SB Course
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Revision as of 08:36, 28 November 2009
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Biomodel database
Running SBML
- SBML softwares - guide table
- KEGG2SBML - KEGG pathway converter to SBML (written in Perl)
R-project
- R package
- BioConductor - based on R package
- SBMLR package - Manual
- getIncidenceMatrix (get incidence/stoichiometry matrix from model)
- RSBML - quick introduction
- SBMLR package - Manual
Matlab
- SimBiology Toolbox provided by Mathworks
M = getstoichmatrix(modelObj) [M,objSpecies] = getstoichmatrix(modelObj) [M,objSpecies,objReactions] = getstoichmatrix(modelObj)
- Systems Biology Toolbox 2 - third party toolbox
Readings
- Math tutorials
- Metabolic Control Analysis (MCA)
Term project
2009 Fall
- Reconstructing central carbon pathways in target organims
- Shewanella oneidensis MR-1 KEGG pathway map
- Lactate metabolism
- PubMed on flux analysis
- Saccharophagus degradans 2-40 KEGG pathway map
- Glucose to Lactate
- converting KEGG pathway map into 'sbml' by kegg2sbml
- or using Keggconverter
- Example
- glycolysis pathway map - sde0010
- detailed information (content) - sde0010
- download pathway map - KEGG pathway_gif ftp - The final GIF version of KEGG PATHWAY (to be removed)
- Shewanella oneidensis MR-1 KEGG pathway map
- Example using SBMLR
- Reference
- Curto, R., Voit, E. O. and Cascante, M. Analysis of abnormalities in purine metabolism leading to gout and to neurological dysfunctions in man. Biochem.J. 329 (Pt 3), 477-487 (1998a).
- Curto, R., Voit, E. O., Sorribas, A. and Cascante, M. Validation and steady-state analysis of a power-law model of purine metabolism in man. Biochem.J. 324 (Pt 3), 761-775 (1997).
- Curto, R., Voit, E. O., Sorribas, A. and Cascante, M. Mathematical models of purine metabolism in man. Math.Biosci. 151, 1-49 (1998b)
- R-script
## installing Bioconductor source("http://bioconductor.org/biocLite.R") biocLite() # install default packages biocLite(c("KEGGgraph","SBMLR")) # install specified packages ## loading packages by 'library' function library(KEGGgraph) ## ##---- The following example performs a perturbation in PRPP from 5 to 50 uM in Curto et al. ## library(SBMLR) library(odesolve) curto=readSBML(file.path(system.file(package="SBMLR"), "models/curto.xml")) summary(curto) names(curto) out1=simulate(curto,seq(-20,0,1)) curto$species$PRPP$ic=50 out2=simulate(curto,0:70) outs=data.frame(rbind(out1,out2)) attach(outs) par(mfrow=c(2,1)) plot(time,IMP,type="l") plot(time,HX,type="l") par(mfrow=c(1,1)) detach(outs) # which should be the same plots as curto=readSBMLR(file.path(system.file(package="SBMLR"), "models/curto.r")) out1=simulate(curto,seq(-20,0,1)) curto$species$PRPP$ic=50 out2=simulate(curto,0:70) outs=data.frame(rbind(out1,out2)) attach(outs) par(mfrow=c(2,1)) plot(time,IMP,type="l") plot(time,HX,type="l") par(mfrow=c(1,1)) detach(outs) ##---- The following example uses fderiv to generate Morrison's folate system response to morr=readSBMLR(file.path(system.file(package="SBMLR"), "models/morrison.r")) out1=simulate(morr,seq(-20,0,1)) morr$species$EMTX$ic=1 out2=simulate(morr,0:30) outs=data.frame(rbind(out1,out2)) attach(outs) pdf(file="output.pdf",paper="A4") par(mfrow=c(3,4)) plot(time,FH2b,type="l",xlab="Hours") plot(time,FH2f,type="l",xlab="Hours") plot(time,DHFRf,type="l",xlab="Hours") plot(time,DHFRtot,type="l",xlab="Hours") plot(time,CHOFH4,type="l",xlab="Hours") plot(time,FH4,type="l",xlab="Hours") plot(time,CH2FH4,type="l",xlab="Hours") plot(time,CH3FH4,type="l",xlab="Hours") plot(time,AICARsyn,type="l",xlab="Hours") plot(time,MTR,type="l",xlab="Hours") plot(time,TYMS,type="l",xlab="Hours") #plot(time,EMTX,type="l",xlab="Hours") plot(time,DHFReductase,type="l",xlab="Hours") dev.off()