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.

Below is a link for a book that focuses on how to use "sf" and "terra" packages for GIS computations. As of 5/1/2023, this book is up to date and examples are error free. The book has a lot of information but provides a good overview and example workflows on how to use these tools.

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!

The MOOSE Navier-Stokes Cahn-Hilliard (NSCH) application is a library for implementing simulation tools that solve the Navier-Stokes Cahn-Hilliard equations with non-matching densities using Galerkin finite element methods with a residual-based stabilization scheme.

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.

Very helpful list of external resources from Trusted CI

Visual Studio Code, commonly known as VSCode, is a popular tool used by programmers worldwide. It serves as a text editor and an Integrated Development Environment (IDE) that supports a wide variety of programming languages. One of its key features is its extensive library of extensions. These extensions add on to the basic functionalities of VSCode, making coding more efficient and convenient. However, there's a catch. When these extensions are installed and used frequently, they generate a multitude of files. These files are typically stored in a folder named .vscode-extension within your home directory. On a cluster computing facility such as the FASTER and Grace clusters at Texas A&M University, there's a limitation on how many files you can have in your home directory. For instance, the file number limit could be 10000, while the .vscode-extension directory can hold around 4000 temporary files even with just a few extensions. Thus, if the number of files in your home directory surpasses this limit due to VSCode extensions, you might face some issues. This restriction can discourage users from taking full advantage of the extensive features and extensions offered by the VSCode editor. To overcome this, we can shift the .vscode-extension directory to the scratch space. The scratch space is another area in the cluster where you can store files and it usually has a much higher limit on the number of files compared to the home directory. We can perform this shift smoothly using a feature called symbolic links (or symlinks for short). Think of a symlink as a shortcut or a reference that points to another file or directory located somewhere else. Here's a step-by-step guide on how to move the .vscode-extension directory to the scratch space and create a symbolic link to it in your home directory: 1. Copy the .vscode-extension directory to the scratch space: Using the cp command, you can copy the .vscode-extension directory (along with all its contents) to the scratch space. Here's how: cp -r ~/.vscode-extension /scratch/user Don't forget to replace /scratch/user with the actual path to your scratch directory. 2. Remove the original .vscode-extension directory: Once you've confirmed that the directory has been copied successfully to the scratch space, you can remove the original directory from your home space. You can do this using the rm command: rm -r ~/.vscode-extension It's important to make sure that the directory has been copied to the scratch space successfully before deleting the original. 3. Create a symbolic link in the home directory: Lastly, you'll create a symbolic link in your home directory that points to the .vscode-extension directory in the scratch space. You can do this as follows: ln -s /scratch/user/.vscode-extension ~/.vscode-extension By following this process, all the files generated by VSCode extensions will be stored in the scratch space. This prevents your home directory from exceeding its file limit. Now, when you access ~/.vscode-extension, the system will automatically redirect you to the directory in the scratch space, thanks to the symlink. This method ensures that you can use VSCode and its various extensions without worrying about hitting the file limit in your home directory.

Spatial Data Science is a growing field across a wide range of industries and disciplines. The open-source programming language Python has many libraries that support spatial analysis, but what do you do when your computer is unable to tackle the massive file sizes of high-resolution data and the computing power required in your analysis? There materials have been prepared to teach you spatial data science and how to execute your analysis using a high-performance computer (HPC).

High Performance Computing (HPC) Cluster

The official MGH / Harvard tutorial page for FreeSurfer. The FreeSurfer group has provided and designed a series of tutorials for using FreeSurfer and for getting acquainted with the concepts needed to perform its various modes of analysis and processing of MRI data. The tutorials are designed to be followed along in a terminal window where commands can be copy/pasted instead of typed.

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.

This code showcases how to work with the header-only nlohmann JSON library for C++. In order to compile, change the extensions from json_test.txt to json_test.cpp and test.txt to test.json. You must also download the header files from https://github.com/nlohmann/json. Complilation instructions are at the bottom of json_test. This code is very helpful for creating config files, for example.

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.

Introductory training materials for working on the UNIX command line.

MediaPipe is Google's open-source framework for building multimodal (e.g., video, audio, etc.) machine learning pipelines. It is highly efficient and versatile, making it perfect for tasks like gesture recognition. This is a tutorial on how to make a custom model for gesture recognition tasks based on the Google MediaPipe API. This tutorial is specifically for video-playback, though could be generalized to image and live-video feed recognition.

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

A compilation of the slides from this year's RMACC Sys Admin Workshop. RMACC Sys Admin Workhop Schedule: Tuesday 12:00 PM Sign-in 1:00 PM Introductions 1:30 PM Lightning Talk - HPC Survival guide 2:00 PM Node Management - Scott Serr 2:30 PM Lightning Talk - Warewulf 3:00 PM Urgent HPC - Coltran Hophan-Nichols and Alexander Salois Wednesday 9:00 AM Breakfast 10:00 AM Round table Sites - BYU, INL, UMT, ASU, MSU 11:00 AM Open OnDemand setup - Dean Anderson 11:30 AM Lightning talk - Long term hardware support 12:00 PM Lunch 1:00 PM HPC Security - Matt Bidwell 2:00 PM Lightning talk- Security 2:30 PM ACCESS resources - Couso 3:00 PM Easybuild tutorial - Alexander Salois 3:30 PM General Q & A Thursday 9:00 AM Breakfast 10:00 AM Lightning Talk- Containers and Virtual Machines 11:00 AM University of Montana - Hellgate Site Tour 11:30 AM Closing Remarks

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.

Hour of Cyberinfrastructure (Hour of CI) is a nationwide campaign to introduce undergraduate and graduate students to cyberinfrastructure and geographic information science (GIS).

Techniques and support for multithreaded geospatial data processing in GRASS.

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.

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.