A parallel algorithm to compute chemical organizations in biological networks.

ABSTRACT

SUMMARY: Analysing genome-scale in silico models with stoichiometry-based methods is computationally demanding. The current algorithms to compute chemical organizations in chemical reaction networks are limited to small-scale networks, prohibiting a thorough analysis of large models. 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 parallelized using the message passing interface (MPI) protocol. The resulting code can be executed on computer clusters making use of an arbitrary number of processors. The algorithm is parallelized in an embarrassing parallel manner, providing good scalability. AVAILABILITY: An implementation of the algorithm including source code can be obtained from http//www.minet.uni-jena.de/csb/prj/ot/tools