Synbio course

From CSBLwiki

Contents 1 2010 Fall LMB904 2 Practices in R 2.1 Practice #1 2.2 Practice #2 2.3 Practice #3

2010 Fall LMB904

• What is Synthetic Biology? - Introduction to Synthetic Biology
  • check readings (recent special issue of various journals) in above link

• We will use R package for simulating several biological processes
  • check bioconductor for more applications in bioinformatics
  • tutorials and course materials in CSBL's R page (some collections)

Practices in R

• We will practice some materials in MIT open courseware (department of physics)

Practice #1

• Simulating Michaelis–Menten kinetics in R
  • underlying assumption: quasi-equilibrium state (pseudosteady state) of enzyme-catalyzed reaction
  • OCW Matlab code ported in R
  • using R
    • install a specific package (e.g. 'odesolve') in R (there are several ways to do this)

# execute 'R' & run a command
# you should have a internet connection

>install.package("odesolve")

• R-code

library(odesolve)
# Michaelis-menten equation
# E + S <-> ES -> E + P
#      k1,k2   k3
# rate equations
# dE = -k1*E*S+k2*ES, dS = -k1*E*S+k2*ES+k3*ES, dES = k1*E*S-k2*ES-k3*ES
# quasi-equilibrium; E0 = E + ES; dES = 0
# dE = -k1*E0*S+(k1*S+k2)*ES, dES = k1*E0*S-(k1*S+k2+k3)*ES, dP = k2*ES
# ode functions
michaelis = function(t,y,p) {
  # S = y[1]; ES = y[2]; P = y[3]
  # k1 = p[1]; k2 = p[2]; k3=p[3]; E0=p[4]
  dS = -p[1]*p[4]*y[1]+(p[1]*y[1]+p[2])*y[2]
  dES = p[1]*p[4]*y[1]-(p[1]*y[1]+p[2]+p[3])*y[2]
  dP = p[2]*y[2]
  list(c(dS,dES,dP))
}
#### initial parameter
k1 = 1000; k2 = 1; k3 = 0.05; E0 = 0.0005
p = c(k1,k2,k3,E0)
t = seq(0,100,1) # time scale
#t = 1
y = c(0.001,0,0) # initial values of S, ES and P

#### solving equations
res = lsoda(y,t,michaelis,p)

#### plotting results
plot(res[,1],res[,2],type="l",col="red",ylim=c(0,0.001))
points(res[,1],res[,3],type="l",col="blue")
E = p[4]-res[,3]
points(res[,1],E,type="l",col="cyan")
points(res[,1],res[,4],type="l",col="green")

• Result (above script is working but the result is not correct; you may find an error in the code)

Practice #2

• A Genetic Switch in Lamba Phage in R

1. Error fetching PMID 10681449: [LAM]

Practice #3

• A Genetic Toggle Switch in R

2. Error fetching PMID 10659857: [TOG]