Knowledge Base Resources

The Biopython Tutorial and Cookbook website is a dedicated online resource for users in the field of computational biology and bioinformatics. It provides a collection of tutorials and practical examples focused on using the Biopython library. The website offers a series of tutorials that cover various aspects of Biopython, catering to users with different levels of expertise. It also includes code snippets and examples, and common solutions to common challenges in computational biology.

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

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!

This tutorial will give you an introduction to neural networks using the ever-famous MNIST handwritten digits database! Presented by Robin Hwang.

Python has become a very popular programming language and software ecosystem for work in Data Science, integrating support for data access, data processing, modeling, machine learning, and visualization. In this webinar, we will describe some of the key Python packages that have been developed to support that work, and highlight some of their capabilities. This webinar will also serve as an introduction and overview of topics addressed in two Cornell Virtual Workshop tutorials, available at https://cvw.cac.cornell.edu/pydatasci1 and https://cvw.cac.cornell.edu/pydatasci2

Goes through in detail on how to build an application that can run on Android and IOS devices, using Qt Creator to develop Qt Quick applications. Goes through the setting up, creation, configuration, optimization, and overall deployment. This provides the fundamental basis, need to click around on the site for more specifics.

Resources and User Guide available at Rockfish

High Performance Computing (HPC) Cluster

HPCwire is a prominent news and information source for the HPC community. Their website offers articles, analysis, and reports on HPC technologies, applications, and industry trends.

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.

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

Often when working with GIS, or spatial data, one encounters the word "datum" and it may require that you choose a "datum" when doing GIS computation tasks. Below is a short video on what are datums from NOAA and UCAR.

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.

The NSF-funded ResearchSOC helps make scientific computing resilient to cyberattacks and capable of supporting trustworthy, productive research through operational cybersecurity services, training, and information sharing necessary to a community as unique and variable as research and education (R&E). ResearchSOC is a service offering from Indiana University's OmniSOC.

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

The "Fairness and Machine Learning" book offers a rigorous exploration of fairness in ML and is suitable for researchers, practitioners, and anyone interested in understanding the complexities and implications of fairness in machine learning.

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.

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

These links take you to visualization resources supported by the University of Arizona's HPC visualization consultant (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. Some of the pages linked are very beginner friendly: getting started, working with cameras and keyframes for rendering, visualizing external files (netcdf climate data), graphs and data exporting. Many of the workflows involve using remote desktops via the Open On Demand interface, but if this isn't set up at your university you can use paraview locally on a desktop. Feel free to post on access ci https://ask.cyberinfrastructure.org/ if you need assistance getting a paraview gui open for your work on HPC.

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.

Training materials for using the bash (and zsh) shell.

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.