TinkerCell is a Computer-Aided Design software tool for Synthetic Biology that promotes collaboration through its plugin interface. This blog is used to keep notes on updates to the project.
Monday, March 7, 2011
Sample Python Code for Creating a Little Network
cds4 = tc_insert("cds4","Coding")
p3 = tc_insert("p3","Inducible Promoter")
cds3 = tc_insert("cds3","Coding")
t3 = tc_insert("t3","Terminator")
p2 = tc_insert("p2","Inducible Promoter")
cds2 = tc_insert("cds2","Coding")
t2 = tc_insert("t2","Terminator")
listOfParts = [cds4, p3, cds3, t3, p2, cds2, t2]
tcArray = toTC(listOfParts) #convert Python data structure to
tc_alignParts(tcArray)
#production of P4
P4 = tc_insert("P4", "Transcription Factor")
x = tc_getX(cds4)
y = tc_getY(cds4)
tc_setPos(P4, x, y - 200)
listToConnect = [cds4, P4]
tcArray = toTC(listToConnect)
R1 = tc_insertConnection(tcArray, "R1", "Protein Production")
#P4 regulates p3
listToConnect = [P4, p3]
tcArray = toTC(listToConnect)
R2 = tc_insertConnection(tcArray, "R2", "Transcription Activation")
#production of P3
P3 = tc_insert("P3", "Transcription Factor")
x = tc_getX(cds3)
y = tc_getY(cds3)
tc_setPos(P3, x, y - 200)
listToConnect = [cds3, P3]
tcArray = toTC(listToConnect)
R3 = tc_insertConnection(tcArray, "R3", "Protein Production")
#P3 regulates p2
listToConnect = [P3, p2]
tcArray = toTC(listToConnect)
R4 = tc_insertConnection(tcArray, "R4", "Transcription Activation")
#production of GFP
GFP = tc_insert("GFP", "Reporter")
x = tc_getX(cds2)
y = tc_getY(cds2)
tc_setPos(GFP, x, y - 200)
listToConnect = [cds2, GFP]
tcArray = toTC(listToConnect)
R5 = tc_insertConnection(tcArray, "R5", "Protein Production")
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