sybil (version 1.0.1)

sybil-package: Systems Biology Library

Description

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

encoding

utf8

Details

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

the beginning (or reading a csv file): ec <- readTSVmod(reactList = "Ec_core.csv")

find double reactions: ec_d <- doubleReact(ec)

remove reactions one and five: ec_r <- rmReact(ec, c(1, 5))

convert to irreversible model: ec_ir <- mod2irrev(ec)

perform FBA: ec_f <- simpleFBA(ec)

perform single gene deletion analysis: ec_o <- oneGeneDel(ec)

References

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.

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 (readSBMLmod).

Examples

data(Ec_core)
  Ec_ofd <- oneFluxDel(Ec_core)
  hist(lp_obj(Ec_ofd))