When epidemiologists investigate a disease outbreak, they do not just match symptoms to known pathogens. They work through complex chains of evidence, test hypotheses, reconsider assumptions when data does not fit, and sometimes completely change their approach based on new information.

Imagine hiring an assistant who never sleeps, never forgets, can work on a thousand tasks simultaneously, and communicates with you in your own language. Now imagine having not just one such assistant, but an entire team of them, each specialized in different areas, all coordinating seamlessly to achieve your goals.

I have a little hobby project I’m working on and I wanted to use the opportunity to fully make the switch to Positron from RStudio. I used Positron here and there when it first came out, but now that it’s out of beta and has a more complete feature set (like remote SSH sessions!) I have everything I need to switch and not look back.

“If health workers do not share their challenges and solutions, we are bound to fail.” This declaration from a participant in the Teach to Reach initiative facilitated by The Geneva Learning Foundation (TGLF) cuts to the heart of a crisis that has long plagued global health technical assistance: the persistent gap between what external experts provide and what practitioners actually need.

Ein Zentralbaustein zum Verständnis der Open-Access-Transformation ist das Monitoring. Die Landesinitiative für Open Research in Berlin betreibt ein solches mit Blick auf Berlin. Wir hier in Brandenburg machen etwas ähnliches. Am Forschungszentrum in Jülich wird der Open Access Monitor mit einer bundesweiten Perspektive betrieben.

The right to asylum is a legacy of the French Revolution. As it recognized the first secular form of asylum for “freedom fighters”, the Revolution gave birth to the myth of France as a “land of asylum”. However, during the so-called “refugee crisis” in 2015, France was not a major destination country for refugees.

Time to update posts again. I know it is not that long ago since the last update post, but there are just so many interesting things I want to share with you. The first thing observant readers probably have already noticed: Every Substack post now has its own historical image. You can watch all of them by browsing through the archive. I tried to find ones that fit the general vibe of the post and I am quite happy with the result.

“I have learned much from my teachers and even more from my friends, but from my students I have learned most of all” Graduation is one of the most enjoyable milestones in the academic calendar.

I had a lot of fun working with the XKCD color survey data, and I think I’ll keep messing around with it here and there in the future. But I also think I’ll want access to the full data. The tidytuesday data set was necessarily boiled down. The answers data frame contained just one hex code associated with one color label, not every color label given to every hex code in the survey.

An LLM Chat Plants the Seed To come up with small projects to do in preparation for job interviews (contact me if you need a cheminformatics scientific software developer!), I interactively asked ChatGPT for suggestions. It suggested The Murcko Scaffolds Blog Post I wrote code to find the Murcko scaffold for a set of molecules, then determine the count of unique scaffolds. That answered the ChapGPT challenge.

Reposted from the original at: https://blog.stephenturner.us/p/tidy-rag-in-r-with-ragnar Retrieval augmented generation in R using the ragnar package. Demonstration: scraping text from relevant links on a website and using RAG to ask about a university's grant funding.