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  • Here, we present the software library pSSAlib, which provides a complete and concise implementation of the most efficient partial-propensity methods for simulating exact stochastic chemical kinetics. Here, we describe pSSAlib in detail and apply it to a new model of the endocytic pathway in eukaryotic cells, leading to the discovery of a stochastic counterpart of the cut-out switch motif underlying early-to-late endosome conversion. pSSAlib is written in C++ and is designed to be highly efficient, also supporting parallel execution on distributed-memory computer clusters. The pSSAlib source code and pre-packaged installers are freely available from mosaic.mpi-cbg.de as open source under the GNU LGPL v3 license.
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