Jeff

#Observability + #AI: a surprisingly helpful combination. Leverage improved observability in #genomics workflows to delegate initial troubleshooting tasks to an AI agent! #Slurm #Nextflow #OpenAI #Python #Loki #Slack jeffjjohnston.github.io/2025/11/30/o...

In this post, I walk through improving the #observability of a typical system one might use in the processing of genomic data: a #Slurm high-performance computing cluster running #Nextflow workflows. #Genomics #Grafana #Loki
jeffjjohnston.github.io/2025/11/22/o...

Connecting the Dots: Understanding the PSF’s Current Financial Outlook As the PSF heads into our end-of-year fundraiser, we want to share information to help “connect the dots” and show a more complete picture of the PSF’s current financial outlook. You’ve heard from us on subjects related to our financial position from several different angles recently (a list of those posts is below). We’ve prioritized proactive communications, because we believe in transparency, we have trust in our community, and we value keeping you informed— we know how invested in and impacted by our work you are. We now want to pull those threads together in order to create some shared clarity on the big picture, and, hopefully, inspire you to action to support our fundraising efforts.  

As the PSF heads into our end-of-year fundraiser this month, we want to “connect the dots” and share a full picture of our current financial outlook: what’s happening, why, and how you can help sustain the future of Python and the PSF. 🧵

remoclip now has a demo video! Access your local clipboard in the CLI - even when connected to remote systems. Free and open-source - see more at remoclip.newmatter.net/video/ #terminal #shell

Do you spend a lot of time in the shell connected to remote systems? Wouldn't it be great if you could access your local clipboard from those remote shells? Introducing remoclip - remote clipboard access for terminal users. My first #Python package! jeffjjohnston.github.io/2025/10/17/i...

I’m frequently asked if I have any guidance for getting started with AI, so I wrote a brief post describing a few concepts I think are important to learn.
#OpenAI #Python
jeffjjohnston.github.io/2025/09/21/g...

GitHub - jeffjjohnston/genomics-rare-disease-ai-workflow: An experimental AI agent workflow. An experimental AI agent workflow. Contribute to jeffjjohnston/genomics-rare-disease-ai-workflow development by creating an account on GitHub.

An experimental agent-based workflow designed to search for disease-causing variants in a patient's genomic sequencing results based on a description of the patient's symptoms.
#OpenAI #Python #Genomics #RareDisease
github.com/jeffjjohnsto...

Part 2 of the Variant Agent - now that we have annotated variants in a searchable database, we can build the AI agent and provide it access to a variant search tool.
#OpenAI #Genomics #Python #Bioinformatics
jeffjjohnston.github.io/2025/09/01/v...

The third agent in my AI-assisted rare disease workflow, the Variant Agent, is complex enough to need two posts! This first post describes the processing needed to get genomic variants annotated and inserted into a database. #OpenAI #Genomics #Bioinformatics jeffjjohnston.github.io/2025/08/24/v...

In my rare disease AI-based workflow proof-of-concept, I built three AI agents, each with their own responsibilities. One agent in the system is the Gene Agent, which selects candidate genes based on HPO terms. Read more:
#OpenAI #Genomics #Python #LLMs
jeffjjohnston.github.io/2025/08/18/g...

Recently, I’ve been thinking about how advanced LLMs might be utilized in my own field, genomic medicine. Read my blog post below for some interesting results!
jeffjjohnston.github.io/2025/07/20/g...
#Genomics #AI #OpenAI #RareDiseases #Bioinformatics #LLMs

Wouldn’t it be great if you could ask an AI model questions that you know are answered somewhere in your email, and have it go find the answer for you? I thought so, and decided to build a tool that could do just that.
#openai #ai #python @fastmail.com
jeffjjohnston.github.io/2025/06/12/f...

If you don't like that they only appear when you hover over the file name, you can activate "Show window title icons" in System Settings -> Accessibility -> Display so that they are always visible.