D3GRN

D3GRN is a Data Driven Dynamic network construction method to infer Gene Regulatory Networks.

System Environment

Ubuntu/Linux Bash, Matlab 2015b.

Running Step

Step 1, DREAM4 Network1-5:

nohup  bash ./main_arni_dream4_multifactorial_network1_5.sh  &

the results of bootstraping runs will be generated for further evaluation.

Or if you want to run the algorithm for DREAM5 Network 1 (sudo privilege perhaps needed according to your running environment):

nohup bash ./main_arni_dream5_network1.sh &

As the DREAM5 networks are large in scale so it will be time consuming, so the task is recommended to run in the background mode.

Step 2, Evaluation:

It is recommended to run the following Matlab script in your desktop IDE, the command will calculate the AUPR as well as plot the curves.

• For DREAM4 Network1-5:

infer_grn_arni_dream4_multifactorial_para.m

• For DREAM5 Network 1:

infer_grn_arni_dream5_para_Network1.m

Any question, please do not hesitate to contact me with following address with bash command for decryption:

echo "Y2hlbnhvZmhpdEBnbWFpbC5jb20K"|base64 -d (use -D instead for Mac users)

or submit issue in the repository directly.