Biowulf High Performance Computing at the NIH
iDEP on Biowulf

iDEP (integrated Differential Expression and Pathway analysis) is shiny application for analyzing RNA-seq data. A public instance is available at http://ge-lab.org/idep/ and on this page we show how an ephemeral instance can be run locally on compute nodes.

iDEP reads in gene-level expression data (read counts or FPKM), performs exploratory data analysis (EDA), differential expression, pathway analysis, biclustering, and co-expression network analysis. iDEP also accepts DNA microarray data or other gene-level expression data, such as those from Chip-seq or proteomics studies.

Documentation

Starting an iDEP Instance

This can be done by submitting either a batch or interactive job. Either way, please do not let an idle iDEP session linger. Shut down your instance when you are done with the analysis. Note that iDEP requires lscratch.

In the demonstration here we'll use sinteractive since it supports automatically creating the part of the tunnel from biowulf to the compute nodes (see here for more detail).

For this example we will allocate an interactive session and start an iDEP instance as shown below. First, we launch tmux (or screen) on the login node so that we don't lose our session if our connection to the login node drops.

[user@biowulf]$ module load tmux # You can use screen instead; you don't need to module load it
[user@biowulf]$ tmux
[user@biowulf]$ sinteractive --mem=16g --cpus-per-task=2 --gres=lscratch:10 --tunnel
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

Created 1 generic SSH tunnel(s) from this compute node to
biowulf for your use at port numbers defined
in the $PORTn ($PORT1, ...) environment variables.


Please create a SSH tunnel from your workstation to these ports on biowulf.
On Linux/MacOS, open a terminal and run:

    ssh  -L 33327:localhost:33327 biowulf.nih.gov

For Windows instructions, see https://hpc.nih.gov/docs/tunneling



[user@cn3144]$ module load idep
[user@cn3144]$ idep-server $PORT1
### INFO  ### server will run on port 33327. Set up a tunnel to view the shiny applications
[2019-03-06T09:38:04.462] [INFO] shiny-server - Shiny Server v1.5.11.2 (Node.js v8.11.3)
[2019-03-06T09:38:04.465] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"
[2019-03-06T09:38:04.586] [INFO] shiny-server - Starting listener on http://127.0.0.1:49308

Keep this running for as long as you are using iDEP. Note the port number and the compute node which are required to connect to your iDEP instance.

Connecting to your iDEP Instance

Connecting to your iDEP instance on a compute node with your local browser requires setting up the second leg of the tunnel (from your computer to biowulf) and connecting it to the tunnel from biowulf to the compute node. This is described in detail on our tunneling page.

Once the tunnel has been established, you can visit the interface of the iDEP shiny app at http://localhost:33327/idep/ (replacing 49308 with the port used by your instance of idep-server).