Knowledge Base Resources
Use these resources “vetted” by the community. Additional Knowledge Base Resources are always welcome.
ACCESS Support Portal
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Metadata Systems
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Metadata is a vital topic in libraries and librarianship, encompassing structured information used for accessing digital resources. The definition of metadata varies but is essentially data about data. It has evolved beyond simply describing metadata schemas and now focuses on topics like interoperability, non-descriptive metadata (administrative and preservation metadata), and the effective application of metadata schemas for user discovery. Interoperability, the ability to seamlessly exchange metadata between systems, is a major concern. Different levels of interoperability are examined, including schema-level, record-level, and repository-level. Challenges to interoperability include variations in standards, collaboration barriers, and costs.Metadata management is discussed in terms of the holistic management of metadata across an entire library. Steps include analyzing metadata requirements, adopting schema, creating metadata content, delivery/access, evaluation, and maintenance. Administrative metadata, which encompasses ownership and production information, is becoming more critical, particularly for electronic resource licensing. Preservation metadata is also gaining importance in ensuring the long-term viability of digital objects.
RRCoP Resources Page
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Very helpful list of Regulated Research Community of Practice's collaborating communities.
Horovod: Distributed deep learning training framework
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Horovod is a distributed deep learning training framework. Using horovod, a single-GPU training script can be scaled to train across many GPUs in parallel. The library supports popular deep learning framework such as TensorFlow, Keras, PyTorch, and Apache MXNet.
Use Windows Subsystem for Linux for HPC Command Line Access from Windows
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Windows Subsystem for Linux (WSL) provides a Linux environment for Windows users to access HPC resources fast and efficiently.
Docker Tutorial for Beginners
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A Docker tutorial for beginners is a course that teaches the basics of Docker, a containerization platform that allows you to package your application and its dependencies into a standardized unit for development, shipment, and deployment.
Linux Tutorial from Ryan's Tutorials
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The following pages are intended to give you a solid foundation in how to use the terminal, to get the computer to do useful work for you. You won't be a Unix guru at the end but you will be well on your way and armed with the right knowledge and skills to get you there if that's what you want (which you should because that will make you even more awesome). Here you will learn the Linux command line (Bash) with our 13 part beginners tutorial. It contains clear descriptions, command outlines, examples, shortcuts and best practice. At first, the Linux command line may seem daunting, complex and scary. It is actually quite simple and intuitive (once you understand what is going on that is), and once you work through the following sections you will understand what is going on. Unix likes to take the approach of giving you a set of building blocks and then letting you put them together. This allows us to build things to suit our needs. With a bit of creativity and logical thinking, mixed in with an appreciation of how the blocks work, we can assemble tools to do virtually anything we want. The aim is to be lazy. Why should we do anything we can get the computer to do for us? The only reason I can think of is that you don't know how (but after working through these pages you will know how, so then there won't be a good reason). A question that may have crossed your mind is "Why should I bother learning the command line? The Graphical User Interface is much easier and I can already do most of what I need there." To a certain extent you would be right, and by no means am I suggesting you should ditch the GUI. Some tasks are best suited to a GUI, word processing and video editing are great examples. At the same time, some tasks are more suited to the command line, data manipulation (reporting) and file management are some good examples. Some tasks will be just as easy in either environment. Think of the command line as another tool you can add to your belt. As always, pick the best tool for the job.
What are LSTMs?
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This reading will explain what a long short-term memory neural network is. LSTMs are a type of neural networks that rely on both past and present data to make decisions about future data. It relies on loops back to previous data to make such decisions. This makes LSTMs very good for predicting time-dependent behavior.
Python
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Python course offered by Texas A&M HPRC
Astronomy data analysis with astropy
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Astropy is a community-driven package that offers core functionalities needed for astrophysical computations and data analysis. From coordinate transformations to time and date handling, unit conversions, and cosmological calculations, Astropy ensures that astronomers can focus on their research without getting bogged down by the intricacies of programming. This guide walks you through practical usage of astropy from CCD data reduction to computing galactic orbits of stars.
Applications of Machine Learning in Engineering and Parameter Tuning Tutorial
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Slides for a tutorial on Machine Learning applications in Engineering and parameter tuning given at the RMACC conference 2019.
Neural Networks in Julia
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Making a neural network has never been easier! The following link directs users to the Flux.jl package, the easiest way of programming a neural network using the Julia programming language. Julia is the fastest growing software language for AI/ML and this package provides a faster alternative to Python's TensorFlow and PyTorch with a 100% Julia native programming and GPU support.
Research Software Engineering Training Materials
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An ongoing collection of RSE training material, workshops, and resources. We are compiling this list as a starting point for future activities. We are especially seeking material that goes beyond basic research computing competency (e.g. what The Carpentries does so well) and is general enough to span multiple domains. Specific tools and technologies used only in one domain, or applicable to only one subset of computing (i.e. HPC) are typically too narrowly focused. When in doubt, submit it to be included or reach out and we’d be happy to discuss.
Slurm Tutorials
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Introduction to the Slurm Workload Manager for users and system administrators, plus some material for Slurm programmers.
Conda
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Conda is a popular package management system. This tutorial introduces you to Conda and walks you through managing Python, your environment, and packages.
Recommended Libraries for Cyberinfrastructure Users Developing Jupyter Notebooks
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This repository contains information about Jupyter Widgets and how they can be used to develop interactive workflows, data dashboards, and web applications that can be run on HPC systems and science gateways. Easy to build web applications are not only useful for scientists. They can also be used by software engineers and system admins who want to quickly create tools tools for file management and more!
Scikit-Learn: Easy Machine Learning and Modeling
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Scikit-learn is free software machine learning library for Python. It has a variety of features you can use on data, from linear regression classifiers to xg-boost and random forests. It is very useful when you want to analyze small parts of data quickly.
Better Scientific Software (BSSw)
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The Better Scientific Software (BSSw) project provides a community to collaborate and learn about best practices in scientific software development. Software—the foundation of discovery in computational science & engineering—faces increasing complexity in computational models and computer architectures. BSSw provides a central hub for the community to address pressing challenges in software productivity, quality, and sustainability.
ACCESS Events and Training
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Listing of upcoming ACCESS related events and training activities.
Biopython Tutorial
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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.
Introduction to Probabilistic Graphical Models
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This website summarizes the notes of Stanford's introductory course on probabilistic graphical models.
It starts from the very basics and concludes by explaining from first principles the variational auto-encoder, an important probabilistic model that is also one of the most influential recent results in deep learning.
Neocortex Documentation
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Neocortex is a new supercomputing cluster at the Pittsburgh Supercomputing Center (PSC) that features groundbreaking AI hardware from Cerebras Systems.
Hour of Ci
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Hour of Cyberinfrastructure (Hour of CI) is a nationwide campaign to introduce undergraduate and graduate students to cyberinfrastructure and geographic information science (GIS).