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

• Introduction to Synthetic Biology
  • check readings in above link
• R package - bioconductor
  • using R
  • tutorials and course materials in R page

Practices in R

• We will practice the materials in MIT open courseware

Practice #1

• Simulating Michaelis–Menten kinetics in R
  • assumption: quasi-equilibrium state (pseudosteady state)
  • OCW Matlab code ported in R
  • 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
# v= dp/dt = k3*E0*S/(S+(k2+k3)/k1)
# E0 = E + ES
# initial parameter
k1 = 1e3
k2 = 1
k3 = 0.05
E0 = 0.5e-3
parms = c(k1,k2,k3)
# ode

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]