Synbio course

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	===Practice #1===		===Practice #1===
	*Simulating [[w:Michaelis-Menten kinetics|Michaelis–Menten kinetics]] in R		*Simulating [[w:Michaelis-Menten kinetics|Michaelis–Menten kinetics]] in R
-	**[http://ocw.mit.edu/courses/physics/8-591j-systems-biology-fall-2004/readings/CodeI1_v2.m Matlab code] will be ported in R	+	**assumption: quasi-equilibrium state (pseudosteady state)
		+	**[http://ocw.mit.edu/courses/physics/8-591j-systems-biology-fall-2004/readings/CodeI1_v2.m OCW Matlab code] ported in R
	**R-code		**R-code
	<pre>		<pre>
		+	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
	</pre>		</pre>

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Revision as of 07:54, 29 October 2010

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]