Software for Building Markov State Models
This chapter briefly describes some of the publicly available software packages for the construction of Markov state models and provides links where they can be downloaded.
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Gregory R. Bowman and Frank Noé
11.1
MSMBuilder
MSMBuilder is an open source software package for constructing Markov state models. The software is primarily written in python to facilitate rapid integration of new methods and readable implementations of existing methods. Timesensitive routines are implemented in C with python wrappers to enhance the performance of the software. At the time of this writing, stable public releases of MSMBuilder are available via the SimTk software repository (https://simtk.org/ home/msmbuilder; http://msmbuilder.org). The current development build is also available via GitHub (https://github.com/SimTk/msmbuilder).
11.2
EMMA
EMMA is a software library and set of commandline tools for constructing, validating and analyzing Markov state models. The library is written in Java, thus being fast and platform-independent without requiring local compilation or installation. At the time of this writing, stable public releases of EMMA are available via the SimTk software repository (https://simtk.org/home/ emma). The Java source code is available on request. As soon as publicly available, it will be linked on the simtk.org website.
G.R. Bowman (B) Departments of Molecular & Cell Biology and Chemistry, University of California, Berkeley, CA 94720, USA e-mail: [email protected] F. Noé Institut für Mathematik II, Freie Universität Berlin, Arnimallee 2-6, 14195 Berlin, Germany G.R. Bowman et al. (eds.), An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation, Advances in Experimental Medicine and Biology 797, DOI 10.1007/978-94-007-7606-7_11, © Springer Science+Business Media Dordrecht 2014
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