sybil – Efficient Constraint Based Modelling in R
The package sybil is a Systems Biology Library for GNU R, implementing algorithms for constraint based analysis of metabolic networks. Among other functions, sybil currently provides efficient methods for flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), flux variability Analysis and robustness Analysis. Sybil makes use of the sparse matrix implementation in the R-package Matrix.
Sybil is available for download on CRAN.
- flux-balance analysis (FBA)
- minimization of metabolic adjustment (MOMA)
- regulatory on/off minimization (ROOM)
- simulate gene knock-outs (single, double, n)
- flux variability analysis
- robustness analysis
- read SBML formatted files
- read output from BiGG database
- interfaceing mathematical programming software: GLPK, COIN-OR Clp, IBM ILOG CPLEX, lp_solve and Gurobi
- set or change all parameters provided by the mathematical programming software
- extendable with new algorithms due to object oriented programming interface
To cite package sybil in publications use:
Gelius-Dietrich, G., Amer Desouki, A., Fritzemeier, C.J. and Lercher, M.J. “sybil – Efficient constraint-based modelling in R”. BMC Systems Biology, 2013. 7:125.
The R-package sybilGUROBI makes the R-interface of Gurobi available to sybil.
- sybilGUROBI_1.0.4.tar.gz source code package.
All packages are compatible with R version 2.15.3.
Sybil, sybilSBML and sybilGUROBI are non-profit projects. They are published under the GNU General Public License (GPL 3).
Contact: Jonathan Fritzemeier