StoChDyn and EvO-ES-
Stochastic modeling of chromatin state dynamics across cell divisions and
evolutionary optimization of epigenetic stability
Arnold, C, Stadler, P.F., Prohaska, S.J. 2013. Chromatin Computation: Epigenetic Inheritance as a Pattern Reconstruction Problem. Journal of Theoretical Biology. 336(7):61-74.
We developed a flexible stochastic simulation system for studying the dynamics of chromatin states across cell divisions. The implementation is based on Gillespie's well-established stochastic simulation algorithm (i.e., it models the master equation of a detailed chemical model). The software may be used to study the propagation of histone modification patterns across cell divisions and therefore its epigenetic inheritance potential.
Importantly, the software can be highly customized. For example, parameters relating to the histone-modifying enzymes (set of possible histone-modifying enzymes along with their individual cellular concentrations, recognition rules, and binding and dissociation reaction rates), the set of histone modifications that are of relevance, the specific modification pattern that should be maintained, DNA replication specifics, the length of the nucleosome string to be considered, or parameters relating to the stochastic simulation algorithm (such as the number of independent runs) may be user-adjusted. For a full list of adjustable parameters, see the Documentation.
We also provide an evolutionary algorithm (called EvO-ES) that allows to search for mixtures of histone-modifying enzymes (among a set of user-defined enzymes) capable of propagating, with high accuracy, arbitrarily complex and user-defined modification patterns across cell divisions. The EvO-ES program is written in Perl and neatly integrates with StoChDyn. The software provides high flexibility, as virtually all relevant parameters may be adjusted by the user (e.g., all parameters of the StoChDyn program as well as various parameters related to the evolutionary algorithm itself).
For more details, see the official Publication.
Current release: StoChDyn Version 1.0 (June 2013, Sourcecode)
see the Documentation
For more information, see the Documentation.