Python Data and Viz Training (CCEP Program)
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Containerization Explained
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Containerization is a software development method in which applications are packaged into standard units for development, shipment, and deployment.
PyTorch Introduction
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This is a very barebones introduction to the PyTorch framework used to implement machine learning. This tutorial implements a feed-forward neural network and is taught completely asynchronously through Stanford University. A good start after learning the theory behind feed-forward neural networks.
How to use Rclone
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Learn how to use Rclone to transfer data, specifically from your local drive to the Open Storage Network, vice versa.
Practical Machine Learning with Python
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This video series provides a holistic understanding of machine learning, covering theory, application, and inner workings of supervised, unsupervised, and deep learning algorithms. It covers topics such as linear regression, K Nearest Neighbors, Support Vector Machines (SVM), flat clustering, hierarchical clustering, and neural networks. Goes over the high level intuitions of the algorithms and how they are logically meant to work. Apply the algorithms in code using real world data sets along with a module, such as with Scikit-Learn.
Slurm User Group Mailing List
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Federated CI Resources
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Discussion about contributing cycles to the Open Science Grid.
Awesome Jupyter Widgets (for building interactive scientific workflows or science gateway tools)
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A curated list of awesome Jupyter widget packages and projects for building interactive visualizations for Python code
Bridges-2 Home Page
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Landing Page for Bridges-2 information
Ask.CI Q&A Platform for Research Computing
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MATLAB with other Programming Languages
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MATLAB is a really useful tool for data analysis among other computational work. This tutorial takes you through using MATLAB with other programming languages including C, C++, Fortran, Java, and Python.
Paraview UArizona HPC links (beginner)
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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.
Ultimate guide to Unix
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Unix is incredibly common and useful. This website provides all the common commands and explanations for one to get started with a unix system.
TensorFlow for Deep Neural Networks
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TensorFlow is a powerful framework for Deep Learning, developed by google. This specifically is their python package, which is easy to use and can be used to train incredibly powerful models.
Probabilistic Semantic Data Association for Collaborative Human-Robot Sensing
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Humans cannot always be treated as oracles for collaborative sensing. Robots thus need to maintain beliefs over unknown world states when receiving semantic data from humans, as well as account for possible discrepancies between human-provided data and these beliefs. To this end, this paper introduces the problem of semantic data association (SDA) in relation to conventional data association problems for sensor fusion. It then, develops a novel probabilistic semantic data association (PSDA) algorithm to rigorously address SDA in general settings. Simulations of a multi-object search task show that PSDA enables robust collaborative state estimation under a wide range of conditions.
Samtools Documentation
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Samtools is a suite of programs for interacting with high-throughput sequencing data, especially in the SAM/BAM format. It offers various utilities for processing, analyzing, and managing sequence data generated from next-generation sequencing (NGS) experiments. Samtools is widely used in bioinformatics and genomics research for tasks such as read alignment, variant calling, and data manipulation.
Wiki for Onboarding onto the C3DDB Cluster at MGHPCC
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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.
ConnectCI
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Connect.Cybinfrastructure is a family of portals, each representing a program that is serving a segment of the research computing and data community. Each portal provides program-specific information, as well a custom "view" into a common database. The portal was originally developed to support project workflows and a knowledge base of self service learning resources for the Northeast Cyberteam. Subsequently, it was expanded to provide support to multiple cyberteams and other research computing communities of practice. We welcome additional communities, please contact us if you are interested in participating. Central to the Portal is an extensive and ever-evolving tagging infrastructure which informs every aspect of the Portal. The tag taxonomy was initially developed by the Northeast Cyberteam to categorize subject matter relevant to practitioners of Research Computing Facilitation and is ever changing due to the frequent introduction of new technology in domains that characterize the field of research computing.
Charliecloud User Group
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Announcements for for users and developers of Charliecloud, which provides lightweight user-defined software stacks for high-performance computing.
GDAL Multi-threading
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Multi-threading guidance when using GDAL.
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.
Implementing Markov Processes with Julia
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The following link provides an easy method of implementing Markov Decision Processes (MDP) in the Julia computing language. MDPs are a class of algorithms designed to handle stochastic situations where the actor has some level of control. For example, used at a low level, MDPs can be used to control an inverted pendulum, but applied in higher level decision making the can also decide when to take evasive action in air traffic management. MDPs can also be extended to the partially observable domain to form the Partially Observable Markov Decision Process (POMDP). This link contains a wealth of information to show one can easily implement basic POMDP and MDP algorithms and apply well known online and offline solvers.
Installing Rocky Linux Operating System
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Rocky Linux is an open-source enterprise operating system. It is compatible with Red Hat Enterprise Linux (RHEL). It is a community-driven project that provides a stable and reliable platform for production workloads. It is one of the best alternatives to Opensource CentOS, since Centos will be on end of life (EoL) soon in 2024 by shifting to CentOS Stream.
Texas A&M HPRC Training Site
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Training Resources and Courses offered by Texas A&M's Research Computing Group
RRCoP Resources Page
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Very helpful list of Regulated Research Community of Practice's collaborating communities.