A Haskell program (and library) for the creation and analysis of gene regulatory networks generated from biological pathway data.
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GRN
pws
tests
.gitignore
GrnSim.hs
LICENSE
README.md
gendat
gold.txt
grnsim
grntools.cabal
simruns

README.md

GRN-Pathways

Welcome to the GRN-Pathways program. This is a program to produce biological genetic regulatory network models from biological pathway data. Simply create a pathway file (see the examples in the pws folder for syntax), and run the program with the appropriate options to generate pathway, state space, or conditional distribution graphs. Also enables setting various conditions and knockout conditions as well.

NB: Must have gnuplot, the fftw3 library, and graphviz installed on the PATH in order for most of the commands to work.

Installing

Assuming you have Haskell installed and the appropriate prerequisites:

cabal configure
cabal build
./grnsim -m d -r -e "tnf=0 lps=1 ltbr=0" "pws/nfkb-super.pw" --n4 1

Or run ./simruns (a short python script) and compare to gold.txt to make sure everything is running alright (I know, its a poor man's way to test, but I've got paper deadlines to worry about!).

Future Work

You can find the paper published from some of this code in the [IEEE Transactions on Biomedical Engineering] 1.

I have moved on to other techniques due to the super-exponential behavior of some of the Hamming graph code in there (there is not much documentation, but if you have the slightest interest, please contact me!).

Problems

Just let me know if you run into any problems or have any questions: (jason@jasonknight.us)