Florian Centler; Christoph Kaleta; Pietro Speroni di Fenizio; Peter Dittrich (2010)
A parallel algorithm to compute chemical organizations in biological networks
Bioinformatics Applications Note 26 (14), 1788 – 1789
Abstract:
Analysing genome-scale in silico models with stoichiometry-based methods is computationally demanding. The current algorithms to compute chemical organisations in chemical reaction networks are limited to small-scale networks, prohibiting a thorough analysis of large models. Here, we introduce a parallelised version of the constructive algorithm to determine chemical organisations. The algorithm is implemented in the Standard C programming language and parallelised 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 parallelised in an embarrassing parallel manner, providing good scalability.