Random Parametric Perturbations of Gene Regulatory Circuit Uncover State Transitions in Cell Cycle, by Ataur Katebi, Vivek Kohar, and Mingyang Lu (submitted). Published in bioRxiv at http://dx.doi.org/10.1101/799965
RACIPE STABLE VERSION: RACIPE_3.1.1
REQUIREMENTS TO RUN RACIPE:
- gcc
- python 3.7 or above
RACIPE INSTALLATION:
-
git clone https://github.com/arkatebi/cellcycle
-
Run make file:
make
This will create the necessary shared object files (such as simulation_clib.so) that will be used by the RACIPE software.
CONFIGURATION FILE: racipe.cfg
This file contains the configuration data for RACIPE. If this file is not in the working directory, the following command will create it:
python racipe.py -M=C -I1=cellcycle.tpo
Here, cellcycle.tpo is circuit topology from user input. In the topology file, each line specifies a regulatory interaction in the format of "A B 1". Here, A is the regulator, B is the targeted gene, and "1" is a number specifying the type of the interaction. 1: transcriptional activation; 2: transcriptional inhibition; 3: activation by inhibiting degradation; 4: inhibition by activating degradation; 5: signaling activation; 6: signaling inhibition.
The parameters in the configuration file can be changed according to the user need.
RACIPE COMMANDS:
-
Generate configuration file (racipe.cfg):
python racipe.py -M=C -I1=cellcycle.tpo
-
Generate both thresholds and models (full mode):
python racipe.py -M=A -I1=cellcycle.tpo
-
Generate and save thresholds in the .prs file:
python racipe.py -M=T -I1=cellcycle.tpo
-
Generate models using thresholds from the .prs file
python racipe.py -M=P -I1=cellcycle.tpo -I2=cellcycle.prs
-
Generate probabilities of the nodes (half-functional rule):
python racipe.py -M=S -I1=cellcycle.tpo
-I4=cellcycle.states.txt
-I5=cellcycle.params
-O=cellcycleOutputs are saved in cellcycle.edge.stat.txt file
OPTIONS FOR KNOCK DOWN PERTURBATIONS:
-
Single gene knock down in (parameter range file is supplied):
python racipe.py -M=P -I1=cellcycle.tpo -I2=cellcycle.prs -KD=Cln1
-
Double gene knock down in (parameter range file is supplied):
python racipe.py -M=P -I1=cellcycle.tpo -I2=cellcycle.prs -KD=Cln1,Clb5
-
Single gene knock down in (full mode):
python racipe.py -M=A -I1=cellcycle.tpo -KD=Cln1
-
Double gene knock down in (full mode):
python racipe.py -M=A -I1=cellcycle.tpo -KD=Cln1,Clb5
OUTPUT FILES FROM RUNNING RACIPE in the full mode
- cellcycle.states.txt - gene expression for the stable states
- cellcycle.limitcycles.txt - gene expression for the stable limit cycles
- cellcycle.summary.txt - summary of the number of states and limit cycles
- cellcycle.mpr.txt - MPR (maximum production rate) values of all the genes in each model
- cellcycle.dnr.txt - DNR (degradation rate) values of all the genes in each model
- cellcycle.tsh.txt - TSH (threshold) values used in all the interactions in each model
- cellcycle.hco.txt - HCO (Hill coefficient) values used in all the interactions in each model
- cellcycle.fch.txt - FCH (fold change) values in all the interactions in each model
- cellcycle.mpr.prs, cellcycle.dnr.prs, cellcycle.tsh.prs, cellcycle.hco.prs, and cellcycle.fch.prs stores the ranges for the MPR, DNR, TSH, HCO, and FCH, respectively.