2012 Workshop: Student Projects and Presentations

Discussion: Most valuable properties of models

Group 1

Group 2

Group 3


Frog Cell Cycle


Math Modeling Paper

Exercise Introduction


Exercise Answers

Stochastic Version

Project Assignments

Team Cyclin: Spratt, Balmick, Ratsimihah

EGFR: bngl file, reference paper

Target protein is Sos (unless/until we get a model including Ras)

Team Cdk: Packer, Rodriguez, Yalkabov

TCR: bngl file, reference paper

Target protein is Erk

Team MPF: Feitzinger, Abbasi, Nunez

FceRI: bngl file, reference paper

Target protein is Syk

Team PreMPF: Miranda, Garib, Green

Apoptosis: bngl file, reference paper 1 (current version) reference paper 2 (extrinsic version)

Target protein is F (subject to future review)

Team APC: Weinberg, Zegel, Lagrange

HMGB1: bngl file, reference paper

Target protein is p53 (subject to future review)


MultBNGSim_8 - run this with -h to get the command line parameters; look at it to find out how to run from a command line

Organize data: shell script (you run this) awk program (just put this in the directory with the shell script)

Discussion of Project

New Scripts and BioNetGen

run_network: Duplicate BioNetGen-2.1.8 in the RuleBender folder, so you get a directory "BioNetGen-2.1.8 copy" in the folder. Change the name of "BioNetGen-2.1.8 copy" to "BioNetGen-2.1.8test". Finally, put this copy of run_network inside the folder "BioNetGen-2.1.8test/bin/"

actions.bngl: The new script uses this. You need to change the file parameter of the readFile command (the string "egfr_net" should be changed to the name of your bngl file, but without the .bngl); both parameters of the setConcentration command to reflect the ligand and dose you are using; and the t_end parameter of simulate_ssa to be the time you want your simulation to run.

To make this file work, you have to add a command to your model file (.bngl) right after an initial simulate_ode (yes, you must have one, but you can set t_end to something small, eg, t_end=>1). The new command is writeNET({suffix=>"write"});

firstpassage.awk: Put this someplace convenient, you will tell the script where it is. But don't put it in your output directory, because things in there may be overwritten or removed. You may want to change the criterion for target activation, which is $2 > 0 in this file. The output has two columns, the first is time and the second is the concentration of the target at that time.

vars.sh: Put this someplace convenient. You use this file to tell the script file where all the other files are. Take a look at it to figure out how it works; it should be readable. Sample values are already there; many of them will work without change if you haven't reorganized your Desktop drastically. You will have to describe where model files are, of course (.bngl)
Things to watch out for: spaces around the "=" signs will totally corrupt the script, don't let them happen!
Paths to directories MUST end in "/" (that's scriptPath)

MultBNGSim.sh: This is the script file. It takes only one parameter, the fully-qualified path to vars.sh

Presentation Schedule for Monday

1 pm HMGB1 (Lagrange, Weinberg, Zegel)

1:30 pm TCR (Packer, Rodriguez, Yalkabov)

2:00 pm FceRI (Abbasi, Feitzinger, Nunez)

2:30 pm ScanBatch tool (Packer)

2:45 pm EGFR (Balmick, Ratsimihah, Spratt)

3:15 pm Apoptosis (Garib, Green, Miranda)

Thoughts on Presentation