Jeff
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Jeff
@jeffjohnston.bsky.social
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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
Can an AI agent help diagnose genetic diseases? | Jeff's site
jeffjjohnston.github.io
We are witnessing the cusp of a sea change in software. It is becoming more diverse and flexible as the cost of adding custom features drops precipitously with more and more of the work delegated to AI models.
#SoftwareEngineering #Developers #OpenAI
jeffjjohnston.github.io/2026/01/10/e...
The evolution of an idea
A tale of using AI to rapidly prototype, build, and evolve a personal software tool.
jeffjjohnston.github.io
January 10, 2026 at 8:25 PM
#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...
Observability part 2: AI assistance
Observability in genomics workflows
jeffjjohnston.github.io
November 30, 2025 at 8:20 PM
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...
Observability in genomic workflows: Part 1
Observability in genomics workflows
jeffjjohnston.github.io
November 24, 2025 at 7:39 PM
Reposted by Jeff
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. 🧵
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.  
pyfound.blogspot.com
November 4, 2025 at 12:12 PM
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
Video Demo - remoclip
Local and remote CLI access to your clipboard
remoclip.newmatter.net
October 25, 2025 at 10:47 AM
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...
Introducing remoclip
Introducing the Python tool remoclip: remote clipboard access for terminal users
jeffjjohnston.github.io
October 17, 2025 at 1:46 PM
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...
Getting started with AI
Guides newcomers through the OpenAI API, structured output, and tool use with Python examples for text and multimodal interactions.
jeffjjohnston.github.io
September 23, 2025 at 11:55 AM
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...
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.
github.com
September 6, 2025 at 2:49 PM
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...
Implementing the Variant Agent: Part 2 | Jeff's site
jeffjjohnston.github.io
September 2, 2025 at 11:20 AM
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...
Implementing the Variant Agent: Part 1 | Jeff's site
jeffjjohnston.github.io
August 25, 2025 at 11:12 AM
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...
Implementing the Gene Agent | Jeff's site
jeffjjohnston.github.io
August 20, 2025 at 3:55 PM
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
Can an AI agent help diagnose genetic diseases? | Jeff's site
jeffjjohnston.github.io
July 21, 2025 at 3:49 PM
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...
Building a chat interface for your inbox | Jeff's site
jeffjjohnston.github.io
June 12, 2025 at 11:36 PM