A compendium with digressions of topics started elsewhere on the interwebs (or things on my mind).
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If you searched against a pre-June 2026 UniProt database, some of your identified proteins no longer exist in the current release… and that means no keywords among other things. If you are using 2026_02 release as the good lord intended then none of this applies to you. But if you are like me, you read Vande Moortele et al. and decided to use the full 2026_01 TrEMBL (and associated Swiss-Prot and…
Alright, so I have been working on something for the last couple months, basically doing some analysis of these stool samples samples. Part of it is showing the “normal” Minnesota two-step in action (search everything then take peptide hits and their species, and search that subset search space in a second pass), but then also making an updated second step where I dump search results from first…
I have been bouncing between LLMs, both for work and for personal, and realized I love having projects on each, but I did not like that they were behind walls. Moreover, some of my early stuff was done where I was manually copying things over. Then I realized the obvious for when I wanted to go cloud to cloud vibe coding: just give the LLM a PAT and let it commit and push to a repo, and if I have…
So way back when in 2023 this popped up on Twitter and it cracked me up so hard. We are constantly trying to avoid reading things and thinking, and so this satirical “Impact Shade” was developed by BioRxIF (venture to twitter if you so dare) to help us easily evaluate a paper using colors: I was thinking of this because of the q.e.d. 1% thing going on , but I won’t lie, I think about it all the…
I needed to put chatGPT through its paces a few weeks ago, so decided to update the oldest website I have. That’s right, the one that is my quasi CV that has been a dark theme since I started it, benjaminneely.com . I still can’t remember where I got the template from, but in my memory it was on Lifehacker, described as a nameplate so that you could control what google thought of you. Since then I…
Yes this is LLM generated, but with my specific questions and goals. There is a short version as well, here . This is for me. B-) Button-driven. Every step shows VS Code and GitHub Desktop side by side. GitLab note: GitHub Desktop only works with GitHub repos. For GitLab, use the VS Code column (it works with any remote). In-editor Pull Requests on GitLab need the GitLab Workflow extension; on the…
I’ve been running this blog on Jekyll and GitHub Pages for a while now. The setup is clean and I like it: no server to maintain, no database, just Markdown files in a repo that build into a site. The problem is the writing workflow. To publish a post I needed to be at my computer, write the Markdown, commit it, push it. On my phone that’s basically impossible without a third-party app, and every…
Okay, so I am realizing I subscribe to the idea (which I don’t know where I read this) that you should choose tasks to off-load to LLMs, but in doing so keep tasks that make you happy or ones that you need to keep so your brain doesn’t rot away. For me, I will totally let an LLM write an internal report, but I don’t want to vibe-write an actual paper, because weirdly enough, I actually enjoy it…
I used the example of finding my dream project car to test ideating in my last posts and here is the follow-up no one wanted as to what the answer is. If you looked at the last post on ideating with hats , which didn’t work super well but was useful to do, my example was a prompt about me and a dream car, or what I am referring to as my final fun car once I get kids out of the house. My first car…
I am going to start some sort of weekly posting here (for a while at least) to focus on what I learned this week (WILTW) or what I built this week (WIBTW). With my new focus on Data Sci and AI, you’re going to get a lot of that, sorry. I am also going to backdate some posts. This week I saw someone on reddit mention making agents that are based on Edward de Bono’s six thinking hats , plus a…
