BiGGR-package {BiGGR} | R Documentation

## Creates an interface to the BiGG database, provides a framework for simulation and produces flux graphs

### Description

This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package aids in performing flux balance analysis (FBA). Metabolic networks and estimated fluxes can be visualized using hypergraphs.

### Details

Package: | BiGGR
Type: | Package
Version: | 0.99.0
Date: | 2013-07-10
Depends: | R (>= 2.14.0), rsbml, hyperdraw, LIM
Imports: | hypergraph
License: | GPL (>=2)
URL: | http://www.bioconductor.org/
Copyright: | see inst/COPYRIGHTS for the license of the BiGG database
biocViews: | NetworkAnalysis, Visualization, Metabolomics
LazyLoad: | yes
Packaged: | 2013-08-05 12:44:08 UTC; hettling
Built: | R 3.0.0; ; 2013-08-05 12:44:22 UTC; unix

Index:

    E.coli_iAF1260                                              Ecoli dataset with ORFs and thermodynamic information
    E.coli_iJR904                                               Ecoli genome-scale model
    Glycolysis                                                  Metabolic reconstruction of Glycolysis pathway
    H.pylori_ilT341                                             H.pylori in silico genome-scale characterization of single and double deletion mutants
    H.sapiens_Recon_1                                           Reconstruction of human metabolism from the BiGG database
    M.barkeri_iAF692                                            Metabolic reconstruction of M.barkeri from the BiGG database
    Recon2                                                      Human metabolic reconstruction Recon2
    S.aureus_iSB619                                             Metabolic reconstruction of S.aureus from the BiGG database
    S.cerevisiae_iND750                                         Metabolic reconstruction of S.cerevisiae from the BiGG database
    buildSBMLFromBiGG                                           Build an SBML model from a given reactions file obtained from the BiGG database
    buildSBMLFromGenes                                          Build an SBML model for specific genes in a given database
    buildSBMLFromPathways                                       Build an SBML model for specific pathway(s) in a given database
    buildSBMLFromReactionIDs                                    Build an SBML model for specific reactions in a given database
    createLIMFromBiGG                                           Create a LIM model object from a BiGG database file
    createLIMFromSBML                                           Create a LIM model object from an SBML file
    extractGeneAssociations                                     Extract informations on genes from a given database
    extractPathways                                             Extract all pathways from given database
    getPathwaysForSBML                                          Extract all pathways from a database that are relevant for a given SBML model
    getRates                                                    Get Optimized Rates
    sbml2hyperdraw                                              Returns a graph representation of an SBML model

Further information is available in the following vignettes:

`BiGGR` | BiGGR (source, pdf)

### Author(s)

Anand K. Gavai, Hannes Hettling

Maintainer: Anand K. Gavai <anand.gavai@bioinformatics.nl>, Hannes Hettling <j.hettling@vu.nl>

### See Also

`rsbml`

### Examples

    # library("BiGGR")

    library(help="BiGGR")

    ##load reaction identifiers from package examples
    file.name <- system.file("extdata",
    					 "Glycolysis_TCA_recon1_reactionIDs.txt",
    					 package="BiGGR")
    reaction.ids <- scan(file.name, what=" ")

    ##load database
    data("H.sapiens_Recon_1")

    ##build SBML model
    sbml.model <- buildSBMLFromReactionIDs(reaction.ids, H.sapiens_Recon_1)

    ##following term is to be maximized
    maximize <- "R_ATPS4m - R_NDPK1m - R_HEX1 - R_PFK - R_PGK + R_PYK"

    ##specify the external metabolites of the system
    externals <- c("M_glc_DASH_D_e", "M_lac_DASH_L_e",
    		   "M_ala_DASH_L_e", "M_gln_DASH_L_c", "M_h2o_e",
    		   "M_co2_e", "M_o2_e", "M_h_e", "M_pi_c",
    		   "M_o2s_m", "M_nh4_m", "M_adp_c",
    		   "M_atp_c", "M_nadp_c", "M_nadph_c", "M_h_c")
    ##specify the values of following fluxes:
    ##R_GLCt1r=0.4, R_O2t=2.4, R_L_LACt2r=R_GLNtm=0

    equation.vars <- c("R_GLCt1r", "R_O2t", "R_L_LACt2r", "R_GLNtm")
    equation.values <- c(0.4, 2.4, 0.0, 0.0)
    eqns <- list(equation.vars, equation.values)

    ##create LIM file
    limfile.name <- tempfile()
    createLIMFromSBML(sbml.model, maximize, equations=eqns,
    			  externals=externals, file.name=limfile.name)

    rates <- getRates(limfile.name)

    relevant.species <- c("M_glc_DASH_D_c", "M_g6p_c", "M_f6p_c",
    				  "M_fdp_c", "M_dhap_c", "M_g3p_c",
    				  "M_13dpg_c", "M_3pg_c", "M_2pg_c",
    				  "M_pep_c", "M_pyr_c")
    ##generate graphical representation
    hd <- sbml2hyperdraw(sbml.model, rates=rates,
    				 relevant.species=relevant.species,
    				 layoutType="dot", plt.margins=c(20, 0, 20, 0))

    ##plot hypergraph
    plot(hd)

[Package BiGGR version 1.16.0 Index]