A parallel algorithm to compute chemical organizations in biological networks
Authors
Abstract
Motivation: Analysing genome-scale in silico models with stoichiometry based methods is computationally demanding. The current algorithm to compute chemical organizations in chemical reaction networks is limited to small-scale networks, prohibiting a thorough analysis of large models.Results: Here, we introduce a parallelized version of the constructive algorithm to determine chemical organizations. The algorithm is implemented in the Standard C programming language and paralellized using the Message Passing Interface (MPI) protocol. The resulting code can be executed on computer clusters making use of an arbitrary number of pocessors. The algorithm is paralellized in an embarrassing parallel manner, providing good scalability.
Availability: The source code can be obtained at http://www.minet.uni-jena.de/csb/prj/ot/tools.
Contact: florian.centler@ufz.de