Knowledge Base Resources
These resources have been contributed and “vetted” by the community of cyberinfrastructure professionals (researchers, research computing facilitators, research software engineers and HPC system administrators) that are participating in programs such as this one, that are supported by the ConnectCI community management platform. Additional Knowledge Base Resources are always welcome!
Intro to Statistical Computing with Stan
0
The Stan language is used to specify a (Bayesian) statistical model with an imperative program calculating the log probability density function. Here are some useful links to start your exploration of this statistical programming language, and a Python interface to Stan.
Jetstream2 Docs Site
0
Jetstream2 makes cutting-edge high-performance computing and software easy to use for your research regardless of your project’s scale—even if you have limited experience with supercomputing systems.Cloud-based and on-demand, the 24/7 system includes discipline-specific apps. You can even create virtual machines that look and feel like your lab workstation or home machine, with thousands of times the computing power.
Wiki for Onboarding onto the C3DDB Cluster at MGHPCC
0
This is a resource for researchers and students looking to on-board onto the c3ddb cluster at MGHPCC. In the code section, there are example job submission scripts for the different queues on c3ddb.
Tutorial for OpenMP Building up and Utilization
0
The following link elaborates the usage of OpenMP API and its related syntax. There are also several exercises available for learners to help them get familiar with this widely-used tool for multi-threaded realization.
Termius - Modern ssh platform
0
**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.
Data Analysis with R for Educators
0
This webinar series is an orientation to R. We start with an overview of R’s history and place in the larger data science ecosystem. Next, we introduce the R Studio user interface and how to access R’s excellent documentation. Finally, we present the fundamental concepts you need to use the R environment and language for data analysis. Along the way, we compare R script files (.R) to R Notebook (.Rmd) files and show how the features of R Notebook support better communication and encourage more dynamic engagement with statistical analysis and code. It is helpful to be familiar with tabular data analysis using statistical software, database tools, or spreadsheet programs.
Workshop materials, including setup directions and slides are available at https://github.com/CornellCAC/r_for_edu/ The Rstudio Cloud project used in the workshop is https://rstudio.cloud/project/4044219.
The Official Documentation of Pandas
0
Pandas is one of the most essential Python libraries for data analysis and manipulation. It provides high-performance, easy-to-use data structures, and data analysis tools for the Python programming language. The official documentation serves as an in-depth guide to using this powerful tool including explanations and examples.
Beautiful Soup - Simple Python Web Scraping
0
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.
Trusted CI
0
The mission of Trusted CI is to lead in the development of an NSF Cybersecurity Ecosystem with the workforce, knowledge, processes, and cyberinfrastructure that enables trustworthy science and NSF’s vision of a nation that is a global leader in research and innovation.
Research Software Development in JupyterLab: A Platform for Collaboration Between Scientists and RSEs
0
Iterative Programming takes place when you can explore your code and play with your objects and functions without needing to save, recompile, or leave your development environment. This has traditionally been achieved with a REPL or an interactive shell. The magic of Jupyter Notebooks is that the interactive shell is saved as a persistant document, so you don't have to flip back and forth between your code files and the shell in order to program iteratively.
There are several editors and IDE's that are intended for notebook development, but JupyterLab is a natural choice because it is free and open source and most closely related to the Jupyter Notebooks/iPython projects. The chief motivation of this repository is to enable an IDE-like development environment through the use of extensions. There are also expositional notebooks to show off the usefulness of these features.
Data Visualization Tools for Julia
0
Plots.jl is the most widely used plotting library for the Julia programming language. It's known for being especially powerful in its versatility and intuitiveness. It's limited set of dependencies and wide applicability across different graphics packages make it especially helpful in visualizing the results of your latest Julia implementation.
However, there are still multiple options available for Julia programmers to visualize their datasets. The second link details a comparison against a variety of Julia packages.
Neurodesk
0
Neurodesk provides a containerised data analysis environment to facilitate reproducible analysis of neuroimaging data. Analysis pipelines for neuroimaging data typically rely on specific versions of packages and software, and are dependent on their native operating system. These dependencies mean that a working analysis pipeline may fail or produce different results on a new computer, or even on the same computer after a software update. Neurodesk provides a platform in which anyone, anywhere, using any computer can reproduce your original research findings given the original data and analysis code.
What is VPN? How It Works, Types of VPN
0
A VPN, or Virtual Private Network, is a technology that creates a secure tunnel between your device and a VPN server. This tunnel encrypts all of your traffic, making it unreadable to anyone who tries to intercept it.
Applications of Machine Learning in Engineering and Parameter Tuning Tutorial
0
Slides for a tutorial on Machine Learning applications in Engineering and parameter tuning given at the RMACC conference 2019.
MATLAB bioinformatics toolbox
0
Bioinformatics Toolbox provides algorithms and apps for Next Generation Sequencing (NGS), microarray analysis, mass spectrometry, and gene ontology. Using toolbox functions, you can read genomic and proteomic data from standard file formats such as SAM, FASTA, CEL, and CDF, as well as from online databases such as the NCBI Gene Expression Omnibus and GenBank.
Introduction to Vizualization on HPC Using Python
0
This workshop has an introduction to the concepts of visualization followed by hands on exercises. The concepts section has Speaker Notes, and the hands on section has an accompanying Jupyter notebook.
The workshop is one in a series of Introduction to HPC
ACCESS KB Guide - Expanse
0
Expanse at SDSC is a cluster designed by Dell and SDSC delivering 5.16 peak petaflops, and offers Composable Systems and Cloud Bursting.
Reinforcement Learning For Beginners with Python
0
This course takes through the fundamentals required to get started with reinforcement learning with Python, OpenAI Gym and Stable Baselines. You'll be able to build deep learning powered agents to solve a varying number of RL problems including CartPole, Breakout and CarRacing as well as learning how to build your very own/custom environment!
Jetstream Home
0
Jetstream2 makes cutting-edge high-performance computing and software easy to use for your research regardless of your project’s scale—even if you have limited experience with supercomputing systems.Cloud-based and on-demand, the 24/7 system includes discipline-specific apps. You can even create virtual machines that look and feel like your lab workstation or home machine, with thousands of times the computing power.
ACCESS HPC Workshop Series
0
Monthly workshops sponsored by ACCESS on a variety of HPC topics organized by Pittsburgh Supercomputing Center (PSC). Each workshop will be telecast to multiple satellite sites and workshop materials are archived.
The Theory Behind Neural Networks (Very Simplified)
0
This video by the YouTube channel 3Blue1Brown provides a very simplified introduction to the theory behind neural networks. This tutorial is perfect for those that don't have much linear algebra or machine learning background and are eager to step into the realm of ML!
Ask.CI Q&A Platform for Research Computing
0
OnShape Documentation
0
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.
Women in HPC
0
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.
Python
0
Python course offered by Texas A&M HPRC