http://msl-libraries.org/api.php?action=feedcontributions&feedformat=atom&user=Sabareeshs 2026-04-09T09:34:26Z User contributions MediaWiki 1.32.6 http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=838 2013-04-01T18:43:10Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> [[File:Msl_hierarchy.png | frame | '''MSL OBJECT HIERARCHY''']] <br /> <br /> ==Goal==<br /> <br /> 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).<br /> <br /> ==History==<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> <br /> 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.<br /> <br /> ==Current development==<br /> <br /> [[File:FtsB.png | frame | '''Structural model of a dimer of a membrane protein obtained with MSL''']] <br /> <br /> 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. <br /> <br /> We are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> There are a number of areas, listed below, in which a GSoC student could contribute to realize these goals.<br /> <br /> <br /> <br /> == Ideas ==<br /> <br /> <br /> ====Embedding MSL code for use in higher-level languages====<br /> <br /> '''Brief explanation:'''<br /> <br /> 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)<br /> <br /> '''Expected results:'''<br /> <br /> Infrastructure and example applications in multiple higher-level languages.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++ and one of Python or R or perl <br /> <br /> <br /> <br /> ====MSL-Light====<br /> <br /> '''Brief explanation:'''<br /> <br /> 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. <br /> <br /> '''Expected results:'''<br /> <br /> A collection of light-weight objects and methods.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++, Data Structures and Algorithms<br /> <br /> <br /> <br /> ====Smart pointers in MSL====<br /> <br /> '''Brief explanation:'''<br /> <br /> MSL uses basic pointers which are prone to bugs due to dangling pointers, memory leaks, etc.,<br /> <br /> '''Expected results:'''<br /> <br /> Replace regular pointers with the appropriate smart pointers in MSL.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> ====Efficient program options management====<br /> <br /> '''Brief explanation:'''<br /> <br /> 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.<br /> <br /> '''Expected results:'''<br /> <br /> The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications. <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> ====MSL Linux Distribution Packages====<br /> <br /> '''Brief explanation:''' <br /> <br /> 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.<br /> <br /> '''Expected results:'''<br /> <br /> One-click/command MSL installation.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Linux, Make<br /> <br /> <br /> ====Developing a website to run MSL applications====<br /> <br /> '''Brief explanation:'''<br /> <br /> 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.<br /> <br /> '''Expected results:'''<br /> <br /> A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> ==Contact==<br /> <br /> Please email '''sabareeshs@gmail.com''' if you are interested in working on any of these ideas and would like to obtain more information.</div>

Sabareeshs http://msl-libraries.org/index.php?title=File:FtsB.png&diff=837 2013-04-01T18:38:16Z

<p>Sabareeshs: </p> <hr /> <div></div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=818 2013-03-29T14:50:05Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> [[File:Msl_hierarchy.png | frame | '''MSL OBJECT HIERARCHY''']] <br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> <br /> 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.<br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Embedding MSL code for use in higher-level languages'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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)<br /> <br /> '''Expected results:'''<br /> <br /> Infrastructure and example applications in multiple higher-level languages.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++ and one of Python or R or perl <br /> <br /> <br /> <br /> 2) '''MSL-Light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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. <br /> <br /> '''Expected results:'''<br /> <br /> A collection of light-weight objects and methods.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++, Data Structures and Algorithms<br /> <br /> <br /> <br /> 3) '''Smart pointers in MSL'''<br /> <br /> '''Brief explanation:'''<br /> <br /> MSL uses basic pointers which are prone to bugs due to dangling pointers, memory leaks, etc.,<br /> <br /> '''Expected results:'''<br /> <br /> Replace regular pointers with the appropriate smart pointers in MSL.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> 4) '''Efficient program options management'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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.<br /> <br /> '''Expected results:'''<br /> <br /> The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications. <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> 5) '''MSL Packages'''<br /> <br /> '''Brief explanation:''' <br /> <br /> The MSL needs to be compiled from source. It would be convenient to distribute MSL as a .deb and/or .rpm package like other open source software.<br /> <br /> '''Expected results:'''<br /> <br /> One-click/command MSL installation.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Linux, Make<br /> <br /> <br /> 6) '''Developing a website to run MSL applications'''<br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use of these applications with a minimal/no knowledge of MSL.<br /> <br /> '''Expected results:'''<br /> <br /> A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''sabareeshs@gmail.com''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=817 2013-03-29T05:24:59Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> [[File:Msl_hierarchy.png | frame | '''MSL OBJECT HIERARCHY''']] <br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> <br /> 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.<br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Embedding MSL code for use in higher-level languages'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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)<br /> <br /> '''Expected results:'''<br /> <br /> Infrastructure and example applications in multiple higher-level languages.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++ and one of Python or R or perl <br /> <br /> <br /> <br /> 2) '''MSL-Light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> The objects in MSL are functionality-rich and sometimes too heavy (in terms of efficiency) for simple operations on large molecules. One idea is to implement light-weight versions of some core objects, for example, the AtomContainer object that is a lighter version of the System object. <br /> <br /> '''Expected results:'''<br /> <br /> We expect a collection of objects that would make some simple, routine operations faster than using core MSL.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++, Data Structures and Algorithms<br /> <br /> <br /> <br /> 3) '''Smart pointers in MSL'''<br /> <br /> '''Brief explanation:'''<br /> <br /> MSL uses basic pointers which are prone to bugs due to dangling pointers, memory leaks, etc.,<br /> <br /> '''Expected results:'''<br /> <br /> Replace regular pointers with the appropriate smart pointers in MSL.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> 4) '''Efficient program options management'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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.<br /> <br /> '''Expected results:'''<br /> <br /> The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications. <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> 5) '''MSL Packages'''<br /> <br /> '''Brief explanation:''' <br /> <br /> The MSL needs to be compiled from source. It would be convenient to distribute MSL as a .deb and/or .rpm package like other open source software.<br /> <br /> '''Expected results:'''<br /> <br /> One-click/command MSL installation.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Linux, Make<br /> <br /> <br /> 6) '''Developing a website to run MSL applications'''<br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use of these applications with a minimal/no knowledge of MSL.<br /> <br /> '''Expected results:'''<br /> <br /> A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''sabareeshs@gmail.com''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=816 2013-03-29T05:10:17Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> [[File:Msl_hierarchy.png | frame | '''MSL OBJECT HIERARCHY''']] <br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> <br /> 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.<br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Embedding MSL code for use in higher-level languages'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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)<br /> <br /> '''Expected results:'''<br /> <br /> Infrastructure and example applications in multiple higher-level languages.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++ and one of Python or R or perl <br /> <br /> <br /> <br /> 2) '''MSL-Light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> The objects in MSL are functionality-rich and sometimes too heavy (in terms of efficiency) for simple operations on large molecules. One idea is to implement light-weight versions of some core objects, for example, the AtomContainer object that is a lighter version of the System object. <br /> <br /> '''Expected results:'''<br /> <br /> We expect a collection of objects that would make some simple, routine operations faster than using core MSL.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++, Data Structures and Algorithms<br /> <br /> <br /> <br /> 3) '''Smart pointers in MSL'''<br /> <br /> '''Brief explanation:'''<br /> <br /> MSL uses basic pointers which are prone to bugs due to dangling pointers, memory leaks, etc.,<br /> <br /> '''Expected results:'''<br /> <br /> An efficient smart pointer implementation for MSL.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> 4) '''Efficient program options management'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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.<br /> <br /> '''Expected results:'''<br /> <br /> The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications. <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> 5) '''MSL Packages'''<br /> <br /> '''Brief explanation:''' <br /> <br /> The MSL needs to be compiled from source. It would be convenient to distribute MSL as a .deb and/or .rpm package like other open source software.<br /> <br /> '''Expected results:'''<br /> <br /> One-click/command MSL installation.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Linux, Make<br /> <br /> <br /> 6) '''Developing a website to run MSL applications'''<br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use of these applications with a minimal/no knowledge of MSL.<br /> <br /> '''Expected results:'''<br /> <br /> A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''sabareeshs@gmail.com''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=815 2013-03-29T05:09:36Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> [[File:Msl_hierarchy.png | frame | '''MSL OBJECT HIERARCHY''']] <br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> <br /> 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.<br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Embedding MSL code for use in higher-level languages'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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)<br /> <br /> '''Expected results:'''<br /> <br /> Infrastructure and example applications in multiple higher-level languages.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++ and one of Python or R or perl <br /> <br /> <br /> <br /> 2) '''MSL-Light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> The objects in MSL are functionality-rich and sometimes too heavy (in terms of efficiency) for simple operations on large molecules. One idea is to implement light-weight versions of some core objects, for example, the AtomContainer object that is a lighter version of the System object. <br /> <br /> '''Expected results:'''<br /> <br /> We expect a collection of objects that would make some simple, routine operations faster than using core MSL.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++, Data Structures and Algorithms<br /> <br /> <br /> <br /> 3) '''Smart pointers in MSL'''<br /> <br /> '''Brief explanation:'''<br /> MSL uses basic pointers which are prone to bugs due to dangling pointers, memory leaks, etc.,<br /> <br /> '''Expected results:'''<br /> An efficient smart pointer implementation for MSL.<br /> <br /> '''Knowledge Prerequisite:'''<br /> C++<br /> <br /> <br /> <br /> 4) '''Efficient program options management'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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.<br /> <br /> '''Expected results:'''<br /> <br /> The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications. <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> 5) '''MSL Packages'''<br /> <br /> '''Brief explanation:''' <br /> <br /> The MSL needs to be compiled from source. It would be convenient to distribute MSL as a .deb and/or .rpm package like other open source software.<br /> <br /> '''Expected results:'''<br /> <br /> One-click/command MSL installation.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Linux, Make<br /> <br /> <br /> 6) '''Developing a website to run MSL applications'''<br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use of these applications with a minimal/no knowledge of MSL.<br /> <br /> '''Expected results:'''<br /> <br /> A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''sabareeshs@gmail.com''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=814 2013-03-29T04:33:40Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> [[File:Msl_hierarchy.png | frame | '''MSL OBJECT HIERARCHY''']] <br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> <br /> 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.<br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Embedding MSL code for use in higher-level languages.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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)<br /> <br /> '''Expected results:'''<br /> <br /> Infrastructure and example applications in multiple higher-level languages.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++ and one of Python or R or perl <br /> <br /> <br /> <br /> 2) '''MSL-Light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> The objects in MSL are functionality-rich and sometimes too heavy (in terms of efficiency) for simple operations on large molecules. One idea is to implement light-weight versions of some core objects, for example, the AtomContainer object that is a lighter version of the System object. <br /> <br /> '''Expected results:'''<br /> <br /> We expect a collection of objects that would make some simple, routine operations faster than using core MSL.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++, Data Structures and Algorithms<br /> <br /> <br /> <br /> 3) '''Smart pointers in MSL'''<br /> <br /> '''Brief explanation:'''<br /> <br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> C++<br /> <br /> <br /> <br /> 4) '''Efficient program options management'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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.<br /> <br /> '''Expected results:'''<br /> <br /> The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications. <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> 5) '''MSL Packages'''<br /> <br /> '''Brief explanation:''' <br /> <br /> The MSL needs to be compiled from source. It would be convenient to distribute MSL as a .deb and/or .rpm package like other open source software.<br /> <br /> '''Expected results:'''<br /> <br /> One-click/command MSL installation.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Linux, Make<br /> <br /> <br /> 6) '''Developing a website to run MSL applications.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use of these applications with a minimal/no knowledge of MSL.<br /> <br /> '''Expected results:'''<br /> <br /> A website to run MSL applications on the lab cluster, post process the output and make the results available to the user.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''sabareeshs@gmail.com''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=813 2013-03-29T02:50:54Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> [[File:Msl_hierarchy.png | frame | '''MSL OBJECT HIERARCHY''']] <br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> <br /> 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.<br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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)<br /> <br /> '''Expected results:'''<br /> <br /> Infrastructure and example applications in multiple higher-level languages.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++ and one of Python or R or perl <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> The objects in MSL are functionality-rich and sometimes too heavy (in terms of memory) for simple operations on large molecules. One idea is to implement light weight versions of some core objects. An example is the AtomContainer object that is a lighter version of the System Object. <br /> <br /> '''Expected results:'''<br /> <br /> New light-weight objects could do away with some inefficiencies in core MSL which were necessary to make MSL flexible. We expect a collection of objects that could make some simple,routine operations faster than using core MSL.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++, Data Structures and Algorithms<br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> C++<br /> <br /> <br /> <br /> 4) '''Create a centralized program options mechanism that makes options management easier.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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.<br /> <br /> '''Expected results:'''<br /> <br /> The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications. <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> <br /> The MSL needs to be compiled from source. It would be convenient to distribute MSL as a .deb and/or .rpm package like other open source software.<br /> <br /> '''Expected results:'''<br /> <br /> One-click/commmand MSL installation.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Linux, Make<br /> <br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''sabareeshs@gmail.com''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=812 2013-03-29T02:23:25Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> [[File:Msl_hierarchy.png | frame | '''MSL OBJECT HIERARCHY''']] <br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> <br /> 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.<br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> 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)<br /> <br /> '''Expected results:'''<br /> Infrastructure and example applications in multiple higher-level languages.<br /> <br /> '''Knowledge Prerequisite:'''<br /> C++ and one of Python or R or perl <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 4) '''Create a centralized program options mechanism that makes options management easier.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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.<br /> <br /> '''Expected results:'''<br /> <br /> The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications. <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> <br /> The MSL needs to be compiled from source. It would be convenient to distribute MSL as a .deb and/or .rpm package like other open source software.<br /> <br /> '''Expected results:'''<br /> <br /> One-click/commmand MSL installation.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Linux, Make<br /> <br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''sabareeshs@gmail.com''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=811 2013-03-29T00:58:06Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> [[File:Msl_hierarchy.png | frame | '''MSL OBJECT HIERARCHY''']] <br /> <br /> 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.<br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 4) '''Create a centralized program options mechanism that makes options management easier.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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.<br /> <br /> '''Expected results:'''<br /> <br /> The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications. <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> <br /> The MSL needs to be compiled from source. It would be convenient to distribute MSL as a .deb and/or .rpm package like other open source software.<br /> <br /> '''Expected results:'''<br /> <br /> One-click/commmand MSL installation.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Linux, Make<br /> <br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''sabareeshs@gmail.com''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=810 2013-03-29T00:56:56Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> [[File:Msl_hierarchy.png | frame | '''MSL OBJECT HIERARCHY''']] <br /> <br /> 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.<br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 4) '''Create a centralized program options mechanism that makes options management easier.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> 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.<br /> <br /> '''Expected results:'''<br /> <br /> The mechanism developed should facilitate option reuse and in general, easy option handling in MSL applications. <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> C++<br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> <br /> The MSL needs to be compiled from source. It would be convenient to distribute MSL as a .deb and/or .rpm package like other open source software.<br /> <br /> '''Expected results:'''<br /> <br /> One-click/commmand MSL installation.<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Linux, Make<br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''sabareeshs@gmail.com''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=809 2013-03-29T00:48:51Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> [[File:Msl_hierarchy.png | frame | '''MSL OBJECT HIERARCHY''']] <br /> <br /> 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.<br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 4) '''Create a centralized program options mechanism that makes options management easier.'''<br /> <br /> '''Brief explanation:'''<br /> 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.<br /> <br /> '''Expected results:'''<br /> The mechanism developed should facilitate easy option handling in MSL applications. <br /> <br /> '''Knowledge Prerequisite:'''<br /> C++<br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> The MSL needs to be compiled from source. It would be convenient to distribute MSL as a .deb and/or .rpm package like other open source software.<br /> <br /> '''Expected results:'''<br /> One-click/commmand MSL installation.<br /> <br /> '''Knowledge Prerequisite:'''<br /> Linux, Make<br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''sabareeshs@gmail.com''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=808 2013-03-28T20:47:22Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> 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.<br /> <br /> <br /> Place some figures here<br /> <br /> [[File:Msl_hierarchy.png]] <br /> <br /> <br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 4) '''Create a centralized options mechanism that makes managing options easier.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''sabareeshs@gmail.com''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=807 2013-03-28T20:45:36Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> 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.<br /> <br /> <br /> Place some figures here<br /> <br /> [[File:Msl_hierarchy.png]] <br /> <br /> <br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 4) '''Create a centralized options mechanism that makes managing options easier.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=806 2013-03-28T20:44:49Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> 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.<br /> <br /> <br /> Place some figures here<br /> <br /> [[File:Msl_hierarchy.png|left|400px]]] <br /> <br /> <br /> <br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 4) '''Create a centralized options mechanism that makes managing options easier.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Main_Page&diff=805 2013-03-28T20:43:22Z

<p>Sabareeshs: </p> <hr /> <div>&lt;big&gt;'''MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.'''<br /> &lt;/big&gt;<br /> [[Image:MSL-logo.png|right|400px]]<br /> <br /> ===Philosophy===<br /> 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).<br /> <br /> The MSL library is '''not''' a program (although some applications are distributed) but a tool for scientist to code their own methods.<br /> <br /> ===Features===<br /> Some of the features supported by the library are:<br /> <br /> * Support for reading and writing PDB and CRD files.<br /> * The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.<br /> * For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.<br /> * Support for rotamer libraries.<br /> * Transformations such as translations, rotations, and alignments.<br /> * The CHARMM force field and other energy funtions.<br /> * Support for CHARMM topology and parameter files.<br /> * Structure building from scratch (using internal coordinates)<br /> * Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.<br /> * Local backbone sampling.<br /> * Crystal lattice generation.<br /> * A '''[[PyMOL Python Interface]]''' for calling MSL code from within PyMOL.<br /> * A R Interface for calling arbitrary R algorithms or plotting routines from within MSL<br /> * And more...<br /> <br /> ===Documentation===<br /> 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.<br /> <br /> ===Status===<br /> Version 1.0 of MSL was released on July 8, 2012, which is suitable for production.<br /> <br /> The libraries are in an advanced are in active development, and a development version is also available (use it at your own risk).<br /> <br /> ===Source===<br /> <br /> The source code can be downloaded on SourceForge. Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page. ([[ToDo|&quot;To do&quot; list]]).<br /> <br /> ===Main development team:===<br /> <br /> * Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']<br /> * Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA<br /> * Jason Donald, Agrivida, Inc., Medford MA<br /> * Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group<br /> * Gevorg Grigoryan, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']<br /> <br /> We have applied to the Google Summer of Code 2013. Please see this page '''[[Google_Summer_of_Code_Ideas]]'''<br /> <br /> === Reference === <br /> Article published using MSL should cite:<br /> &lt;pubmed&gt;22565567&lt;/pubmed&gt;<br /> <br /> '''MSL (including early versions) has been used in the following work:'''<br /> &lt;pubmed&gt;23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646&lt;/pubmed&gt;</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=804 2013-03-28T20:24:29Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> 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.<br /> <br /> [[Media:Msl_hierarchy.png]]<br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 4) '''Create a centralized options mechanism that makes managing options easier.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=803 2013-03-28T20:24:12Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> 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.<br /> <br /> [[Media:Example.ogg]]<br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. This will continue to be the main theme of MSL development and we are striving to improve the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> * implementing more modeling algorithms and protocols <br /> <br /> Another important direction is making MSL more accessible to a wider audience by<br /> * creating interfaces to other programming languages<br /> * making distribution of MSL easier <br /> * building ready-to-use applications <br /> * hosting MSL applications on web servers for public use<br /> <br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 4) '''Create a centralized options mechanism that makes managing options easier.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=File:Msl_hierarchy.png&diff=802 2013-03-28T20:22:35Z

<p>Sabareeshs: </p> <hr /> <div></div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=801 2013-03-28T20:11:31Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> 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.<br /> <br /> '''Current development'''<br /> <br /> The focus so far has been on creating a flexible yet powerful software framework that is easily accessible to programmers familiar with C++/object-orientation. While this will continue to be the main theme of MSL development, another important direction is making MSL more accessible to a wider audience by<br /> <br /> 1) creating interfaces to other programming languages<br /> <br /> 2) making distribution of MSL easier <br /> <br /> 3) building ready-to-use applications <br /> <br /> 4) hosting MSL applications on web servers for public use<br /> <br /> 5) improving the core framework through<br /> * more advanced objects<br /> * more efficient implementations<br /> <br /> With these goals in mind, we have come up with a list of project ideas that will greatly help MSL developers and users.<br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 4) '''Create a centralized options mechanism that makes managing options easier.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=800 2013-03-28T19:45:50Z

<p>Sabareeshs: </p> <hr /> <div>'''MSL (Molecular Software Libraries)''' is an open source C++ library of objects related to macromolecular modeling.<br /> <br /> '''Goal'''<br /> <br /> 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).<br /> <br /> '''History'''<br /> <br /> MSL has been developed in the past 5 year (9 years if we include its early predecessor). It has an extensive code base (over 150 objects and 100,000 lines of code). After years in beta, the first stable version (1.0) was released in 2012.<br /> <br /> 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]. <br /> <br /> MSL is described in its primary citation:<br /> * Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A &quot;Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)&quot;, ''J Comput. Chem.'' 2012 '''33(20)''', 1645-61 ([http://senes.biochem.wisc.edu/pdf/22968_ftp.pdf Download PDF])<br /> <br /> 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.<br /> <br /> '''Current development'''<br /> <br /> Write a paragraph linking to the following ideas...<br /> <br /> <br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 4) '''Create a centralized options mechanism that makes managing options easier.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=796 2013-03-28T19:20:31Z

<p>Sabareeshs: </p> <hr /> <div>The goal of MSL is to create a toolbox that enables the study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a the distance between two atoms) to complex applications (protein design).<br /> <br /> The MSL is not just a program (although some applications are distributed) but a tool for scientists to develop their own methods.<br /> <br /> The core of MSL has stabilized over years of development and can be easily extended to create a wide range of applications.<br /> <br /> MSL has been extensively used in scientific publications encompassing a variety of applications. <br /> <br /> <br /> 1) [http://senes.biochem.wisc.edu/pdf/FtsBdimer-preprint.pdf Protein structure prediction]<br /> <br /> 2) [http://www.ncbi.nlm.nih.gov/pubmed/23422424 Protein design]<br /> <br /> 3) [http://www.ncbi.nlm.nih.gov/pubmed/23089864 Protein Engineering]<br /> <br /> 4) [http://senes.biochem.wisc.edu/pdf/EBL-2012-Proteins.pdf Modeling algorithms/methods]<br /> <br /> <br /> <br /> <br /> == Ideas ==<br /> <br /> <br /> 1) '''Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 2) '''MSL-light'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 3) '''Convert MSL pointers to using a Smart/Owning pointer system'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 4) '''Create a centralized options mechanism that makes managing options easier.'''<br /> <br /> '''Brief explanation:'''<br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> <br /> <br /> 5) '''Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation.''' <br /> <br /> '''Brief explanation:''' <br /> <br /> '''Expected results:'''<br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> <br /> 6) '''Creating a web interface to run MSL programs.'''<br /> <br /> <br /> '''Brief explanation:'''<br /> <br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal/no knowledge of MSL.<br /> <br /> <br /> '''Expected results:'''<br /> <br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> <br /> '''Knowledge Prerequisite:'''<br /> <br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=795 2013-03-28T19:02:17Z

<p>Sabareeshs: </p> <hr /> <div>The goal of MSL is to create a toolbox that enables the study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a the distance between two atoms) to complex applications (protein design).<br /> <br /> The MSL is not just a program (although some applications are distributed) but a tool for scientists to develop their own methods.<br /> <br /> The core of MSL has stabilized over years of development and can be easily extended to create a wide range of applications.<br /> <br /> MSL has been extensively used in scientific publications encompassing a variety of applications. <br /> <br /> <br /> 1) [http://senes.biochem.wisc.edu/pdf/FtsBdimer-preprint.pdf Protein structure prediction]<br /> <br /> 2) [http://www.ncbi.nlm.nih.gov/pubmed/23422424 Protein design]<br /> <br /> 3) [http://www.ncbi.nlm.nih.gov/pubmed/23089864 Protein Engineering]<br /> <br /> 4) [http://senes.biochem.wisc.edu/pdf/EBL-2012-Proteins.pdf Modeling algorithms/methods]<br /> <br /> <br /> <br /> <br /> == Ideas ==<br /> <br /> <br /> 1) Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.<br /> <br /> Brief explanation:<br /> <br /> Expected results:<br /> <br /> Knowledge Prerequisite:<br /> <br /> <br /> <br /> <br /> 2) MSL-light<br /> <br /> Brief explanation:<br /> <br /> Expected results:<br /> <br /> Knowledge Prerequisite:<br /> <br /> <br /> <br /> <br /> 3) Convert MSL pointers to using a Smart/Owning pointer system<br /> <br /> Brief explanation:<br /> <br /> Expected results:<br /> <br /> Knowledge Prerequisite:<br /> <br /> <br /> <br /> <br /> 4) Create a centralized options mechanism that makes managing options easier.<br /> <br /> Brief explanation:<br /> <br /> Expected results:<br /> <br /> Knowledge Prerequisite:<br /> <br /> <br /> <br /> <br /> 5) Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation. <br /> <br /> Brief explanation: <br /> <br /> Expected results:<br /> <br /> Knowledge Prerequisite:<br /> <br /> <br /> 6) Creating a web interface to run MSL programs.<br /> <br /> Brief explanation:<br /> There are several MSL applications that are directly useful to structural biologists. For example, the sidechain modeling programs, the structure prediction programs, etc., are of general interest and it would be useful to create a web interface that allows the use these applications with a minimal knowledge of MSL.<br /> <br /> Expected results:<br /> A page on the lab website that manages jobs submitted by users. This may also involve running multiple programs on the lab cluster, post processing, and making the results available.<br /> <br /> <br /> Knowledge Prerequisite:<br /> Scripting Languages and Web Design<br /> <br /> <br /> Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=794 2013-03-28T18:27:08Z

<p>Sabareeshs: </p> <hr /> <div>The main goal of MSL is to create a set of tools that enable the computational study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a distance or edit a dihedral) to complex applications (protein modeling or design).<br /> The MSL library is not a program (although some applications are distributed) but a tool for scientist to code their own methods.<br /> <br /> MSL has been extensively used in scientific publications encompassing a variety of applications. <br /> <br /> 1) [http://senes.biochem.wisc.edu/pdf/FtsBdimer-preprint.pdf Protein structure prediction]<br /> <br /> 2) [http://www.ncbi.nlm.nih.gov/pubmed/23422424 Protein design]<br /> <br /> 3) [http://www.ncbi.nlm.nih.gov/pubmed/23089864 Protein Engineering]<br /> <br /> 4) [http://senes.biochem.wisc.edu/pdf/EBL-2012-Proteins.pdf Modeling algorithms/methods]<br /> <br /> <br /> <br /> == Ideas ==<br /> <br /> <br /> 1) Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.<br /> <br /> 2) MSL-light<br /> <br /> 3) Convert MSL pointers to using a Smart/Owning pointer system<br /> <br /> 4) Create a centralized options mechanism that makes managing options easier.<br /> <br /> 5) Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation. <br /> <br /> Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=793 2013-03-28T17:20:59Z

<p>Sabareeshs: </p> <hr /> <div>'''List of ideas for Google Summer of Code 2013'''<br /> <br /> 1) Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.<br /> <br /> 2) MSL-light<br /> <br /> 3) Convert MSL pointers to using a Smart/Owning pointer system<br /> <br /> 4) Create a centralized options mechanism that makes managing options easier.<br /> <br /> 5) Create Debian/Ubuntu deb packages and Redhat rpm packages to facilitate distribution and installation. <br /> <br /> Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=792 2013-03-27T19:04:32Z

<p>Sabareeshs: </p> <hr /> <div>'''List of ideas for Google Summer of Code 2013'''<br /> <br /> 1) Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.<br /> <br /> 2) MSL-light<br /> <br /> 3) Convert MSL pointers to using a Smart/Owning pointer system<br /> <br /> 4) Create a centralized options mechanism that makes managing options easier.<br /> <br /> Please email '''mslib-discussion@lists.sourceforge.net''' if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=791 2013-03-27T19:04:21Z

<p>Sabareeshs: </p> <hr /> <div>'''List of ideas for Google Summer of Code 2013'''<br /> <br /> 1) Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.<br /> <br /> 2) MSL-light<br /> <br /> 3) Convert MSL pointers to using a Smart/Owning pointer system<br /> <br /> 4) Create a centralized options mechanism that makes managing options easier.<br /> <br /> Please email mslib-discussion@lists.sourceforge.net if you would like to work on any of these ideas.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=790 2013-03-27T18:28:58Z

<p>Sabareeshs: </p> <hr /> <div>'''List of ideas for Google Summer of Code 2013'''<br /> <br /> 1) Implementing a generic language-interface (swig.org) allowing for easy MSL use in python, R, perl, octave, etc.<br /> <br /> 2) MSL-light<br /> <br /> 3) Convert MSL pointers to using a Smart/Owning pointer system<br /> <br /> 4) Create a centralized options mechanism that makes managing options easier.</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=785 2013-03-27T17:46:13Z

<p>Sabareeshs: </p> <hr /> <div>'''List of ideas for Google Summer of Code 2013'''</div>

Sabareeshs http://msl-libraries.org/index.php?title=Google_Summer_of_Code_Ideas&diff=784 2013-03-27T17:44:52Z

<p>Sabareeshs: Created page with &quot;'''List of Ideas for Google Summer of Code 2013'''&quot;</p> <hr /> <div>'''List of Ideas for Google Summer of Code 2013'''</div>

Sabareeshs