A parallel algorithm to compute chemical organizations in biological networks.
CONCLUSIONS
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.


BACKGROUND
An implementation of the algorithm including source code can be obtained from http://www.minet.uni-jena.de/csb/prj/ot/tools
Centler
Florian
F
Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstrasse 15, D-04318 Leipzig, Germany. florian.centler@ufz.de
Kaleta
Christoph
C
Speroni di Fenizio
Pietro
P
Dittrich
Peter
P
D000465:Algorithms; D008954:Models, Biological; D008956:Models, Chemical; D049490:Systems Biology