SB Course

From CSBLwiki

Contents 1 Biomodel database 2 Running SBML 3 R-project 4 Matlab 5 Readings 6 Term project 6.1 2009 Fall

Biomodel database

• Biomodel DB@EBI
• Simulating Biomodels in JWS online

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

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
  • Ken Miller's Math Notes - UCSF
• Metabolic Control Analysis (MCA)
  • Tutorial

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)
• Example using SBMLR

## 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()