Knowledge Base Resources
Contributed by cyberinfrastructure professionals (researchers, research computing facilitators, research software engineers and HPC system administrators), these resources are shared through the ConnectCI community platform. Add resources you find helpful!
Enhanced Sampling for MD simulations
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Quick and Robust Data Augmentation with Albumentations Library
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Data augmentation is a crucial step in the pipeline for image classification with deep learning. Albumentations is an extremely versatile Python library that can be used to easily augment images. Transformations include rotations, flips, downscaling, distortions, blurs, and many more.
Citation:
Buslaev A, Iglovikov VI, Khvedchenya E, Parinov A, Druzhinin M, Kalinin AA. Albumentations: Fast and Flexible Image Augmentations. Information. 2020; 11(2):125. https://doi.org/10.3390/info11020125
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.
Electric field analyses for molecular simulations
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Tool to compute electric fields from molecular simulations
marimo | a next generation python notebook
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Introduction seminar for new reactive python notebook from marimo ambassador.
AI powered VsCode Editor
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**Cursor: The AI-Powered Code Editor**
Cursor is a cutting-edge, AI-first code editor designed to revolutionize the way developers write, debug, and understand code. Built upon the premise of pair-programming with artificial intelligence, Cursor harnesses the capabilities of advanced AI models to offer real-time coding assistance, bug detection, and code generation.
**How Cursor Benefits High-Performance Computing (HPC) Work:**
1. **Efficient Code Development:** With AI-assisted code generation, researchers and developers in the HPC realm can quickly write optimized code for simulations, data processing, or modeling tasks, reducing the time to deployment.
2. **Debugging Assistance:** Handling complex datasets and simulations often lead to intricate bugs. Cursor's capability to automatically investigate errors and determine root causes can save crucial time in the HPC workflow.
3. **Tailored Code Suggestions:** Cursor's AI provides context-specific code suggestions by understanding the entire codebase. For HPC applications where performance is paramount, this means receiving recommendations that align with optimization goals.
4. **Improved Code Quality:** With AI-driven bug scanning and linter checks, Cursor ensures that HPC codes are not only fast but also robust and free of common errors.
5. **Easy Integration:** Being a fork of VSCode, Cursor allows seamless migration, ensuring that developers working in HPC can swiftly integrate their existing VSCode setups and extensions.
In essence, for HPC tasks that demand speed, precision, and robustness, Cursor acts as an invaluable co-pilot, guiding developers towards efficient and optimized coding solutions.
It is free if you provide your own OPEN AI API KEY.
MDAnalysis - Python library for the analysis of molecular dynamics simulations
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MDAnalysis is a python based library of tools for the analysis of molecular dynamics simulations. It is able to read and write many popular simulation formats including CHARMM, LAMMPS, GROMACS, and AMBER and more. This link contains the documentation pages of all MDAnalysis functions and has links to tutorials using Jupyter Notebooks.
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.