sybil-package: sybil - Efficient Constrained Based Modelling in R

In sybil: Efficient Constrained Based Modelling

Description

The package sybil is a collection of functions designed for in silico analysis—in particular constrained based analysis—of metabolic networks.

Details

The package sybil is designed to read metabolic networks from csv files. This is done by the function readTSVmod. The function returns an object of the class modelorg.

Read csv files (example files included):

mpath <- system.file(package = "sybil", "extdata")
model <- readTSVmod(prefix = "Ec_core",
                    fpath = mpath, quote = "\"")
  

Perform flux balance analysis (FBA):
ec_f <- optimizeProb(model)

Perform single gene deletion analysis:
ec_g <- oneGeneDel(model)

Plot the values of the objective function after optimization in a histogram:
plot(ec_g)

Perform flux variability analysis:
ec_v <- fluxVar(model)

Plot the result:
plot(ec_v)

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

References

Gelius-Dietrich, G., Desouki, A. A., Fritzemeier, C. J., and Lercher, M. J. (2013). sybil – Efficient constraint-based modelling in R. BMC Systems Biology 7, 125.

The BiGG database http://bigg.ucsd.edu/.

Schellenberger, J., Park, J. O., Conrad, T. C., and Palsson, B. Ø., (2010) BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11, 213.

The openCOBRA project https://opencobra.github.io/.

Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. Ø. and Herrgard, M. J. (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2, 727–738.

Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., Kang, J., Hyduke, D. R. and Palsson, B. Ø. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6, 1290–1307.

See Also

Package sybilSBML and there the function readSBMLmod to read metabolic models written in SBML language.

Examples

  data(Ec_core)
  Ec_ofd <- oneGeneDel(Ec_core)
  plot(Ec_ofd)

Example output

Loading required package: Matrix
Loading required package: lattice
compute affected fluxes ... OK
Loading required package: glpkAPI
using GLPK version 4.65
calculating 137 optimizations ... 
|            :            |            :            | 100 %
|===================================================| :-) 
OK
Done.

sybil documentation built on May 31, 2021, 5:08 p.m.