Name
Abstract | ||
|---|---|---|
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.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 faster than previous implementations when calculating the effect of whole-genome single gene deletions in silico on a complete E. coli metabolic model.Due to the object-oriented architecture of sybil, users can easily build analysis pipelines in R or even implement their own constraint-based algorithms. Based on its highly efficient communication with different mathematical optimisation programs, sybil facilitates the exploration of high-dimensional optimisation problems on small time scales. Sybil and all its dependencies are open source. Sybil and its documentation are available for download from the comprehensive R archive network (CRAN). |
Year | DOI | Venue |
|---|---|---|
2013 | 10.1186/1752-0509-7-125 | BMC systems biology |
Keywords | Field | DocType |
systems biology,escherichia coli,bioinformatics,algorithms,computer simulation,programming languages,computational biology,computer graphics | Pairwise comparison,Computer science,Systems biology,Implementation,Theoretical computer science,Bioinformatics,Computer graphics,Flux balance analysis,Computation | Journal |
Volume | Issue | ISSN |
7 | 1 | 1752-0509 |
Citations | PageRank | References |
13 | 0.68 | 18 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Gabriel Gelius-Dietrich | 1 | 13 | 0.68 |
| Abdelmoneim Amer Desouki | 2 | 13 | 0.68 |
| Claus Jonathan Fritzemeier | 3 | 17 | 1.16 |
| Martin J Lercher | 4 | 55 | 5.89 |