BiGGR-package {BiGGR} | R Documentation |
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.
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) |
Anand K. Gavai, Hannes Hettling
Maintainer: Anand K. Gavai <anand.gavai@bioinformatics.nl>, Hannes Hettling <j.hettling@vu.nl>
rsbml
# 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)