Secretariat OnDemand
Tip
Contact Secretariat System Administrators with HPC Questions!
vshanka@clemson.edu,jopoole@clemson.edu,madonay@clemson.edu
Contact IHG Research Cores with Research Questions!
ihgcores@clemson.edu
Open OnDemand (OOD) is a web-based interface that is designed to be a user-friendly method for accessing HPC resources and services through your browser. To access Secretariat’s OOD Page, navigate to secretariat-master.clemson.edu or 130.127.173.136 using your web browser. (Or click on the image, below!)
Make sure to use the Google Chrome browser when accessing Secretariat via OOD!
Log in using your Secretariat credentials and complete DUO two-factor authentication when prompted.
Note
Although you may encounter a warning message that says the connection is not private, it is safe to proceed to the site. To proceed, you may need to click a button labeled something like “Advanced” in the lower portion of the window. If you have any trouble during this process, send us a message!
After a successful login, you will arrive at the Dashboard, which provides quick access to Secretariat resources and tools!
Dashboard Overview
Section |
Description |
|---|---|
Files |
Access your /home directory immediately, or navigate to other permitted locations. Upload / download / edit small text files! |
Jobs |
Create, submit, and monitor Slurm batch jobs on Secretariat. |
Clusters |
Launch a browser-based terminal session on Secretariat. (Note: Launches on the head node!) |
Interactive Apps |
Launch GUI-based scientific applications in the browser. |
Interactive Apps
View our current apps, below:
App |
Description |
|---|---|
Cytoscape |
Network analysis and visualization of gene / protein / etc interactions, pathways, and omics networks. |
DGRP2 Webserver |
Tool for Drosophila Genetic Reference Panel analyses and population genomics workflows. |
Dynamic Bic Flows |
Biclustering-based visualization for exploring complex gene expression or phenotypic datasets. |
IGV |
Genome browser for inspecting alignments, variants, and annotation tracks. |
Spyder |
Python IDE for scripting, statistical analysis, and data exploration workflows. |
Secretariat Remote Desktop |
Full Linux desktop environment for GUI-based applications and point-and-click navigation. |
ASC Seurat |
Single-cell RNA-seq analysis environment using Seurat for clustering, visualization, and downstream interpretation. |
Code Server |
Browser-based VS Code environment for editing scripts and running computational pipelines. |
Jupyter Notebook |
Interactive notebooks for Python / R / etc analysis, visualization, and reproducible research. |
RStudio 1.4 |
IDE for R-based statistical analysis and visualization. |
ShinyR DAM |
Interactive R Shiny app for Drosophila Activity Monitor data analysis and visualization. |
iDEP & ShinyGO |
Web tools for differential expression analysis, enrichment, and functional genomics interpretation. |
List last updated: 11 May 2026.