Biowulf High Performance Computing at the NIH
Bio3D-web: online interactive analysis of protein structure ensembles

Bio3D-web is an online application for analyzing the sequence, structure and conformational heterogeneity of protein families. This application facilitates the identification of protein structure sets for analysis, their alignment and refined structure superposition, sequence and structure conservation analysis, mapping and clustering of conformations, and the quantitative comparison of their predicted structural dynamics.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

Connect to the Biowulf using NX.
[user@biowulf ~]$ sinteractive  --mem=4g --gres=lscratch:10
[user@cn0868 ~]$ module load bio3d-web
[+] Loading gcc  7.3.0  ...
[+] Loading GSL 2.4 for GCC 7.2.0 ...
[+] Loading openmpi 3.0.2  for GCC 7.3.0
[+] Loading ImageMagick  7.0.8  on cn2353
[+] Loading HDF5  1.10.4
[+] Loading pandoc  2.13  on cn2353
[+] Loading R 3.5.2
[+] Loading bio3d-web  20210525

[user@cn0868 ~]$ cp -r $BIO3DWEB_SRC/* .
[user@cn0868 ~]$ R

>  .libPaths(c(Sys.getenv("R_LIBS_USER"), .libPaths())) 
>   library(shiny) 
>   runApp("./pca-app") 
   Listening on
    - the port number, in this case: 7136
    - the entire URL, in this case:
    - an id of the compute node you have been using, in this case cn0868
On your local system (PC or Mac), open a terminal/linux shell and type:
   ssh -t -L 7136:localhost:7136 biowulf "ssh -L 7136:localhost:7136 cn0868"
(Make sure to substitute the stored port number and the compute node id into this command.)

Now open a Web browser on your local computer (Mac or PC) and navigate to the URL you stored, in this case 
You should see the view shown below:

[user@cn0868 ~]$ exit
salloc.exe: Relinquishing job allocation 49998864

[user@biowulf ~]$