High-Performance Computing at the NIH
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Hotnet2 on NIH HPC Systems

HotNet2 is an algorithm for finding significantly altered subnetworks in a large gene interaction network. While originally developed for use with cancer mutation data, the current release also supports any application in which meaningful scores can be assigned to genes in the network.

Note, example files can be copied from /usr/local/apps/hotnet2/1.0.1/example

Follow instruction in /usr/local/apps/hotnet2/1.0.1/example/README

Make sure to use full path in the *.config files in the examples.

On Helix

Sample session:


[USER@helix ~]$ module load hotnet2
[USER@helix ~]$ commands.....

Batch job on Biowulf

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash

cd /data/$USER/dir
module load hotnet2
hotnet2 commands .........

Then submit the file on biowulf

sbatch batch.sh

Please read user guide for more sbatch options

Useful utilities for job monitoring and debugging

Swarm of Jobs on Biowulf

Create a swarmfile (e.g. script.swarm). For example:

# this file is called script.swarm
cd dir1; hotnet2 command 
cd dir2; hotnet2 command 
cd dir3; hotnet2 command
[...]

Submit this job using the swarm command.

biowulf >$ swarm -f script.swarm --module hotnet2

More options for swarm job can be viewed here.

Interactive job on Biowulf
Allocate an interactive session. Sample session:
[USER@biowulf ~]$ sinteractive 
salloc.exe: Pending job allocation 15194042
salloc.exe: job 15194042 queued and waiting for resources
salloc.exe: job 15194042 has been allocated resources
salloc.exe: Granted job allocation 15194042
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1719 are ready for job

[USER@cn1719 ~]$ module load hotnet2

[USER@cn1719 ~]$ hotnet2 command ....
Documentation