Computational biology and genomics
gpt-oss is OpenAI’s open-weight models designed for powerful reasoning, agentic tasks, and versatile developer use cases. You can easily use it via Ollama and read more about it in their blog post. Let’s see how long it takes to generate some output using the same prompt on some of my computers at home. For this…
Back in February I learned about Open WebUI and have been wanting to test it out with Retrieval-Augmented Generation (RAG). I’ll follow the tutorial available on Open WebUI’s site. The goal of RAG is to provide Large Language Models (LLMs) with specific information with the goal of improving the output. My main interest in RAG…
Since it was Halloween and all, I shared an article with some scary Linux commands that one should never run to some of my colleagues. One of them was a fork bomb, which looks like this: :(){:|:&};: In Bash, a function is defined like so: function_name () { commands } So the fork bomb starts…
I came across this question last night on some trivia app I have on my phone: When you let fruits consisting of 99% water by weight dry so that they become 98% water, what percentage of weight do they lose? Stop scrolling (or looking) down right now, if you want to give it some thought…
I keep forgetting amino acid abbreviations and their classes because I never bothered learning them. To see if I can teach an old dog (me) new tricks, I wrote this simple Python script that asks questions about amino acids. I’ll keep doing the quiz until I can finally remember. Below is the Python code for…
In this post, I outline an approach for retrieving weather conditions from the command line. There are websites and widgets that provide weather details but I like using the command line because I find that it’s more efficient than pointing and clicking on stuff. In addition, this approach enables us to program specific tasks. For…
I saw this question on Quora: A teacher assigns each of her 18 students a different integer from 1 through 18. The teacher forms pairs of study partners by using the rule that the sum of the pair of numbers is a perfect square. Assuming the 9 pairs of students follow this rule, the student…
This is my third post on learning R through the BetaBit package, which contains three mini games for learning R. I wrote about the first game, called proton, late last year and the second game, called frequon, a week and a half ago. The third game is called regression and it’s much more statistical than…
Just last night I found this educational mini game written in R and decided to have a go at it: This was a fairly fun #Rstats game: https://t.co/0zGCQqCxvw (Only after brute-forcing it, I realised I didn't have to.) — Dave Tang (@davetang31) December 5, 2015 I completed it but as I alluded to in my…
At the start of this year I created a Twitter account that automatically tweets out papers related to transcriptomes, i.e. a Twitter literature bot. This idea isn’t new and there are over 200 Twitter literature bots. However, I wrote my Twitter bot using R (and using the RISmed package to search PubMed for papers) and…