github
36 posts
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Managing projects with GitHub and AI agents
Organizing conferences and workshops can quickly become overwhelming when plans, decisions, contracts, and meeting notes are scattered across multiple platforms.
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Running AlphaFold3 and OpenFold3 protein-ligand structure prediction on SDSC Expanse
I built two self-contained, reproducible projects that run realistic (non-toy) protein structure prediction on a single SDSC Expanse GPU node: one with DeepMind AlphaFold3 (via nf-core/proteinfold) and one with the fully open OpenFold3 (MCL1 protein-ligand ensemble).
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Synchronizing Google Docs and GitHub with gdrivemd
Managing documentation often requires choosing between the collaborative ease of Google Docs and the version-controlled structure of GitHub.
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Terminal-based AI assistant with GitHub for Education
GitHub offers to all academic people a free GitHub Pro account which allows you to use GitHub Copilot Pro, which includes access to the latest and most powerful models from OpenAI, Anthropic, and Google.
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Cosmosage Unshelver
This post describes the Cosmosage Unshelver. You can find the project on GitHub: zonca/openstackunshelverwebapp. There is an active pull request for further development. You can find the branch I am working on here: cosmosageunshelver branch.
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Software Citation Station
This post introduces the "Software Citation Station" by Tom Wagg, a tool designed to help researchers generate accurate and comprehensive citations for software. It simplifies the process of giving credit to software used in academic work, ensuring proper attribution and reproducibility.
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Take control of your Kaiser Permanente blood test results (no coding knowledge required)
Want to make sense of your Kaiser Permanente blood test results without needing to be a coding expert? This guide will walk you through using readily available tools to analyze your health summary, specifically focusing on lipid panels, with a step-by-step approach.
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Going full agentic for scientific software development
The landscape of scientific software development is being transformed by AI coding agents. Over the past few weeks, I've been exploring GitHub Copilot's AI coding agent capabilities for maintaining healpy, and the experience has been remarkable.
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Auto-merge GitHub pull requests after GitHub Actions pass
Pull request auto-merge is a small feature that keeps teams from babysitting green builds. Once every required check is green, GitHub merges the PR for you—no extra clicks, no late-night merges. Here is how to get it running safely with GitHub Actions.
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How to use GitHub Copilot for scientific computing
GitHub Copilot is rapidly transforming the landscape of scientific computing by streamlining code development and accelerating research workflows. This guide outlines how computational scientists can leverage Copilot, with a focus on professional and research-oriented use cases.
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Authenticate to GitHub in the browser with the device flow
Authenticating to GitHub in the browser using the device flow is essential for applications that cannot directly handle OAuth redirects.
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Save Jupyterlite notebooks to GitHub
JupyterLite runs entirely inside the browser, which means it doesn't have access to the underlying operating system. Its storage is persistent across restarts of the machine but could be deleted if the browser cache is cleared.
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Using GitHub Releases to keep track of large artifacts
GitHub Releases provide a way to attach large artifacts, such as binaries or large autogenerated files, without polluting the repository. A release points to a specific commit in a repository and can include files up to 2GB in size.
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Authenticate FastAPI endpoints with a GitHub organization
FastAPI is a framework that simplifies building APIs in Python. Authentication via Google, Github and many more is provided by FastAPI-SSO.
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2-way synchronization of Overleaf and GitHub via a GitHub Action
Updated: 2025-02-20 In the past I wrote tutorials on how to handle Github and Overleaf, the latest for example is this. However the Github button in Overleaf is fragile, it often gets disconnected for unknown reasons, and it cannot be reconnected, it forces deletion of the Github repository. Moreover, it seems it is now a Premium feature. Finally, it needs to be triggered manually, and nobody remembers to do that.