A parallel algorithm to compute chemical organizations in biological networks | Zendy

Florian Centler | Zendy; Christoph Kaleta | Zendy; Pietro Speroni di Fenizio | Zendy; Peter Dittrich | Zendy

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A parallel algorithm to compute chemical organizations in biological networks

Author(s) -

Florian Centler,

Christoph Kaleta,

Pietro Speroni di Fenizio,

Peter Dittrich

Publication year - 2010

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btq263

Subject(s) - computer science , scalability , message passing interface , algorithm , code (set theory) , parallel algorithm , parallel computing , interface (matter) , source code , scale (ratio) , message passing , theoretical computer science , programming language , physics , set (abstract data type) , bubble , quantum mechanics , maximum bubble pressure method , database

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.

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