Knowledge Base Resources

Chameleon is an NSF-funded testbed system for Computer Science experimentation. It is designed to be deeply reconfigurable, with a wide variety of capabilities for researching systems, networking, distributed and cluster computing and security.

Expanse at SDSC is a cluster designed by Dell and SDSC delivering 5.16 peak petaflops, and offers Composable Systems and Cloud Bursting.

DeepChem is an open-source library built on TensorFlow and PyTorch. It is helpful in applying machine learning algorithms to molecular data.

Through collaboration and networking, WHPC strives to bring together women in HPC and technical computing while encouraging women to engage in outreach activities and improve the visibility of inspirational role models.

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a widely distributed molecular simulation program with a broad array of applications. CHARMM has the capabilities to setup and run simulations on both biological and materials systems, contains a comprehensive set of analysis and tools, and has high performance on a variety of platforms. Here you will find links to the CHARMM website, forum, and registration/download page.

WarpX is an advanced particle-in-cell code used to model particle accelerators, which needs to be run on HPC. This website contains the tutorial on how to build WarpX on various HPC systems such as NERSC along with examples on how to set up post-processing/visualization tools for different physics cases.

Trinity is one of the most popular tool to assemble transcripts from RNA-Seq short reads. In this tutorial, we will cover the basic usage of Trinity, best practice and common problems.

Tableau is a popular and capable software product for creating charts that present data and dashboards that allow you to explore data. It is typically used to present business or statistical data, but can also create compelling visualizations of scientific data. However, scientific data is often generated or stored in formats that are not immediately accessible by Tableau. This seminar will explore the data formats that work best with Tableau and the available mechanisms for generating scientific data in (or converting it to) those formats so that you can apply the full power of Tableau to create the best possible visualizations of your data.

Regular expressions (sometimes referred to as RegEx) is an incredibly powerful tool that is used to define string patterns for "find" or "find and replace" operations on strings, or for input validation. Regular Expressions are used in search engines, in search and replace dialogs of word processors and text editors, and text-processing Linux utilities such as sed and awk. They are supported in many programming languages, including Python, R, Perl, Java, and others.

Snakemake is a powerful and versatile workflow management system that simplifies the creation, execution, and management of data analysis pipelines. It uses a user-friendly, Python-based language to define workflows, making it particularly valuable for automating and reproducibly managing complex computational tasks in research and data analysis.

tutorial on introduction to making a AI Chat assistant using GenAI API

Singularity/Apptainer is a free and open-source container platform that allows users to build and run containers on high performance computing resources. SingularityCE is the community edition of Singularity maintained by Sylabs, a company that also offers commercial Singularity products and services. Apptainer is a fork of Singularity, maintained by the Linux foundation, a community of developers and users who are passionate about open source software.

This contains documentation for getting started with using OnShape for CAD. OnShape cloud-hosted CAD software that lets you work with others like on a Google Doc, with the power and capabilities of any other software like Solidworks or Inventor.

These links take you to visualization resources supported by the University of Arizona's HPC visualization consultant ([rtdatavis.github.io](http://rtdatavis.github.io/)). The following links are specific to the Paraview program and the workflows that have been used my researchers at the U of Arizona. These links are distinct from the others posted in the beginner paraview access ci links from the University of Arizona in that they are for more complex workflows. The links included explain how to use the terminal with paraview (pvpython), and the steps to leverage HPC resources for headless batch rendering. The batch rendering tutorial is significantly more complex than the others so if you find yourself stuck please post on the https://ask.cyberinfrastructure.org/ and I will try to troubleshoot with you.

R for Data Science is a comprehensive resource for individuals looking to harness the power of the R programming language for data analysis, visualization, and statistical modeling. Whether you're a beginner or an experienced data scientist, this guide will help you unlock the full potential of R in the realm of data science.

Learn Python online with these distance learning courses.

**Termius: The Modern SSH Client for 2023** Termius is the future-facing SSH client that's redefining remote server access in 2023. Designed for ease and efficiency, Termius offers a seamless connection experience across all devices, be it mobile or desktop. Gone are the days of re-inputting IP addresses, ports, and passwords; with Termius, one-click connectivity is the new norm. **How Termius Elevates Remote Server Access:** 1. **One-Click Connectivity:** Save the hassle of remembering and re-entering connection details. Termius provides an immediate connection to your infrastructure with a single click. 2. **Synchronized Across Devices:** Termius ensures that your data, connection settings, and preferences are consistent across all your devices, from mobile to desktop. 3. **Unparalleled Security:** With the Cloud Vault feature, users can securely store their data in an encrypted environment, accessible only from their specific devices. Shared vaults allow for safe connection sharing within teams. 4. **AI-Powered Terminal Experience:** Advanced AI-driven autocomplete means users can input command descriptions, and Termius will swiftly convert them into accurate bash commands, simplifying and enhancing the terminal interaction. 5. **Collaborative Troubleshooting:** Share terminal sessions with teammates, facilitating cooperative problem-solving or knowledge sharing. No additional server-side installations needed. 6. **Automation and Snippets:** Streamline routine processes with the ability to save and run frequently used shell scripts. Sharing these Snippets with your team can lead to increased productivity and fewer manual errors. 7. **All-Device Compatibility:** Whether on iPad, iPhone, Android, macOS, Windows, or Linux, Termius ensures a consistent and fluid experience. The platform's synchronization capability means you're always ready to respond swiftly, irrespective of the device in use. For professionals and businesses aiming for top-notch server access efficiency, Termius is the gold standard in 2023. Experience the revolution in SSH connectivity and optimize your workflow with Termius.

ACCESS requests proposals to be written following NSF proposal guidelines. The link provides an example of an ACCESS proposal using an NSF LaTeX template. The request is at the DISCOVER level appropriate for Campus Champions. The file is 2 pages: the first page details the motivation, approach, and resources requested; and the second page is a 1-page bio.

Discover Data Science is all about making connections between prospective students and educational opportunities in an exciting new, hot, and growing field – data science.

It's not uncommon to see beautiful visualizations in HPC center galleries, but the majority of these are either rendered off the HPC or created using programs that run on OpenGL or custom rasterization techniques. To put it simply the next generation of graphics provided by OpenGL's successor Vulkan is strangely absent in the super computing world. The aim of this survey of available resources is to determine the systems that can support Vulkan workflows and programs. This will assist users in getting past some of the first hurdles in using Vulkan in HPC contexts.

This package lets you easily scrape websites and extract information based on html tags and various other metadata found in the page. It can be useful for large-scale web analysis and other tasks requiring automated data gathering.