Jump to contentJump to search

sybil

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.

Download

Sybil is available for download on CRAN.

Features

  • 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

Citation

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.

doi:10.1186/1752-0509-7-125

Article: http://www.biomedcentral.com/1752-0509/7/125

 

Additional Packages

sybilSBML

The package sybilSBML is an extension for sybil to use SBML format files.

The package can be installed on Windows, Mac OS and linux systems. License information can be found in the source package.

Windows 10, 64-bit

For Windows 10, 64-bit we have a binary version of the package, that is able to use additional functions of the libSBML FBC and Groups plugins, because it has been built with the respective building options. The binary version of the package was build against the static library of libSBML, therefore an additional installation of libSBML is not necessary.

The binary version of the package can be installed by opening the GNU R environment in Windows 10 and typing the following commands (modify example file path shown here for the correct location of the .zip file):

install.packages("sybil")
install.packages("C:/Users/traes/Desktop/sybilSBML_3.1.3.zip", repos = NULL)

If you want to install the source package on Windows 10, the procedure is more comprehensive. It involves the installation of the Windows Toolset (Rtools40) and libSBML, the setting of environment variables, and building of the source package of sybilSBML.

The document Installing_sybil_and_sybilSBML_on_Windows_10_64bit.pdf contains examples of the installation procedure of the binary and source code package on Windows 10, 64-bit.

Mac OS 11 (Big Sur)

For Mac OS 11 (Big Sur) we have a binary version of the package, that is able to use additional functions of the libSBML FBC and Groups plugins, because it has been built with the respective building options. The binary version of the package was build against the static library of libSBML, therefore an additional installation of libSBML is not necessary.

The binary version of the package can be installed by opening the GNU R environment in Mac OS  and typing the following commands (modify example file path shown here for the correct location of the .tgz file):

install.packages("sybil")
install.packages("/Users/traes/sybilSBML_3.1.3.tgz", repos = NULL)

If you want to install the source package on Mac OS, the procedure is more comprehensive. It involves the installation of the libSBML source distribution, the setting of environment variables and system settings, and installation of the source package of sybilSBML.

The document Installing_sybil_and_sybilSBML_on_Mac_OS_11.pdf contains examples of the installation procedure of the binary and source code package on Mac OS 11 (Big Sur).

Linux

If you want to install the source package on Linux, the installation of the libSBML-software and installation of the source package of sybilSBML is necessary.

The document Installing_sybil_and_sybilSBML_on_Debian_10.pdf contains examples of the installation procedure of the source code package on Debian 10 (Buster).

sybilGUROBI

The R-package sybilGUROBI makes the R-interface of Gurobi available to sybil.

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:

Responsible for the content: