Secretariat OnDemand ==================== .. tip:: **Contact** `Secretariat System Administrators`_ **with HPC Questions!** +------------------+----------------+--------------------+ | `Vijay Shankar`_ | `John Poole`_ | `Maria E. Adonay`_ | +------------------+----------------+--------------------+ .. code-block:: text vshanka@clemson.edu,jopoole@clemson.edu,madonay@clemson.edu .. raw:: html
**Contact** `IHG Research Cores`_ **with Research Questions!** .. code-block:: text 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. .. image:: ../_static/images/ood.png :width: 630 px :height: 150 px :scale: 100% :alt: Secretariat Open OnDemand Dashboard :target: https://130.127.173.136/ .. 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. .. _Open OnDemand: https://www.openondemand.org/ .. _Google Chrome: https://www.google.com/chrome/ .. _secretariat-master.clemson.edu: https://secretariat-master.clemson.edu .. _130.127.173.136: https://130.127.173.136 .. _Vijay Shankar: https://scienceweb.clemson.edu/chg/dr-vijay-shankar-2/ .. _John Poole: https://scienceweb.clemson.edu/chg/dr-john-poole/ .. _Maria E. Adonay: https://scienceweb.clemson.edu/chg/maria-adonay/ .. _Secretariat System Administrators: https://scienceweb.clemson.edu/ihg/research-cores/bsc-core/ .. _IHG Research Cores: https://scienceweb.clemson.edu/ihg/research-cores/