Sybil--efficient constraint-based modelling in R.

ABSTRACT:

Background

Constraint-based analyses of metabolic networks are widely used to simulate the properties of genome-scale metabolic networks. Publicly available implementations tend to be slow, impeding large scale analyses such as the genome-wide computation of pairwise gene knock-outs, or the automated search for model improvements. Furthermore, available implementations cannot easily be extended or adapted by users.

Results

Here, we present sybil, an open source software library for constraint-based analyses in R; R is a free, platform-independent environment for statistical computing and graphics that is widely used in bioinformatics. Among other functions, sybil currently provides efficient methods for flux-balance analysis (FBA), MOMA, and ROOM that are about ten times fas

SUBMITTER: Gelius-Dietrich G 

PROVIDER: S-EPMC3843580 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature