LMB562
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Class Description
- This is introductory class to cover topics in synthetic biology by its past (origin), present and future.
- The course can be divided into three sessions
- Fundamental principles of synthetic biology
- Landmark papers in synthetic biology
- Current topics and future direction
- Additional topics - ethical issues and risks in synthetic biology
- Presentation schedule
- 9/10 Hongjae (RM1), Jeehee (RM2), Areum (RM3)
- Reading report
- Reading 1 - Hanseong, Hyeok-Jin, Byungnam, Saeyoung, Woo-chang, Jeehee
- Reading 2 - Hanseong, Hyeok-Jin, Byungnam, Saeyoung, Woo-chang
- Reading 3 - Hanseong, Hyeok-Jin, Byungnam, Saeyoung, Woo-chang, Jeehee
- Reading report
- 9/17 No class - 2012 IBS (Daegu) symposium
- 9/24 Babu (RM4), Woochang (RM5), Byungho (RM6)
- Reading report
- Reading 4 - Hanseong, Hyeok-Jin, Byungnam, Saeyoung, Woo-chang, Jeehee, Byungho, Hongjae, Babu
- Reading 5 - Hanseong, Hyeok-Jin, Byungnam, Saeyoung, Byungho, Hongjae, Jeehee
- Reading 6 - Hanseong, Hyeok-Jin, Byungnam, Saeyoung, Woo-chang, Hongjae, Jeehee, Babu
- Reading report
- 10/1 No class - August Full Moon (Holiday)
- 10/8 No class - iGEM 2012 (Hong Kong)
- 10/15 Self study (R code)
- 10/22 Hyeokjin (RM7), Saeyoung (RM9), Byungnam (RM8)
- Reading report
- Reading 7 - Byungnam, Woo-chang, Hongjae, Areum, Babu
- Reading 8 - Hyeok-Jin, Woo-chang, Hongjae, Areum, Babu
- Reading 9 - Hyeok-Jin, Byungnam, Woo-chang, Hongjae, Areum, Babu
- Reading report
- 10/29 Hongjae (RM11), Areum (RM12), Jeehee (RM13)
- 11/5 Babu, Woochang, Byungho
- 11/12 Hyeokjin, Saeyoung, Byungnam
- 11/19 Hongjae, Areum, Jeehee
- 11/26 Babu, Woochang, Byungho
- 12/3 Hyeokjin, Saeyoung, Byungnam
- 12/10 Final exam
Reading materials (RMs)
- Fundamental principles
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- Landmarks
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- Selected from external links
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Practice with R package
- Preparation
- install R package
- install required library package
- how to install packages
>install.pacakages("deSolve")
- Repressilater
- R-code
library(deSolve) ### Repressilator ### Elowitz & Leibler (2000) repress = function(t,y,p) { dy = rep(0,6); dy[1] = -y[1] + p[1]/(1.+y[4]^p[4])+p[2]; # dy[1] lacI; dy[4] CI dy[2] = -y[2] + p[1]/(1.+y[5]^p[4])+p[2]; # dy[2] tetR; dy[5] LacI dy[3] = -y[3] + p[1]/(1.+y[6]^p[4])+p[2]; # dy[3] cI; dy[6] TetR dy[4] = -p[3]*(y[4]-y[3]); # cI dy[5] = -p[3]*(y[5]-y[1]); # lacI dy[6] = -p[3]*(y[6]-y[2]); # tetR return(list(dy)) # p[1..4] = c(alpha,alpha0,beta,hill) } # initial parameters x0 = 2*runif(6); p = c(50,0,.2,2); t = seq(0,500,by=0.1) out = lsoda(x0,t,repress,p) matplot(out[,1],out[,2:4],type="l")
- Genetic toggle switch
- R-code
### Genetic toggle switch ### Gardner & Collins (2000) Toggle=function(t,y,parms) { u=y[1]; v=y[2]; du= -u + parms[1]/(1+v^parms[2]); dv= -v + parms[1]/(1+u^parms[3]); dY=c(du,dv); return(list(dY)); } x0=c(.2,.1); times=seq(0,50,by=0.2) out=lsoda(x0,times,Toggle,parms=c(3,2,2)) matplot(out[,1],out[,2:3],type="l",ylim=c(0,3),xlab="time t",ylab="u,v"); # phase portrait plot(out[,2],out[,3],type="l",xlab="u",ylab="v")
External links
- PLoS collections
- PLoS ONE organized Synthetic Biology Collections
- Nature WEB focus
- Science
- PubMed database
- synthetic biology - search results
- Google scholar
- synthetic biology - search results
Open questions
- What is 'synthetic biology'?
- How is synthetic biology different with traditional genetic engineering?