]]''' section

===Distributed Programs===
A number of programs and utilities are distributed with MSL. Check the '''[[MSL Programs]]''' section.

=== MSL by example ===
A number of example on how to do simple or complex tasks: '''[[MSL by example]]'''

=== Developers of MSL ===
* '''[[Committing code to MSL]]'''
* '''[[Creating branches]]'''

Documentation

2013-09-26T01:25:46Z

Senes: /* Developers of MSL */

==MSL Documentation==

=== Getting started ===
An introduction for first users and some simple programs that illustrate how to use different features of the library are provided in the '''[[Tutorial]]'''.

=== MSL Objects ===
A description of the objects and link to the source code on SourceForge is provided in the '''[[MSL Objects]]''' section

===Distributed Programs===
A number of programs and utilities are distributed with MSL. Check the '''[[MSL Programs]]''' section.

=== MSL by example ===
A number of example on how to do simple or complex tasks: '''[[MSL by example]]'''

=== Developers of MSL ===
'''[[Committing code to MSL]]'''
'''[[Creating branches]]'''

Tutorial:Getting started: Downloading MSL

2013-09-26T01:17:14Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

===Download links===
* '''v.1.1 (v.1.1.0.7), stable release, created Apr 3, 2013, last update Sep 25, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.7.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.7.tgz]'''

* '''v.1.0 (v.1.0.0.13), old release (bug fixes back-ported), created Jul 8, 2012, last update Sep 18, 2013'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Compiling MSL with external libraries

2013-09-25T22:15:30Z

Senes:

Certain functions of MSL require the installation of some open-source external libraries.

* '''GSL''' (GNU Scientific Library) [[http://www.gnu.org/software/gsl/]]
* '''BOOST''' (portable C++ source libraries) [[http://www.boost.org]]
* '''GLPK''' (GNU linear programming kit) [[http://www.gnu.org/software/glpk/]]
* '''R''' (R statistical and graphics project) [[http://www.r-project.org/]]

=== What external libraries are really needed? ===
Only '''GLS''' is currently recommend and turned on by default in the Makefile

The other external libraries are needed only to support particular object or applications.

=== How to enable inclusion of the external libraries===

By default MSL '''requires the GSL''' library and will be compiled _without_ the support of the other external libraries and some functionality won't be available. To include the libraries, you need to set some environmental variables.

If you use '''bash''', add the following lines to your .bashrc

<source lang="bash">
# $MSL_GSL set to "T" if GSL is installed or else to "F" (default is T)
# $MSL_BOOST set to "T" if BOOST is installed or else to "F" (default is F)
# $MSL_GLPK set to "T" if GLPK is installed or else to "F" (default is F)
# $MSL_R set to "T" if R is installed or else to "F" (default is F)
export MSL_GSL=T
export MSL_GLPK=F
export MSL_BOOST=F
export MSL_R=F
#export MSL_EXTERNAL_LIB_DIR=/usr/lib
#export MSL_EXTERNAL_INCLUDE_DIR=/usr/include
#export MSL_MACOS=T
#export MSL_DEBUG=F
#export MSL_DIR=$HOME/software/mslib

</source>

If you use '''tcsh''', add the following lines to your .cshrc
<source lang="text">
# $MSL_GSL set to "T" if GSL is installed or else to "F" (default)
# $MSL_BOOST set to "T" if BOOST is installed or else to "F" (default)
# $MSL_GLPK set to "T" if GLPK is installed or else to "F" (default)
# $MSL_R set to "T" if R is installed or else to "F" (default)
setenv MSL_GSL T
setenv MSL_GLPK T
setenv MSL_BOOST T
setenv MSL_R T
#setenv MSL_EXTERNAL_LIB_DIR /usr/lib
#setenv MSL_EXTERNAL_INCLUDE_DIR /usr/include
</source>

The default location of the libraries is '''/usr/lib'''. If you have installed them in a custom location (such as that used below, ~/software/mslib/ext_libs) set the $MSL_EXTERNAL_LIB_DIR environmental variable to the correct location. You will also want to set the $MSL_EXTERNAL_LIB_INCLUDE_DIR if using a custom location (such as that used below, ~/software/mslib/ext_includes).

=== GSL ===
Many functions of MSL depend on [[http://www.gnu.org/software/gsl/ GNU Scientific library (GSL)]], which is therefore highly recommended.

For example, GSL is required by the following objects:
* [[MSL_Objects:RandomNumberGenerator | RandomNumberGenerator]]
* [[MSL_Objects:GSLMinimizer | GSLMinimizer]]
* [[MSL_Objects:MonteCarloOptimization| MonteCarloOptimization]]
* [[MSL_Objects:CCD | CCD]]
* [[MSL_Objects:BackRub | BackRub]]
* [[MSL_Objects:Quench | Quench]]
* [[MSL_Objects:SurfaceAreaAndVolume | SurfaceAreaAndVolume]]

If '''GSL''' is enabled, you should see ''-D__GSL_'' in the compilation command when using make.

====To compile GSL====
GSL can be installed from the software repository (in Ubuntu, libgsl0-dev) or downloaded and installed from a tar file. For a more specific reference see the GSL homepage, but here is an example of the installation procedure:

>tar xzvf gsl-1.14.tar.gz
>cd gsl-1.14
>./configure --prefix=/path/to/desired/directory
>make
>make check
>make install
>cp .libs/libgsl.a ~/software/mslib/ext_libs/
>cp cblas/.libs/libgslcblas.a ~/software/mslib/ext_libs/

# Note the -H, this should follow the symlinks, otherwise you get copies of links with relative paths and then you get errors making MSL that say gsl/gsl_rng.h not found, when you see it there!
> mkdir ~/software/mslib/ext_includes/gsl
> cp -H gsl/* ~/software/mslib/ext_includes/gsl

=== BOOST ===
The following libraries from the [http://www.boost.org/ Boost C++ Libraries] are used in some MSL objects and programs. In Ubuntu, it is available in the package libboost-all-dev.
* Serialization, used for ... in the following objects
** [[MSL_Objects:Atom|Atom]]
** [[MSL_Objects:AtomPointerVector|AtomPointerVector]]
** [[MSL_Objects:CartesianPoint|CartesianPoint]]
** [[MSL_Objects:EnvironmentDatabase|EnvironmentDatabase]]
** [[MSL_Objects:EnvironmentDescriptor|EnvironmentDescriptor]]
** [[MSL_Objects:Frame|Frame]]
** [[MSL_Objects:IcEntry|IcEntry]]
** [[MSL_Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]]
** [[MSL_Objects:Line|Line]]
** [[MSL_Objects:Matrix|Matrix]]
** [[MSL_Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]]
** [[MSL_Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]]
** [[MSL_Objects:SphericalPoint|SphericalPoint]]

* Archive, used for ... in the following objects
** [[MSL_Objects:Atom|Atom]]
** [[MSL_Objects:AtomPointerVector|AtomPointerVector]]
** [[MSL_Objects:CartesianPoint|CartesianPoint]]
** [[MSL_Objects:EnvironmentDatabase|EnvironmentDatabase]]
** [[MSL_Objects:Frame|Frame]]
** [[MSL_Objects:IcEntry|IcEntry]]
** [[MSL_Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]]
** [[MSL_Objects:Line|Line]]
** [[MSL_Objects:Matrix|Matrix]]
** [[MSL_Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]]
** [[MSL_Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]]
** [[MSL_Objects:Selectable|Selectable]]
** [[MSL_Objects:SphericalPoint|SphericalPoint]]

* Regex, used for ... in the following objects
** [[MSL_Objects:MslTools|MslTools]]
** [[MSL_Objects:RegEx|RegEx]]

* Random, used for ... in the following objects
** [[MSL_Objects:RandomSeqGenerator|RandomSeqGenerator]]

Note: if boost is included, version 1.40 (???) or later is required.

If '''BOOST''' is enabled, you should see ''-D__BOOST__ -DBOOST_DISABLE_THREADS'' in the compilation command when using make.

====To Compile BOOST====
>tar xzvf boost-VERSION.tar.gz
>cd boost-VERSION
>./bootstrap.sh --prefix=~/software/mslib/ext_libs
>./b2
> cp ./stage/lib/libboost_*.a ~/software/mslib/ext_libs
> cp -r boost ~/software/mslib/ext_includes/

Assuming MSL library is installed in ~/software/mslib/. You will need to make the ext_includes and ext_libs directories before copying.

=== GLPK ===
The [http://www.gnu.org/software/glpk/ GNU linear programming kit] is required by the [[MSL_Objects:LinearProgrammingOptimization | LinearProgrammingOptimization]] object.

If '''GLPK''' is enabled, you should see ''-D__GLPK__'' in the compilation command when using make.

./configure --prefix=/usr/lib --disable-dl --disable-odbc --disable-mysql --enable-static --without-gmp --without-zlib
make
make install
cp /usr/lib/libglpk.a MSLHOME/ext_libs/
cp /usr/include/glpk.h MSLHOME/ext_includes/

'''NOTE: the current libglpk in Ubuntu appears to be incompatible with MSL'''

=== R ===
The [http://www.r-project.org/ R project] is used by the getDihedrals program. In Ubuntu the package is r-base.

If '''R''' is enabled, you should see ''-D__R__'' in the compilation command when using make.

==== To Compile R ====

===== Compiling R on MAC OS =====
Install R and copy headers into MSL_EXTERNAL_INCLUDE_DIR
cp -r /Library/Frameworks/R.framework/Resources/include/ $MSL_EXTERNAL_INCLUDE_DIR

Download Rcpp
R CMD INSTALL Rcpp_0.8.5.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/Rcpp/lib/x86_64/libRcpp.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/Rcpp/include $MSL_EXTERNAL_INCLUDE_DIR/

R CMD INSTALL RInside_0.2.3.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/RInside/lib/x86_64/libRInside.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/RInside/include $MSL_EXTERNAL_INCLUDE_DIR/

If the above install does not work, one can install from source here is a good resource:
http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Quick-start

===== Compiling R on LINUX OS =====
Success using shared libraries and compiling MSL as shared lib, but static lib has not been done yet. I will link my Makefile for shared-R compile once its cleaned up a bit

First try using the 'apt' system in linux:
sudo apt-get install r-base

If the 'apt' version is not the latest version that you need, then install latest version of R:
sudo apt-get build-dep r-base
tar xvzf R-2.11.1.tar.gz
cd R-2.11.1
./configure
make
sudo make install

Install Rcpp:
sudo /usr/local/bin/R CMD INSTALL Rcpp_0.8.5.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/Rcpp/lib/x86_64/libRcpp.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/Rcpp/include $MSL_EXTERNAL_INCLUDE_DIR/

Install RInside:

R CMD INSTALL RInside_0.2.3.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/RInside/lib/x86_64/libRInside.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/RInside/include $MSL_EXTERNAL_INCLUDE_DIR/

Copy headers into MSL_EXTERNAL_INCLUDE_DIR
cp -r /Library/Frameworks/R.framework/Resources/include/ $MSL_EXTERNAL_INCLUDE_DIR

Tutorial:Getting started: Compiling MSL with external libraries

2013-09-25T22:14:10Z

Senes:

Certain functions of MSL require the installation of some open-source external libraries.

* '''GSL''' (GNU Scientific Library) [[http://www.gnu.org/software/gsl/]]
* '''BOOST''' (portable C++ source libraries) [[http://www.boost.org]]
* '''GLPK''' (GNU linear programming kit) [[http://www.gnu.org/software/glpk/]]
* '''R''' (R statistical and graphics project) [[http://www.r-project.org/]]

=== What external libraries are really needed? ===
Only '''GLS''' is currently recommend and turned on by default in the Makefile

The other external libraries are needed only to support particular object or applications.

=== How to enable inclusion of the external libraries===

By default MSL '''requires the GSL''' library and will be compiled _without_ the support of the other external libraries and some functionality won't be available. To include the libraries, you need to set some environmental variables.

If you use '''bash''', add the following lines to your .bashrc

<source lang="bash">
# $MSL_GSL set to "T" if GSL is installed or else to "F" (default is T)
# $MSL_BOOST set to "T" if BOOST is installed or else to "F" (default is F)
# $MSL_GLPK set to "T" if GLPK is installed or else to "F" (default is F)
# $MSL_R set to "T" if R is installed or else to "F" (default is F)
export MSL_GSL=T
export MSL_GLPK=F
export MSL_BOOST=F
export MSL_R=F
#export MSL_EXTERNAL_LIB_DIR=/usr/lib
#export MSL_EXTERNAL_INCLUDE_DIR=/usr/include
#export MSL_MACOS=T
#export MSL_DEBUG=F
#export MSL_DIR=$HOME/software/mslib

</source>

If you use '''tcsh''', add the following lines to your .cshrc
<source lang="text">
# $MSL_GSL set to "T" if GSL is installed or else to "F" (default)
# $MSL_BOOST set to "T" if BOOST is installed or else to "F" (default)
# $MSL_GLPK set to "T" if GLPK is installed or else to "F" (default)
# $MSL_R set to "T" if R is installed or else to "F" (default)
setenv MSL_GSL T
setenv MSL_GLPK T
setenv MSL_BOOST T
setenv MSL_R T
#setenv MSL_EXTERNAL_LIB_DIR /usr/lib
#setenv MSL_EXTERNAL_INCLUDE_DIR /usr/include
</source>

The default location of the libraries is '''/usr/lib'''. If you have installed them in a custom location (such as that used below, ~/software/mslib/ext_libs) set the $MSL_EXTERNAL_LIB_DIR environmental variable to the correct location. You will also want to set the $MSL_EXTERNAL_LIB_INCLUDE_DIR if using a custom location (such as that used below, ~/software/mslib/ext_includes).

=== GSL ===
Many functions of MSL depend on [[http://www.gnu.org/software/gsl/ GNU Scientific library (GSL)]], which is therefore highly recommended.

For example, GSL is required by the following objects:
* [[MSL_Objects:RandomNumberGenerator | RandomNumberGenerator]]
* [[MSL_Objects:GSLMinimizer | GSLMinimizer]]
* [[MSL_Objects:MonteCarloOptimization| MonteCarloOptimization]]
* [[MSL_Objects:CCD | CCD]]
* [[MSL_Objects:BackRub | BackRub]]
* [[MSL_Objects:Quench | Quench]]
* [[MSL_Objects:SurfaceAreaAndVolume | SurfaceAreaAndVolume]]

If '''GSL''' is enabled, you should see ''-D__GSL_'' in the compilation command when using make.

====To compile GSL====
GSL can be installed from the software repository (in Ubuntu, libgsl0-dev) or downloaded and installed from a tar file. For a more specific reference see the GSL homepage, but here is an example of the installation procedure:

>tar xzvf gsl-1.14.tar.gz
>cd gsl-1.14
>./configure --prefix=/path/to/desired/directory
>make
>make check
>make install
>cp .libs/libgsl.a ~/software/mslib/ext_libs/
>cp cblas/.libs/libgslcblas.a ~/software/mslib/ext_libs/

# Note the -H, this should follow the symlinks, otherwise you get copies of links with relative paths and then you get errors making MSL that say gsl/gsl_rng.h not found, when you see it there!
> mkdir ~/software/mslib/ext_includes/gsl
> cp -H gsl/* ~/software/mslib/ext_includes/gsl

=== BOOST ===
The following libraries from the [http://www.boost.org/ Boost C++ Libraries] are used in some MSL objects and programs. In Ubuntu, it is available in the package libboost-all-dev.
* Serialization, used for ... in the following objects
** [[MSL_Objects:Atom|Atom]]
** [[MSL_Objects:AtomPointerVector|AtomPointerVector]]
** [[MSL_Objects:CartesianPoint|CartesianPoint]]
** [[MSL_Objects:EnvironmentDatabase|EnvironmentDatabase]]
** [[MSL_Objects:EnvironmentDescriptor|EnvironmentDescriptor]]
** [[MSL_Objects:Frame|Frame]]
** [[MSL_Objects:IcEntry|IcEntry]]
** [[MSL_Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]]
** [[MSL_Objects:Line|Line]]
** [[MSL_Objects:Matrix|Matrix]]
** [[MSL_Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]]
** [[MSL_Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]]
** [[MSL_Objects:SphericalPoint|SphericalPoint]]

* Archive, used for ... in the following objects
** [[MSL_Objects:Atom|Atom]]
** [[MSL_Objects:AtomPointerVector|AtomPointerVector]]
** [[MSL_Objects:CartesianPoint|CartesianPoint]]
** [[MSL_Objects:EnvironmentDatabase|EnvironmentDatabase]]
** [[MSL_Objects:Frame|Frame]]
** [[MSL_Objects:IcEntry|IcEntry]]
** [[MSL_Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]]
** [[MSL_Objects:Line|Line]]
** [[MSL_Objects:Matrix|Matrix]]
** [[MSL_Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]]
** [[MSL_Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]]
** [[MSL_Objects:Selectable|Selectable]]
** [[MSL_Objects:SphericalPoint|SphericalPoint]]

* Regex, used for ... in the following objects
** [[MSL_Objects:MslTools|MslTools]]
** [[MSL_Objects:RegEx|RegEx]]

* Random, used for ... in the following objects
** [[MSL_Objects:RandomSeqGenerator|RandomSeqGenerator]]

Note: if boost is included, version 1.40 (???) or later is required.

If '''BOOST''' is enabled, you should see ''-D__BOOST__ -DBOOST_DISABLE_THREADS'' in the compilation command when using make.

====To Compile BOOST====
>tar xzvf boost-VERSION.tar.gz
>cd boost-VERSION
>./bootstrap.sh --prefix=~/software/mslib/ext_libs
>./b2
> cp ./stage/lib/libboost_*.a ~/software/mslib/ext_libs
> cp -r boost ~/software/mslib/ext_includes/

Assuming MSL library is installed in ~/software/mslib/. You will need to make the ext_includes and ext_libs directories before copying.

=== GLPK ===
The [http://www.gnu.org/software/glpk/ GNU linear programming kit] is required by the [[MSL_Objects:LinearProgrammingOptimization | LinearProgrammingOptimization]] object.

If '''GLPK''' is enabled, you should see ''-D__GLPK__'' in the compilation command when using make.

./configure --prefix=/usr/lib --disable-dl --disable-odbc --disable-mysql --enable-static --without-gmp --without-zlib
make
make install
cp /usr/lib/libglpk.a MSLHOME/ext_libs/
cp /usr/include/glpk.h MSLHOME/ext_includes/

'''NOTE: the current libglpk in Ubuntu appears to be incompatible with MSL'''

=== R ===
The [http://www.r-project.org/ R project] is used by the getDihedrals program. In Ubuntu the package is r-base.

If '''R''' is enabled, you should see ''-D__R__'' in the compilation command when using make.

==== To Compile R ====

===== MAC OS =====
Install R and copy headers into MSL_EXTERNAL_INCLUDE_DIR
cp -r /Library/Frameworks/R.framework/Resources/include/ $MSL_EXTERNAL_INCLUDE_DIR

Download Rcpp
R CMD INSTALL Rcpp_0.8.5.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/Rcpp/lib/x86_64/libRcpp.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/Rcpp/include $MSL_EXTERNAL_INCLUDE_DIR/

R CMD INSTALL RInside_0.2.3.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/RInside/lib/x86_64/libRInside.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/RInside/include $MSL_EXTERNAL_INCLUDE_DIR/

If the above install does not work, one can install from source here is a good resource:
http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Quick-start

===== LINUX OS =====
Success using shared libraries and compiling MSL as shared lib, but static lib has not been done yet. I will link my Makefile for shared-R compile once its cleaned up a bit

First try using the 'apt' system in linux:
sudo apt-get install r-base

If the 'apt' version is not the latest version that you need, then install latest version of R:
sudo apt-get build-dep r-base
tar xvzf R-2.11.1.tar.gz
cd R-2.11.1
./configure
make
sudo make install

Install Rcpp:
sudo /usr/local/bin/R CMD INSTALL Rcpp_0.8.5.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/Rcpp/lib/x86_64/libRcpp.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/Rcpp/include $MSL_EXTERNAL_INCLUDE_DIR/

Install RInside:

R CMD INSTALL RInside_0.2.3.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/RInside/lib/x86_64/libRInside.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/RInside/include $MSL_EXTERNAL_INCLUDE_DIR/

Copy headers into MSL_EXTERNAL_INCLUDE_DIR
cp -r /Library/Frameworks/R.framework/Resources/include/ $MSL_EXTERNAL_INCLUDE_DIR

=== OpenMP ===
[http://openmp.org OpenMP] is used by the OnTheFlyManager. In Ubuntu the package is usually installed by default, but may be found under libgomp1.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Compiling MSL with external libraries

2013-09-25T22:12:45Z

Senes: /* How to enable inclusion of the external libraries */

Certain functions of MSL require the installation of some open-source external libraries.

* '''GSL''' (GNU Scientific Library) [[http://www.gnu.org/software/gsl/]]
* '''BOOST''' (portable C++ source libraries) [[http://www.boost.org]]
* '''GLPK''' (GNU linear programming kit) [[http://www.gnu.org/software/glpk/]]
* '''R''' (R statistical and graphics project) [[http://www.r-project.org/]]
* '''OPENMP''' (Open multi-processing) [[http://openmp.org/]]

=== What external libraries are really needed? ===
Only '''GLS''' is currently recommend and turned on by default in the Makefile

The other external libraries are needed only to support particular object or applications.

=== How to enable inclusion of the external libraries===

By default MSL '''requires the GSL''' library and will be compiled _without_ the support of the other external libraries and some functionality won't be available. To include the libraries, you need to set some environmental variables.

If you use '''bash''', add the following lines to your .bashrc

<source lang="bash">
# $MSL_GSL set to "T" if GSL is installed or else to "F" (default is T)
# $MSL_BOOST set to "T" if BOOST is installed or else to "F" (default is F)
# $MSL_GLPK set to "T" if GLPK is installed or else to "F" (default is F)
# $MSL_R set to "T" if R is installed or else to "F" (default is F)
export MSL_GSL=T
export MSL_GLPK=F
export MSL_BOOST=F
export MSL_R=F
#export MSL_EXTERNAL_LIB_DIR=/usr/lib
#export MSL_EXTERNAL_INCLUDE_DIR=/usr/include
#export MSL_MACOS=T
#export MSL_DEBUG=F
#export MSL_DIR=$HOME/software/mslib

</source>

If you use '''tcsh''', add the following lines to your .cshrc
<source lang="text">
# $MSL_GSL set to "T" if GSL is installed or else to "F" (default)
# $MSL_BOOST set to "T" if BOOST is installed or else to "F" (default)
# $MSL_GLPK set to "T" if GLPK is installed or else to "F" (default)
# $MSL_R set to "T" if R is installed or else to "F" (default)
# $MSL_OPENMP set to "T" if OPENMP is installed (default) or else to "F"
setenv MSL_GSL T
setenv MSL_GLPK T
setenv MSL_BOOST T
setenv MSL_R T
setenv MSL_OPENMP T
#setenv MSL_EXTERNAL_LIB_DIR /usr/lib
#setenv MSL_EXTERNAL_INCLUDE_DIR /usr/include
</source>

The default location of the libraries is '''/usr/lib'''. If you have installed them in a custom location (such as that used below, ~/software/mslib/ext_libs) set the $MSL_EXTERNAL_LIB_DIR environmental variable to the correct location. You will also want to set the $MSL_EXTERNAL_LIB_INCLUDE_DIR if using a custom location (such as that used below, ~/software/mslib/ext_includes).

=== GSL ===
Many functions of MSL depend on [[http://www.gnu.org/software/gsl/ GNU Scientific library (GSL)]], which is therefore highly recommended.

For example, GSL is required by the following objects:
* [[MSL_Objects:RandomNumberGenerator | RandomNumberGenerator]]
* [[MSL_Objects:GSLMinimizer | GSLMinimizer]]
* [[MSL_Objects:MonteCarloOptimization| MonteCarloOptimization]]
* [[MSL_Objects:CCD | CCD]]
* [[MSL_Objects:BackRub | BackRub]]
* [[MSL_Objects:Quench | Quench]]
* [[MSL_Objects:SurfaceAreaAndVolume | SurfaceAreaAndVolume]]

If '''GSL''' is enabled, you should see ''-D__GSL_'' in the compilation command when using make.

====To compile GSL====
GSL can be installed from the software repository (in Ubuntu, libgsl0-dev) or downloaded and installed from a tar file. For a more specific reference see the GSL homepage, but here is an example of the installation procedure:

>tar xzvf gsl-1.14.tar.gz
>cd gsl-1.14
>./configure --prefix=/path/to/desired/directory
>make
>make check
>make install
>cp .libs/libgsl.a ~/software/mslib/ext_libs/
>cp cblas/.libs/libgslcblas.a ~/software/mslib/ext_libs/

# Note the -H, this should follow the symlinks, otherwise you get copies of links with relative paths and then you get errors making MSL that say gsl/gsl_rng.h not found, when you see it there!
> mkdir ~/software/mslib/ext_includes/gsl
> cp -H gsl/* ~/software/mslib/ext_includes/gsl

=== BOOST ===
The following libraries from the [http://www.boost.org/ Boost C++ Libraries] are used in some MSL objects and programs. In Ubuntu, it is available in the package libboost-all-dev.
* Serialization, used for ... in the following objects
** [[MSL_Objects:Atom|Atom]]
** [[MSL_Objects:AtomPointerVector|AtomPointerVector]]
** [[MSL_Objects:CartesianPoint|CartesianPoint]]
** [[MSL_Objects:EnvironmentDatabase|EnvironmentDatabase]]
** [[MSL_Objects:EnvironmentDescriptor|EnvironmentDescriptor]]
** [[MSL_Objects:Frame|Frame]]
** [[MSL_Objects:IcEntry|IcEntry]]
** [[MSL_Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]]
** [[MSL_Objects:Line|Line]]
** [[MSL_Objects:Matrix|Matrix]]
** [[MSL_Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]]
** [[MSL_Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]]
** [[MSL_Objects:SphericalPoint|SphericalPoint]]

* Archive, used for ... in the following objects
** [[MSL_Objects:Atom|Atom]]
** [[MSL_Objects:AtomPointerVector|AtomPointerVector]]
** [[MSL_Objects:CartesianPoint|CartesianPoint]]
** [[MSL_Objects:EnvironmentDatabase|EnvironmentDatabase]]
** [[MSL_Objects:Frame|Frame]]
** [[MSL_Objects:IcEntry|IcEntry]]
** [[MSL_Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]]
** [[MSL_Objects:Line|Line]]
** [[MSL_Objects:Matrix|Matrix]]
** [[MSL_Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]]
** [[MSL_Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]]
** [[MSL_Objects:Selectable|Selectable]]
** [[MSL_Objects:SphericalPoint|SphericalPoint]]

* Regex, used for ... in the following objects
** [[MSL_Objects:MslTools|MslTools]]
** [[MSL_Objects:RegEx|RegEx]]

* Random, used for ... in the following objects
** [[MSL_Objects:RandomSeqGenerator|RandomSeqGenerator]]

Note: if boost is included, version 1.40 (???) or later is required.

If '''BOOST''' is enabled, you should see ''-D__BOOST__ -DBOOST_DISABLE_THREADS'' in the compilation command when using make.

====To Compile BOOST====
>tar xzvf boost-VERSION.tar.gz
>cd boost-VERSION
>./bootstrap.sh --prefix=~/software/mslib/ext_libs
>./b2
> cp ./stage/lib/libboost_*.a ~/software/mslib/ext_libs
> cp -r boost ~/software/mslib/ext_includes/

Assuming MSL library is installed in ~/software/mslib/. You will need to make the ext_includes and ext_libs directories before copying.

=== GLPK ===
The [http://www.gnu.org/software/glpk/ GNU linear programming kit] is required by the [[MSL_Objects:LinearProgrammingOptimization | LinearProgrammingOptimization]] object.

If '''GLPK''' is enabled, you should see ''-D__GLPK__'' in the compilation command when using make.

./configure --prefix=/usr/lib --disable-dl --disable-odbc --disable-mysql --enable-static --without-gmp --without-zlib
make
make install
cp /usr/lib/libglpk.a MSLHOME/ext_libs/
cp /usr/include/glpk.h MSLHOME/ext_includes/

=== R ===
The [http://www.r-project.org/ R project] is used by the getDihedrals program. In Ubuntu the package is r-base.

If '''R''' is enabled, you should see ''-D__R__'' in the compilation command when using make.

==== To Compile R ====

===== MAC OS =====
Install R and copy headers into MSL_EXTERNAL_INCLUDE_DIR
cp -r /Library/Frameworks/R.framework/Resources/include/ $MSL_EXTERNAL_INCLUDE_DIR

Download Rcpp
R CMD INSTALL Rcpp_0.8.5.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/Rcpp/lib/x86_64/libRcpp.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/Rcpp/include $MSL_EXTERNAL_INCLUDE_DIR/

R CMD INSTALL RInside_0.2.3.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/RInside/lib/x86_64/libRInside.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/RInside/include $MSL_EXTERNAL_INCLUDE_DIR/

If the above install does not work, one can install from source here is a good resource:
http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Quick-start

===== LINUX OS =====
Success using shared libraries and compiling MSL as shared lib, but static lib has not been done yet. I will link my Makefile for shared-R compile once its cleaned up a bit

First try using the 'apt' system in linux:
sudo apt-get install r-base

If the 'apt' version is not the latest version that you need, then install latest version of R:
sudo apt-get build-dep r-base
tar xvzf R-2.11.1.tar.gz
cd R-2.11.1
./configure
make
sudo make install

Install Rcpp:
sudo /usr/local/bin/R CMD INSTALL Rcpp_0.8.5.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/Rcpp/lib/x86_64/libRcpp.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/Rcpp/include $MSL_EXTERNAL_INCLUDE_DIR/

Install RInside:

R CMD INSTALL RInside_0.2.3.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/RInside/lib/x86_64/libRInside.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/RInside/include $MSL_EXTERNAL_INCLUDE_DIR/

Copy headers into MSL_EXTERNAL_INCLUDE_DIR
cp -r /Library/Frameworks/R.framework/Resources/include/ $MSL_EXTERNAL_INCLUDE_DIR

=== OpenMP ===
[http://openmp.org OpenMP] is used by the OnTheFlyManager. In Ubuntu the package is usually installed by default, but may be found under libgomp1.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Compiling MSL with external libraries

2013-09-25T21:58:56Z

Senes:

Certain functions of MSL require the installation of some open-source external libraries.

* '''GSL''' (GNU Scientific Library) [[http://www.gnu.org/software/gsl/]]
* '''BOOST''' (portable C++ source libraries) [[http://www.boost.org]]
* '''GLPK''' (GNU linear programming kit) [[http://www.gnu.org/software/glpk/]]
* '''R''' (R statistical and graphics project) [[http://www.r-project.org/]]
* '''OPENMP''' (Open multi-processing) [[http://openmp.org/]]

=== What external libraries are really needed? ===
Only '''GLS''' is currently recommend and turned on by default in the Makefile

The other external libraries are needed only to support particular object or applications.

=== How to enable inclusion of the external libraries===

By default MSL '''requires the GSL''' library and will be compiled _without_ the support of the other external libraries and some functionality won't be available. To include the libraries, you need to set some environmental variables.

If you use '''bash''', add the following lines to your .bashrc

<source lang="bash">
# $MSL_GSL set to "T" if GSL is installed or else to "F" (default)
# $MSL_BOOST set to "T" if BOOST is installed or else to "F" (default)
# $MSL_GLPK set to "T" if GLPK is installed or else to "F" (default)
# $MSL_R set to "T" if R is installed or else to "F" (default)
# $MSL_OPENMP set to "T" if OPENMP is installed (default) or else to "F"
export MSL_GSL=T
export MSL_GLPK=T
export MSL_BOOST=T
export MSL_R=T
export MSL_OPENMP=T
#export MSL_EXTERNAL_LIB_DIR=/usr/lib
#export MSL_EXTERNAL_INCLUDE_DIR=/usr/include
#export MSL_MACOS=T
#export MSL_DEBUG=F
#export MSL_DIR=$HOME/software/mslib

</source>

If you use '''tcsh''', add the following lines to your .cshrc
<source lang="text">
# $MSL_GSL set to "T" if GSL is installed or else to "F" (default)
# $MSL_BOOST set to "T" if BOOST is installed or else to "F" (default)
# $MSL_GLPK set to "T" if GLPK is installed or else to "F" (default)
# $MSL_R set to "T" if R is installed or else to "F" (default)
# $MSL_OPENMP set to "T" if OPENMP is installed (default) or else to "F"
setenv MSL_GSL T
setenv MSL_GLPK T
setenv MSL_BOOST T
setenv MSL_R T
setenv MSL_OPENMP T
#setenv MSL_EXTERNAL_LIB_DIR /usr/lib
#setenv MSL_EXTERNAL_INCLUDE_DIR /usr/include
</source>

The default location of the libraries is '''/usr/lib'''. If you have installed them in a custom location (such as that used below, ~/software/mslib/ext_libs) set the $MSL_EXTERNAL_LIB_DIR environmental variable to the correct location. You will also want to set the $MSL_EXTERNAL_LIB_INCLUDE_DIR if using a custom location (such as that used below, ~/software/mslib/ext_includes).

=== GSL ===
Many functions of MSL depend on [[http://www.gnu.org/software/gsl/ GNU Scientific library (GSL)]], which is therefore highly recommended.

For example, GSL is required by the following objects:
* [[MSL_Objects:RandomNumberGenerator | RandomNumberGenerator]]
* [[MSL_Objects:GSLMinimizer | GSLMinimizer]]
* [[MSL_Objects:MonteCarloOptimization| MonteCarloOptimization]]
* [[MSL_Objects:CCD | CCD]]
* [[MSL_Objects:BackRub | BackRub]]
* [[MSL_Objects:Quench | Quench]]
* [[MSL_Objects:SurfaceAreaAndVolume | SurfaceAreaAndVolume]]

If '''GSL''' is enabled, you should see ''-D__GSL_'' in the compilation command when using make.

====To compile GSL====
GSL can be installed from the software repository (in Ubuntu, libgsl0-dev) or downloaded and installed from a tar file. For a more specific reference see the GSL homepage, but here is an example of the installation procedure:

>tar xzvf gsl-1.14.tar.gz
>cd gsl-1.14
>./configure --prefix=/path/to/desired/directory
>make
>make check
>make install
>cp .libs/libgsl.a ~/software/mslib/ext_libs/
>cp cblas/.libs/libgslcblas.a ~/software/mslib/ext_libs/

# Note the -H, this should follow the symlinks, otherwise you get copies of links with relative paths and then you get errors making MSL that say gsl/gsl_rng.h not found, when you see it there!
> mkdir ~/software/mslib/ext_includes/gsl
> cp -H gsl/* ~/software/mslib/ext_includes/gsl

=== BOOST ===
The following libraries from the [http://www.boost.org/ Boost C++ Libraries] are used in some MSL objects and programs. In Ubuntu, it is available in the package libboost-all-dev.
* Serialization, used for ... in the following objects
** [[MSL_Objects:Atom|Atom]]
** [[MSL_Objects:AtomPointerVector|AtomPointerVector]]
** [[MSL_Objects:CartesianPoint|CartesianPoint]]
** [[MSL_Objects:EnvironmentDatabase|EnvironmentDatabase]]
** [[MSL_Objects:EnvironmentDescriptor|EnvironmentDescriptor]]
** [[MSL_Objects:Frame|Frame]]
** [[MSL_Objects:IcEntry|IcEntry]]
** [[MSL_Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]]
** [[MSL_Objects:Line|Line]]
** [[MSL_Objects:Matrix|Matrix]]
** [[MSL_Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]]
** [[MSL_Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]]
** [[MSL_Objects:SphericalPoint|SphericalPoint]]

* Archive, used for ... in the following objects
** [[MSL_Objects:Atom|Atom]]
** [[MSL_Objects:AtomPointerVector|AtomPointerVector]]
** [[MSL_Objects:CartesianPoint|CartesianPoint]]
** [[MSL_Objects:EnvironmentDatabase|EnvironmentDatabase]]
** [[MSL_Objects:Frame|Frame]]
** [[MSL_Objects:IcEntry|IcEntry]]
** [[MSL_Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]]
** [[MSL_Objects:Line|Line]]
** [[MSL_Objects:Matrix|Matrix]]
** [[MSL_Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]]
** [[MSL_Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]]
** [[MSL_Objects:Selectable|Selectable]]
** [[MSL_Objects:SphericalPoint|SphericalPoint]]

* Regex, used for ... in the following objects
** [[MSL_Objects:MslTools|MslTools]]
** [[MSL_Objects:RegEx|RegEx]]

* Random, used for ... in the following objects
** [[MSL_Objects:RandomSeqGenerator|RandomSeqGenerator]]

Note: if boost is included, version 1.40 (???) or later is required.

If '''BOOST''' is enabled, you should see ''-D__BOOST__ -DBOOST_DISABLE_THREADS'' in the compilation command when using make.

====To Compile BOOST====
>tar xzvf boost-VERSION.tar.gz
>cd boost-VERSION
>./bootstrap.sh --prefix=~/software/mslib/ext_libs
>./b2
> cp ./stage/lib/libboost_*.a ~/software/mslib/ext_libs
> cp -r boost ~/software/mslib/ext_includes/

Assuming MSL library is installed in ~/software/mslib/. You will need to make the ext_includes and ext_libs directories before copying.

=== GLPK ===
The [http://www.gnu.org/software/glpk/ GNU linear programming kit] is required by the [[MSL_Objects:LinearProgrammingOptimization | LinearProgrammingOptimization]] object.

If '''GLPK''' is enabled, you should see ''-D__GLPK__'' in the compilation command when using make.

./configure --prefix=/usr/lib --disable-dl --disable-odbc --disable-mysql --enable-static --without-gmp --without-zlib
make
make install
cp /usr/lib/libglpk.a MSLHOME/ext_libs/
cp /usr/include/glpk.h MSLHOME/ext_includes/

=== R ===
The [http://www.r-project.org/ R project] is used by the getDihedrals program. In Ubuntu the package is r-base.

If '''R''' is enabled, you should see ''-D__R__'' in the compilation command when using make.

==== To Compile R ====

===== MAC OS =====
Install R and copy headers into MSL_EXTERNAL_INCLUDE_DIR
cp -r /Library/Frameworks/R.framework/Resources/include/ $MSL_EXTERNAL_INCLUDE_DIR

Download Rcpp
R CMD INSTALL Rcpp_0.8.5.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/Rcpp/lib/x86_64/libRcpp.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/Rcpp/include $MSL_EXTERNAL_INCLUDE_DIR/

R CMD INSTALL RInside_0.2.3.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/RInside/lib/x86_64/libRInside.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/RInside/include $MSL_EXTERNAL_INCLUDE_DIR/

If the above install does not work, one can install from source here is a good resource:
http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Quick-start

===== LINUX OS =====
Success using shared libraries and compiling MSL as shared lib, but static lib has not been done yet. I will link my Makefile for shared-R compile once its cleaned up a bit

First try using the 'apt' system in linux:
sudo apt-get install r-base

If the 'apt' version is not the latest version that you need, then install latest version of R:
sudo apt-get build-dep r-base
tar xvzf R-2.11.1.tar.gz
cd R-2.11.1
./configure
make
sudo make install

Install Rcpp:
sudo /usr/local/bin/R CMD INSTALL Rcpp_0.8.5.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/Rcpp/lib/x86_64/libRcpp.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/Rcpp/include $MSL_EXTERNAL_INCLUDE_DIR/

Install RInside:

R CMD INSTALL RInside_0.2.3.tar.gz
cp /Library/Frameworks/R.framework/Resources/library/RInside/lib/x86_64/libRInside.a $MSL_EXTERNAL_LIB_DIR/
cp -r /Library/Frameworks/R.framework/Resources/library/RInside/include $MSL_EXTERNAL_INCLUDE_DIR/

Copy headers into MSL_EXTERNAL_INCLUDE_DIR
cp -r /Library/Frameworks/R.framework/Resources/include/ $MSL_EXTERNAL_INCLUDE_DIR

=== OpenMP ===
[http://openmp.org OpenMP] is used by the OnTheFlyManager. In Ubuntu the package is usually installed by default, but may be found under libgomp1.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-09-18T14:42:20Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

===Download links===
* '''v.1.1 (v.1.1.0.6), stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.6.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.6.tgz]'''

* '''v.1.0 (v.1.0.0.13), old release (bug fixes back-ported)'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.13.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Main Page

2013-09-12T12:50:49Z

Senes: /* Main development team: */

=MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.=

[[Image:MSL-logo.png|right|400px]]

===Philosophy===
The main goal 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).

The MSL library is '''not''' a program (although some applications are distributed) but a tool for scientist to code their own methods.

===Features===
Some of the features supported by the library are:

* Support for reading and writing PDB and CRD files.
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
* Support for rotamer libraries.
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other energy funtions.
* Support for CHARMM topology and parameter files.
* Structure building from scratch (using internal coordinates)
* Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
* Local backbone sampling.
* Crystal lattice generation.
* A '''[[PyMOL Python Interface]]''' for calling MSL code from within PyMOL.
* A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
* And more...

===Documentation===
The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]'''. A step by step '''[[Tutorial|tutorial]]''' is being assembled.

===Status===
Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.

===Source===

The source code can be downloaded on SourceForge. Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page. ([[ToDo|"To do" list]]).

===Main development team:===

* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA
* Jason Donald, Agrivida, Inc., Medford MA
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
* Gevorg Grigoryan, James Zhang, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']

=== Reference ===
Article published using MSL should cite:
<pubmed>22565567</pubmed>

'''MSL (including early versions) has been used in the following work:'''
<pubmed>23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>

Tutorial:Getting started: Downloading MSL

2013-09-12T04:17:11Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

===Download links===
* '''v.1.1 (v.1.1.0.5), stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.5.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.5.tgz]'''

* '''v.1.0 (v.1.0.0.12), old release (bug fixes back-ported)'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.12.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.12.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-09-12T01:49:42Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

===Download links===
* '''v.1.1 (v.1.1.0.3), stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.3.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.3.tgz]'''

* '''v.1.0 (v.1.0.0.11), old release (bug fixes back-ported)'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.11.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.11.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command (the command will create a subdirectory mslib/trunk)
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/trunk mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-06-15T23:45:58Z

Senes:

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://sourceforge.net/p/mslib/code/HEAD/tree/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

===Download links===
* '''v.1.1 (v.1.1.0.3), stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.3.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.3.tgz]'''

* '''v.1.0 (v.1.0.0.11), old release (bug fixes back-ported)'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.11.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.11.tgz]'''

* '''Development version (trunk)'''
** Download a snapshot from the SourceForge SVN repository at '''[http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/ http://sourceforge.net/p/mslib/code/HEAD/tree/trunk/]'''
** ... or check out the trunk using Subversion (snv) with the following command
<source lang="text">
svn checkout svn://svn.code.sf.net/p/mslib/code/ mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Main Page

2013-04-26T15:31:47Z

Senes: /* Main development team: */

=MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.=

[[Image:MSL-logo.png|right|400px]]

===Philosophy===
The main goal 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).

The MSL library is '''not''' a program (although some applications are distributed) but a tool for scientist to code their own methods.

===Features===
Some of the features supported by the library are:

* Support for reading and writing PDB and CRD files.
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
* Support for rotamer libraries.
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other energy funtions.
* Support for CHARMM topology and parameter files.
* Structure building from scratch (using internal coordinates)
* Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
* Local backbone sampling.
* Crystal lattice generation.
* A '''[[PyMOL Python Interface]]''' for calling MSL code from within PyMOL.
* A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
* And more...

===Documentation===
The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]'''. A step by step '''[[Tutorial|tutorial]]''' is being assembled.

===Status===
Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.

===Source===

The source code can be downloaded on SourceForge. Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page. ([[ToDo|"To do" list]]).

===Main development team:===

* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA
* Jason Donald, Agrivida, Inc., Medford MA
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
* Gevorg Grigoryan, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']

=== Reference ===
Article published using MSL should cite:
<pubmed>22565567</pubmed>

'''MSL (including early versions) has been used in the following work:'''
<pubmed>23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>

Main Page

2013-04-26T15:31:22Z

Senes:

=MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.=

[[Image:MSL-logo.png|right|400px]]

===Philosophy===
The main goal 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).

The MSL library is '''not''' a program (although some applications are distributed) but a tool for scientist to code their own methods.

===Features===
Some of the features supported by the library are:

* Support for reading and writing PDB and CRD files.
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
* Support for rotamer libraries.
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other energy funtions.
* Support for CHARMM topology and parameter files.
* Structure building from scratch (using internal coordinates)
* Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
* Local backbone sampling.
* Crystal lattice generation.
* A '''[[PyMOL Python Interface]]''' for calling MSL code from within PyMOL.
* A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
* And more...

===Documentation===
The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]'''. A step by step '''[[Tutorial|tutorial]]''' is being assembled.

===Status===
Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.

===Source===

The source code can be downloaded on SourceForge. Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page. ([[ToDo|"To do" list]]).

===Main development team:===

* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA
* Jason Donald, Agrivida, Inc., Medford MA
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
* Gevorg Grigoryan, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']

We have applied to the Google Summer of Code 2013. Please see this page '''[[Google_Summer_of_Code_Ideas]]'''

=== Reference ===
Article published using MSL should cite:
<pubmed>22565567</pubmed>

'''MSL (including early versions) has been used in the following work:'''
<pubmed>23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>

Main Page

2013-04-26T15:31:07Z

Senes:

=MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.=
</big>
[[Image:MSL-logo.png|right|400px]]

===Philosophy===
The main goal 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).

The MSL library is '''not''' a program (although some applications are distributed) but a tool for scientist to code their own methods.

===Features===
Some of the features supported by the library are:

* Support for reading and writing PDB and CRD files.
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
* Support for rotamer libraries.
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other energy funtions.
* Support for CHARMM topology and parameter files.
* Structure building from scratch (using internal coordinates)
* Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
* Local backbone sampling.
* Crystal lattice generation.
* A '''[[PyMOL Python Interface]]''' for calling MSL code from within PyMOL.
* A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
* And more...

===Documentation===
The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]'''. A step by step '''[[Tutorial|tutorial]]''' is being assembled.

===Status===
Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.

===Source===

The source code can be downloaded on SourceForge. Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page. ([[ToDo|"To do" list]]).

===Main development team:===

* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA
* Jason Donald, Agrivida, Inc., Medford MA
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
* Gevorg Grigoryan, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']

We have applied to the Google Summer of Code 2013. Please see this page '''[[Google_Summer_of_Code_Ideas]]'''

=== Reference ===
Article published using MSL should cite:
<pubmed>22565567</pubmed>

'''MSL (including early versions) has been used in the following work:'''
<pubmed>23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>

Tutorial:Getting started: Downloading MSL

2013-04-15T02:35:48Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://mslib.svn.sourceforge.net/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

===Download links===
* '''v.1.1 (v.1.1.0.3), stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.3.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.3.tgz]'''

* '''v.1.0 (v.1.0.0.11), old release (bug fixes back-ported)'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.11.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.11.tgz]'''

* '''Development version (trunk)'''
** Download a tar ball (.tgz file) from the SourceForge SVN repository '''[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar]'''
** ... or check out the trunk using Subversion (snv) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-04-14T19:42:51Z

Senes:

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://mslib.svn.sourceforge.net/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

===Download links===
* '''v.1.1 (v.1.1.0.2), stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.2.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.2.tgz]'''

* '''v.1.0 (v.1.0.0.10), old release (bug fixes back-ported)'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.10.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.10.tgz]'''

* '''Development version (trunk)'''
** Download a tar ball (.tgz file) from the SourceForge SVN repository '''[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar]'''
** ... or check out the trunk using Subversion (snv) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-04-14T19:42:23Z

Senes:

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://mslib.svn.sourceforge.net/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

===Download links===
* '''v.1.1 (v.1.1.0.2), stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.2.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.1.tgz]'''

* '''v.1.0 (v.1.0.0.10), old release (bug fixes back-ported)'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.10.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.10.tgz]'''

* '''Development version (trunk)'''
** Download a tar ball (.tgz file) from the SourceForge SVN repository '''[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar]'''
** ... or check out the trunk using Subversion (snv) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-04-13T19:52:01Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://mslib.svn.sourceforge.net/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

===Download links===
* '''v.1.1 (v.1.1.0.0), stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.1.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.1.tgz]'''

* '''v.1.0 (v.1.0.0.9), old release (bug fixes back-ported)'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.9.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.9.tgz]'''

* '''Development version (trunk)'''
** Download a tar ball (.tgz file) from the SourceForge SVN repository '''[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar]'''
** ... or check out the trunk using Subversion (snv) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-04-04T02:55:34Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://mslib.svn.sourceforge.net/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

===Download links===
* '''v.1.1 (v.1.1.0.0), stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.0.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.0.tgz]'''
** ...or check out the v.1.1 branch using Subversion (svn) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/branches/v.1.1
</source>

* '''v.1.0 (v.1.0.0.9), old release (bug fixes back-ported)'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.9.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.9.tgz]'''
** ...or check out the v.1.0 branch using Subversion (svn) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/branches/v.1.0
</source>

* '''Development version (trunk)'''
** Download a tar ball (.tgz file) from the SourceForge SVN repository '''[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar]'''
** ... or check out the trunk using Subversion (snv) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-04-04T01:57:36Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://mslib.svn.sourceforge.net/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

====Download links====
* '''v.1.1 (v.1.1.0.0), stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.0.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.0.tgz]'''
** ...or check out the v.1.1 branch using Subversion (svn) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/branches/v.1.1
</source>

* '''v.1.0 (v.1.0.0.9), old release (bug fixes back-ported)'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.9.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.9.tgz]'''
** ...or check out the v.1.0 branch using Subversion (svn) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/branches/v.1.0
</source>

* '''Development version (trunk)'''
** Download a tar ball (.tgz file) from the SourceForge SVN repository '''[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar]'''
** ... or check out the trunk using Subversion (snv) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Tutorial:Getting started: Downloading MSL

2013-04-04T01:57:26Z

Senes: /* Download links */

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://mslib.svn.sourceforge.net/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

====Download links====
* '''v.1.1 (v.1.1.0.0), stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.0.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.0.tgz]'''
** ...or check out the v.1.1 branch using Subversion (svn) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/branches/v.1.1
</source>

* '''v.1.0 (v.1.0.0.9), old stable release (bug fixes back-ported)'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.9.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.9.tgz]'''
** ...or check out the v.1.0 branch using Subversion (svn) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/branches/v.1.0
</source>

* '''Development version (trunk)'''
** Download a tar ball (.tgz file) from the SourceForge SVN repository '''[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar]'''
** ... or check out the trunk using Subversion (snv) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Main Page

2013-04-04T01:55:32Z

Senes: /* Status */

<big>'''MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.'''
</big>
[[Image:MSL-logo.png|right|400px]]

===Philosophy===
The main goal 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).

The MSL library is '''not''' a program (although some applications are distributed) but a tool for scientist to code their own methods.

===Features===
Some of the features supported by the library are:

* Support for reading and writing PDB and CRD files.
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
* Support for rotamer libraries.
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other energy funtions.
* Support for CHARMM topology and parameter files.
* Structure building from scratch (using internal coordinates)
* Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
* Local backbone sampling.
* Crystal lattice generation.
* A '''[[PyMOL Python Interface]]''' for calling MSL code from within PyMOL.
* A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
* And more...

===Documentation===
The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]'''. A step by step '''[[Tutorial|tutorial]]''' is being assembled.

===Status===
Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.

===Source===

The source code can be downloaded on SourceForge. Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page. ([[ToDo|"To do" list]]).

===Main development team:===

* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA
* Jason Donald, Agrivida, Inc., Medford MA
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
* Gevorg Grigoryan, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']

We have applied to the Google Summer of Code 2013. Please see this page '''[[Google_Summer_of_Code_Ideas]]'''

=== Reference ===
Article published using MSL should cite:
<pubmed>22565567</pubmed>

'''MSL (including early versions) has been used in the following work:'''
<pubmed>23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>

Tutorial:Getting started: Downloading MSL

2013-04-04T01:47:35Z

Senes:

'''MSL''' is open source software distributed under the terms of the GNU Lesser General Public.

MSL is available from SourceForge, at [https://sourceforge.net/projects/mslib/ the project page] (stable releases) and at the [http://mslib.svn.sourceforge.net/ SVN repository] (stable, betas, development version).

==== Version 1.1 released (04/03/2013) ====
'''New Features'''
* Added IMM1 solvation model
* Added a facility to temporarily hide identities (amini acid types) at positions that contain more than one identity
* Initial implementation of clustering algorithms (SingleLinkage, Average-Linkage, Complete-Linkage and PAM/Kmedoids) in src/Clustering.h
* Object for fitting a coiled coil to parameters, in src/CoiledCoilFitter.h

'''Bug fixes'''
* Fixed bug with linked position during on-the-fly energy computation
* Fixed bugs in the implementation of SCWRL4 hydrogen bond

====Download links====
* '''v.1.1 (v.1.1.0.0), stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.0.tgz http://sourceforge.net/projects/mslib/files/v.1.1/mslib-1.1.0.0.tgz]'''
** ...or check out the v.1.1 branch using Subversion (svn) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/branches/v.1.1
</source>

* '''v.1.0 (v.1.0.0.9), old stable release'''
** Download a tar ball (.tgz file) from the SourceForge MSL page '''[http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.9.tgz http://sourceforge.net/projects/mslib/files/v.1.0/mslib-1.0.0.9.tgz]'''
** ...or check out the v.1.0 branch using Subversion (svn) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/branches/v.1.0
</source>

* '''Development version (trunk)'''
** Download a tar ball (.tgz file) from the SourceForge SVN repository '''[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/?view=tar]'''
** ... or check out the trunk using Subversion (snv) with the following command
<source lang="text">
svn co https://mslib.svn.sourceforge.net/svnroot/mslib/trunk
</source>

For compiling instructions refer to the [[Tutorial]] page.

'''NOTE''': by default, MSL assumes that you have installed [http://www.gnu.org/software/gsl GSL]. We highly recommend that you install [http://www.gnu.org/software/gsl GSL] prior to MSL compilation.

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

Google Summer of Code Ideas

2013-04-02T18:28:16Z

Senes: /* Developing a website to run MSL applications */

'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.
[[File:Msl_hierarchy.png | frame | Hierarchy of molecular objects in MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:FtsB.png | frame | Structural model of a membrane protein obtained with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/23520975 LaPointe et al. 2013])]]
[[File:side_chains.png | frame | A unique feature of MSL is that it can hold multiple type of side-chain types (c, d) and/or multiple conformations of the side-chain (a, b) at the same position in a protein ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:TRP_EBL.png | frame | A library of side chain conformations created with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22576292 Subramaniam et. al Proteins 2012])]]

==Goal==

The goal of MSL is to be an efficient toolbox to enable a programmer to design powerful and advanced applications for molecular analysis, modeling, prediction and design. At the same time, MSL is designed with simplicity in mind to 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 years (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) was released in 2012.

The code can be downloaded at the [https://sourceforge.net/projects/mslib/ MSL SourceForge page] and the entire development tree is available at the [http://mslib.svn.sourceforge.net/ MSL SVN repository]. Several examples are now available in the repository that demonstrate the capabilities of MSL objects in modeling applications.

MSL is described in its primary citation:
* 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])

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], and others.

==Current development==

The main theme of MSL development will continue to be the creation of a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation.

We are striving to improve the core framework through
* more advanced objects
* more efficient implementations
* implementing more modeling algorithms and protocols

Another important direction is making MSL more accessible to a wider audience by
* creating interfaces to other programming languages
* making distribution of MSL easier
* building ready-to-use applications
* hosting MSL applications on web servers for public use

There are a number of areas, listed below, in which GSoC students of different background and skills could contribute to realize these goals.

== Ideas ==

====Embedding MSL code for use in higher-level languages====

'''Brief explanation:'''

The idea is to make MSL code available to programs in other higher-level languages. This could be done using an interface compiler like the SWIG (see swig.org)

'''Expected results:'''

Infrastructure and example applications in multiple higher-level languages.

'''Knowledge Prerequisite:'''

C++ and one of Python or R or perl

====MSL-Light====

'''Brief explanation:'''

The objects in MSL are sometimes too complex for simple operations on large molecules. The idea is to implement light-weight versions of some core objects, for example, the AtomContainer object is a lighter version of the System object.

'''Expected results:'''

A collection of light-weight objects and methods.

'''Knowledge Prerequisite:'''

C++, Data Structures and Algorithms

====Smart pointers in MSL====

'''Brief explanation:'''

MSL uses basic pointers which are prone to bugs due to dangling pointers, memory leaks, etc.,

'''Expected results:'''

Replace regular pointers with the appropriate smart pointers in MSL.

'''Knowledge Prerequisite:'''

C++

====Efficient program options management====

'''Brief explanation:'''

MSL has an advanced OptionParser object that supports name/value based program options. A mechanism needs to be implemented to group program options for MSL that uses the underlying OptionParser.

'''Expected results:'''

The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications.

'''Knowledge Prerequisite:'''

C++

====MSL Linux Distribution Packages====

'''Brief explanation:'''

The MSL needs to be compiled from source. The distribution of the software as a .deb and/or .rpm package will simplify installation in some of the most popular Linux distros.

'''Expected results:'''

One-click/command MSL installation.

'''Knowledge Prerequisite:'''

Linux, Make

====Developing a website to run MSL applications====

'''Brief explanation:'''

There are several MSL applications that are directly useful to structural biologists. For example, the side-chain 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 of these applications with a minimal/no knowledge of MSL.

'''Expected results:'''

A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.

'''Knowledge Prerequisite:'''

Scripting Languages and Web Design

====Expansion and improvement of the example and test programs====

'''Brief explanation:'''

MSL ships with a number of small example programs which are to be used as starting points for a programmer interested in adopting the software. MSL also has a number of quality control test programs of known output that are run every time a new commit is performed.

'''Expected results:'''

Expansion and improvement of example and test programs. This is an area that will allow a student to get familiar with the molecular modeling principles implemented in MSL.

'''Knowledge Prerequisite:'''

C++. Knowledge of proteins and modeling is beneficial but not required.

==Contact==

Please email '''sabareeshs@gmail.com''' if you are interested in working on any of these ideas and would like to obtain more information.

Google Summer of Code Ideas

2013-04-02T18:22:46Z

Senes: /* Current development */

'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.
[[File:Msl_hierarchy.png | frame | Hierarchy of molecular objects in MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:FtsB.png | frame | Structural model of a membrane protein obtained with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/23520975 LaPointe et al. 2013])]]
[[File:side_chains.png | frame | A unique feature of MSL is that it can hold multiple type of side-chain types (c, d) and/or multiple conformations of the side-chain (a, b) at the same position in a protein ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:TRP_EBL.png | frame | A library of side chain conformations created with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22576292 Subramaniam et. al Proteins 2012])]]

==Goal==

The goal of MSL is to be an efficient toolbox to enable a programmer to design powerful and advanced applications for molecular analysis, modeling, prediction and design. At the same time, MSL is designed with simplicity in mind to 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 years (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) was released in 2012.

The code can be downloaded at the [https://sourceforge.net/projects/mslib/ MSL SourceForge page] and the entire development tree is available at the [http://mslib.svn.sourceforge.net/ MSL SVN repository]. Several examples are now available in the repository that demonstrate the capabilities of MSL objects in modeling applications.

MSL is described in its primary citation:
* 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])

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], and others.

==Current development==

The main theme of MSL development will continue to be the creation of a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation.

We are striving to improve the core framework through
* more advanced objects
* more efficient implementations
* implementing more modeling algorithms and protocols

Another important direction is making MSL more accessible to a wider audience by
* creating interfaces to other programming languages
* making distribution of MSL easier
* building ready-to-use applications
* hosting MSL applications on web servers for public use

There are a number of areas, listed below, in which GSoC students of different background and skills could contribute to realize these goals.

== Ideas ==

====Embedding MSL code for use in higher-level languages====

'''Brief explanation:'''

The idea is to make MSL code available to programs in other higher-level languages. This could be done using an interface compiler like the SWIG (see swig.org)

'''Expected results:'''

Infrastructure and example applications in multiple higher-level languages.

'''Knowledge Prerequisite:'''

C++ and one of Python or R or perl

====MSL-Light====

'''Brief explanation:'''

The objects in MSL are sometimes too complex for simple operations on large molecules. The idea is to implement light-weight versions of some core objects, for example, the AtomContainer object is a lighter version of the System object.

'''Expected results:'''

A collection of light-weight objects and methods.

'''Knowledge Prerequisite:'''

C++, Data Structures and Algorithms

====Smart pointers in MSL====

'''Brief explanation:'''

MSL uses basic pointers which are prone to bugs due to dangling pointers, memory leaks, etc.,

'''Expected results:'''

Replace regular pointers with the appropriate smart pointers in MSL.

'''Knowledge Prerequisite:'''

C++

====Efficient program options management====

'''Brief explanation:'''

MSL has an advanced OptionParser object that supports name/value based program options. A mechanism needs to be implemented to group program options for MSL that uses the underlying OptionParser.

'''Expected results:'''

The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications.

'''Knowledge Prerequisite:'''

C++

====MSL Linux Distribution Packages====

'''Brief explanation:'''

The MSL needs to be compiled from source. The distribution of the software as a .deb and/or .rpm package will simplify installation in some of the most popular Linux distros.

'''Expected results:'''

One-click/command MSL installation.

'''Knowledge Prerequisite:'''

Linux, Make

====Developing a website to run MSL applications====

'''Brief explanation:'''

There are several MSL applications that are directly useful to structural biologists. For example, the side-chain 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 of these applications with a minimal/no knowledge of MSL.

'''Expected results:'''

A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.

'''Knowledge Prerequisite:'''

Scripting Languages and Web Design

==Contact==

Please email '''sabareeshs@gmail.com''' if you are interested in working on any of these ideas and would like to obtain more information.

Google Summer of Code Ideas

2013-04-02T18:21:50Z

Senes: /* Goal */

'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.
[[File:Msl_hierarchy.png | frame | Hierarchy of molecular objects in MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:FtsB.png | frame | Structural model of a membrane protein obtained with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/23520975 LaPointe et al. 2013])]]
[[File:side_chains.png | frame | A unique feature of MSL is that it can hold multiple type of side-chain types (c, d) and/or multiple conformations of the side-chain (a, b) at the same position in a protein ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:TRP_EBL.png | frame | A library of side chain conformations created with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22576292 Subramaniam et. al Proteins 2012])]]

==Goal==

The goal of MSL is to be an efficient toolbox to enable a programmer to design powerful and advanced applications for molecular analysis, modeling, prediction and design. At the same time, MSL is designed with simplicity in mind to 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 years (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) was released in 2012.

The code can be downloaded at the [https://sourceforge.net/projects/mslib/ MSL SourceForge page] and the entire development tree is available at the [http://mslib.svn.sourceforge.net/ MSL SVN repository]. Several examples are now available in the repository that demonstrate the capabilities of MSL objects in modeling applications.

MSL is described in its primary citation:
* 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])

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], and others.

==Current development==

The main theme of MSL development will continue to be the creation of a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation.

We are striving to improve the core framework through
* more advanced objects
* more efficient implementations
* implementing more modeling algorithms and protocols

Another important direction is making MSL more accessible to a wider audience by
* creating interfaces to other programming languages
* making distribution of MSL easier
* building ready-to-use applications
* hosting MSL applications on web servers for public use

There are a number of areas, listed below, in which a GSoC student could contribute to realize these goals.

== Ideas ==

====Embedding MSL code for use in higher-level languages====

'''Brief explanation:'''

The idea is to make MSL code available to programs in other higher-level languages. This could be done using an interface compiler like the SWIG (see swig.org)

'''Expected results:'''

Infrastructure and example applications in multiple higher-level languages.

'''Knowledge Prerequisite:'''

C++ and one of Python or R or perl

====MSL-Light====

'''Brief explanation:'''

The objects in MSL are sometimes too complex for simple operations on large molecules. The idea is to implement light-weight versions of some core objects, for example, the AtomContainer object is a lighter version of the System object.

'''Expected results:'''

A collection of light-weight objects and methods.

'''Knowledge Prerequisite:'''

C++, Data Structures and Algorithms

====Smart pointers in MSL====

'''Brief explanation:'''

MSL uses basic pointers which are prone to bugs due to dangling pointers, memory leaks, etc.,

'''Expected results:'''

Replace regular pointers with the appropriate smart pointers in MSL.

'''Knowledge Prerequisite:'''

C++

====Efficient program options management====

'''Brief explanation:'''

MSL has an advanced OptionParser object that supports name/value based program options. A mechanism needs to be implemented to group program options for MSL that uses the underlying OptionParser.

'''Expected results:'''

The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications.

'''Knowledge Prerequisite:'''

C++

====MSL Linux Distribution Packages====

'''Brief explanation:'''

The MSL needs to be compiled from source. The distribution of the software as a .deb and/or .rpm package will simplify installation in some of the most popular Linux distros.

'''Expected results:'''

One-click/command MSL installation.

'''Knowledge Prerequisite:'''

Linux, Make

====Developing a website to run MSL applications====

'''Brief explanation:'''

There are several MSL applications that are directly useful to structural biologists. For example, the side-chain 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 of these applications with a minimal/no knowledge of MSL.

'''Expected results:'''

A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.

'''Knowledge Prerequisite:'''

Scripting Languages and Web Design

==Contact==

Please email '''sabareeshs@gmail.com''' if you are interested in working on any of these ideas and would like to obtain more information.

Google Summer of Code Ideas

2013-04-01T22:38:25Z

Senes:

'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.
[[File:Msl_hierarchy.png | frame | Hierarchy of molecular objects in MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:FtsB.png | frame | Structural model of a membrane protein obtained with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/23520975 LaPointe et al. 2013])]]
[[File:side_chains.png | frame | A unique feature of MSL is that it can hold multiple type of side-chain types (c, d) and/or multiple conformations of the side-chain (a, b) at the same position in a protein ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:TRP_EBL.png | frame | A library of side chain conformations created with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22576292 Subramaniam et. al Proteins 2012])]]

==Goal==

The goal of MSL is to be an efficient toolbox to enable a programmer to design powerful and advanced applications for molecular analysis, modeling, prediction and design. At the same time, MSL is designed to 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 years (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) was released in 2012.

The code can be downloaded at the [https://sourceforge.net/projects/mslib/ MSL SourceForge page] and the entire development tree is available at the [http://mslib.svn.sourceforge.net/ MSL SVN repository]. Several examples are now available in the repository that demonstrate the capabilities of MSL objects in modeling applications.

MSL is described in its primary citation:
* 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])

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], and others.

==Current development==

The main theme of MSL development will continue to be the creation of a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation.

We are striving to improve the core framework through
* more advanced objects
* more efficient implementations
* implementing more modeling algorithms and protocols

Another important direction is making MSL more accessible to a wider audience by
* creating interfaces to other programming languages
* making distribution of MSL easier
* building ready-to-use applications
* hosting MSL applications on web servers for public use

There are a number of areas, listed below, in which a GSoC student could contribute to realize these goals.

== Ideas ==

====Embedding MSL code for use in higher-level languages====

'''Brief explanation:'''

The idea is to make MSL code available to programs in other higher-level languages. This could be done using an interface compiler like the SWIG (see swig.org)

'''Expected results:'''

Infrastructure and example applications in multiple higher-level languages.

'''Knowledge Prerequisite:'''

C++ and one of Python or R or perl

====MSL-Light====

'''Brief explanation:'''

The objects in MSL are sometimes too complex for simple operations on large molecules. The idea is to implement light-weight versions of some core objects, for example, the AtomContainer object is a lighter version of the System object.

'''Expected results:'''

A collection of light-weight objects and methods.

'''Knowledge Prerequisite:'''

C++, Data Structures and Algorithms

====Smart pointers in MSL====

'''Brief explanation:'''

MSL uses basic pointers which are prone to bugs due to dangling pointers, memory leaks, etc.,

'''Expected results:'''

Replace regular pointers with the appropriate smart pointers in MSL.

'''Knowledge Prerequisite:'''

C++

====Efficient program options management====

'''Brief explanation:'''

MSL has an advanced OptionParser object that supports name/value based program options. A mechanism needs to be implemented to group program options for MSL that uses the underlying OptionParser.

'''Expected results:'''

The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications.

'''Knowledge Prerequisite:'''

C++

====MSL Linux Distribution Packages====

'''Brief explanation:'''

The MSL needs to be compiled from source. The distribution of the software as a .deb and/or .rpm package will simplify installation in some of the most popular Linux distros.

'''Expected results:'''

One-click/command MSL installation.

'''Knowledge Prerequisite:'''

Linux, Make

====Developing a website to run MSL applications====

'''Brief explanation:'''

There are several MSL applications that are directly useful to structural biologists. For example, the side-chain 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 of these applications with a minimal/no knowledge of MSL.

'''Expected results:'''

A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.

'''Knowledge Prerequisite:'''

Scripting Languages and Web Design

==Contact==

Please email '''sabareeshs@gmail.com''' if you are interested in working on any of these ideas and would like to obtain more information.

Google Summer of Code Ideas

2013-04-01T22:38:07Z

Senes:

'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.
[[File:Msl_hierarchy.png | frame | Hierarchy of molecular objects in MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:FtsB.png | frame | Structural model of a membrane protein obtained with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/23520975 LaPointe et al. 2013])]]
[[File:side_chains.png | frame | A unique feature of MSL is that it can hold multiple type of side-chain types (c, d) and/or multiple conformations of the side-chain (a, b) at the same position in a protein ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:TRP_EBL.png | frame | A library of side chain conformations created with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22576292 Subramaniam et. al Proteins 2012])]]

==Goal==

The goal of MSL is to be an efficient 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 years (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) was released in 2012.

The code can be downloaded at the [https://sourceforge.net/projects/mslib/ MSL SourceForge page] and the entire development tree is available at the [http://mslib.svn.sourceforge.net/ MSL SVN repository]. Several examples are now available in the repository that demonstrate the capabilities of MSL objects in modeling applications.

MSL is described in its primary citation:
* 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])

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], and others.

==Current development==

The main theme of MSL development will continue to be the creation of a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation.

We are striving to improve the core framework through
* more advanced objects
* more efficient implementations
* implementing more modeling algorithms and protocols

Another important direction is making MSL more accessible to a wider audience by
* creating interfaces to other programming languages
* making distribution of MSL easier
* building ready-to-use applications
* hosting MSL applications on web servers for public use

There are a number of areas, listed below, in which a GSoC student could contribute to realize these goals.

== Ideas ==

====Embedding MSL code for use in higher-level languages====

'''Brief explanation:'''

The idea is to make MSL code available to programs in other higher-level languages. This could be done using an interface compiler like the SWIG (see swig.org)

'''Expected results:'''

Infrastructure and example applications in multiple higher-level languages.

'''Knowledge Prerequisite:'''

C++ and one of Python or R or perl

====MSL-Light====

'''Brief explanation:'''

The objects in MSL are sometimes too complex for simple operations on large molecules. The idea is to implement light-weight versions of some core objects, for example, the AtomContainer object is a lighter version of the System object.

'''Expected results:'''

A collection of light-weight objects and methods.

'''Knowledge Prerequisite:'''

C++, Data Structures and Algorithms

====Smart pointers in MSL====

'''Brief explanation:'''

MSL uses basic pointers which are prone to bugs due to dangling pointers, memory leaks, etc.,

'''Expected results:'''

Replace regular pointers with the appropriate smart pointers in MSL.

'''Knowledge Prerequisite:'''

C++

====Efficient program options management====

'''Brief explanation:'''

MSL has an advanced OptionParser object that supports name/value based program options. A mechanism needs to be implemented to group program options for MSL that uses the underlying OptionParser.

'''Expected results:'''

The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications.

'''Knowledge Prerequisite:'''

C++

====MSL Linux Distribution Packages====

'''Brief explanation:'''

The MSL needs to be compiled from source. The distribution of the software as a .deb and/or .rpm package will simplify installation in some of the most popular Linux distros.

'''Expected results:'''

One-click/command MSL installation.

'''Knowledge Prerequisite:'''

Linux, Make

====Developing a website to run MSL applications====

'''Brief explanation:'''

There are several MSL applications that are directly useful to structural biologists. For example, the side-chain 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 of these applications with a minimal/no knowledge of MSL.

'''Expected results:'''

A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.

'''Knowledge Prerequisite:'''

Scripting Languages and Web Design

==Contact==

Please email '''sabareeshs@gmail.com''' if you are interested in working on any of these ideas and would like to obtain more information.

Google Summer of Code Ideas

2013-04-01T22:36:57Z

Senes:

'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.
[[File:Msl_hierarchy.png | frame | Hierarchy of molecular objects in MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:FtsB.png | frame | Structural model of a membrane protein obtained with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/23520975 LaPointe et al. 2013])]]
[[File:side_chains.png | frame | A unique feature of MSL is that it can hold multiple type of side-chain types (c, d) and/or multiple conformations of the side-chain (a, b) at the same position in a protein ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:TRP_EBL.png | frame | A library of side chain conformations created with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22576292 Subramaniam et. al Proteins 2012])]]

==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 years (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) was released in 2012.

The code can be downloaded at the [https://sourceforge.net/projects/mslib/ MSL SourceForge page] and the entire development tree is available at the [http://mslib.svn.sourceforge.net/ MSL SVN repository]. Several examples are now available in the repository that demonstrate the capabilities of MSL objects in modeling applications.

MSL is described in its primary citation:
* 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])

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], and others.

==Current development==

The main theme of MSL development will continue to be the creation of a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation.

We are striving to improve the core framework through
* more advanced objects
* more efficient implementations
* implementing more modeling algorithms and protocols

Another important direction is making MSL more accessible to a wider audience by
* creating interfaces to other programming languages
* making distribution of MSL easier
* building ready-to-use applications
* hosting MSL applications on web servers for public use

There are a number of areas, listed below, in which a GSoC student could contribute to realize these goals.

== Ideas ==

====Embedding MSL code for use in higher-level languages====

'''Brief explanation:'''

The idea is to make MSL code available to programs in other higher-level languages. This could be done using an interface compiler like the SWIG (see swig.org)

'''Expected results:'''

Infrastructure and example applications in multiple higher-level languages.

'''Knowledge Prerequisite:'''

C++ and one of Python or R or perl

====MSL-Light====

'''Brief explanation:'''

The objects in MSL are sometimes too complex for simple operations on large molecules. The idea is to implement light-weight versions of some core objects, for example, the AtomContainer object is a lighter version of the System object.

'''Expected results:'''

A collection of light-weight objects and methods.

'''Knowledge Prerequisite:'''

C++, Data Structures and Algorithms

====Smart pointers in MSL====

'''Brief explanation:'''

MSL uses basic pointers which are prone to bugs due to dangling pointers, memory leaks, etc.,

'''Expected results:'''

Replace regular pointers with the appropriate smart pointers in MSL.

'''Knowledge Prerequisite:'''

C++

====Efficient program options management====

'''Brief explanation:'''

MSL has an advanced OptionParser object that supports name/value based program options. A mechanism needs to be implemented to group program options for MSL that uses the underlying OptionParser.

'''Expected results:'''

The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications.

'''Knowledge Prerequisite:'''

C++

====MSL Linux Distribution Packages====

'''Brief explanation:'''

The MSL needs to be compiled from source. The distribution of the software as a .deb and/or .rpm package will simplify installation in some of the most popular Linux distros.

'''Expected results:'''

One-click/command MSL installation.

'''Knowledge Prerequisite:'''

Linux, Make

====Developing a website to run MSL applications====

'''Brief explanation:'''

There are several MSL applications that are directly useful to structural biologists. For example, the side-chain 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 of these applications with a minimal/no knowledge of MSL.

'''Expected results:'''

A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.

'''Knowledge Prerequisite:'''

Scripting Languages and Web Design

==Contact==

Please email '''sabareeshs@gmail.com''' if you are interested in working on any of these ideas and would like to obtain more information.

Google Summer of Code Ideas

2013-04-01T19:04:37Z

Senes:

'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.
[[File:Msl_hierarchy.png | frame | Hierarchy of molecular objects in MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:FtsB.png | frame | Structural model of a dimer of a membrane protein obtained with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/23520975 LaPointe et al. 2013])]]
[[File:side_chains.png | frame | A unique feature of MSL is that it can hold multiple type of side-chain types (c, d) and/or multiple conformations of the side-chain (a, b) at the same position in a protein ([http://www.ncbi.nlm.nih.gov/pubmed/22565567 Kulp et al. 2012])]]
[[File:TRP_EBL.png | frame | A library of side chain conformations created with MSL ([http://www.ncbi.nlm.nih.gov/pubmed/22576292 Subramaniam et. al Proteins 2012])]]

==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 years (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) was released in 2012.

The code can be downloaded at the [https://sourceforge.net/projects/mslib/ MSL SourceForge page] and the entire development tree is available at the [http://mslib.svn.sourceforge.net/ MSL SVN repository]. Several examples are now available in the repository that demonstrate the capabilities of MSL objects in modeling applications.

MSL is described in its primary citation:
* 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])

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], and others.

==Current development==

The main theme of MSL development will continue to be the creation of a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation.

We are striving to improve the core framework through
* more advanced objects
* more efficient implementations
* implementing more modeling algorithms and protocols

Another important direction is making MSL more accessible to a wider audience by
* creating interfaces to other programming languages
* making distribution of MSL easier
* building ready-to-use applications
* hosting MSL applications on web servers for public use

There are a number of areas, listed below, in which a GSoC student could contribute to realize these goals.

== Ideas ==

====Embedding MSL code for use in higher-level languages====

'''Brief explanation:'''

The idea is to make MSL code available to programs in other higher-level languages. This could be done using an interface compiler like the SWIG (see swig.org)

'''Expected results:'''

Infrastructure and example applications in multiple higher-level languages.

'''Knowledge Prerequisite:'''

C++ and one of Python or R or perl

====MSL-Light====

'''Brief explanation:'''

The objects in MSL are sometimes too complex for simple operations on large molecules. The idea is to implement light-weight versions of some core objects, for example, the AtomContainer object is a lighter version of the System object.

'''Expected results:'''

A collection of light-weight objects and methods.

'''Knowledge Prerequisite:'''

C++, Data Structures and Algorithms

====Smart pointers in MSL====

'''Brief explanation:'''

MSL uses basic pointers which are prone to bugs due to dangling pointers, memory leaks, etc.,

'''Expected results:'''

Replace regular pointers with the appropriate smart pointers in MSL.

'''Knowledge Prerequisite:'''

C++

====Efficient program options management====

'''Brief explanation:'''

MSL has an advanced OptionParser object that supports name/value based program options. A mechanism needs to be implemented to group program options for MSL that uses the underlying OptionParser.

'''Expected results:'''

The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications.

'''Knowledge Prerequisite:'''

C++

====MSL Linux Distribution Packages====

'''Brief explanation:'''

The MSL needs to be compiled from source. The distribution of the software as a .deb and/or .rpm package will simplify installation in some of the most popular Linux distros.

'''Expected results:'''

One-click/command MSL installation.

'''Knowledge Prerequisite:'''

Linux, Make

====Developing a website to run MSL applications====

'''Brief explanation:'''

There are several MSL applications that are directly useful to structural biologists. For example, the side-chain 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 of these applications with a minimal/no knowledge of MSL.

'''Expected results:'''

A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.

'''Knowledge Prerequisite:'''

Scripting Languages and Web Design

==Contact==

Please email '''sabareeshs@gmail.com''' if you are interested in working on any of these ideas and would like to obtain more information.

File:TRP EBL.png

2013-04-01T19:00:18Z

Senes: TRP conformers from EBL paper

TRP conformers from EBL paper