C&T Round Up for October 2023!

Hey everyone,

I’m writing this from the Melbourne Docklands library, as Jessica is presenting her work on systematizing Phage Australia’s phage production pipeline — with systems like AKTA — over at the Bioprocessing Network Conference. We’ll do a writeup (on the very cool results) in Capsid soon!

You might have noticed a slight redesign breezing through Capsid & Tail! We’re trying out a light refresh to Capsid, and I’m slowly rebuilding some data services which will support an (eventually) updated website. We’ve been building a lot of data tools for managing phages, bacteria, and biobank assets for Phage Australia, and I’ve been wanting to roll those updates back through Phage Directory’s website. I’m excited to update the way we list labs and phages, and completely revamp the sign up process to actually have accounts. But as you know, Phage Directory’s become a sort of hobby project at this point, as we’re spending most of our time working on Phage Australia’s process trial — I’m spending most of my time thinking about the “data stuff” and Jess is doing the “wet lab stuff.”

Recently there’s also been a lot more “AI stuff” in the mix, and we’re going to roll out more articles about how AI is shifting how we’re thinking about things: both from the “using ChatGPT for lab work” side to using OpenAI and other “foundation models” to do NLP and generative work. There’s a lot of experimentation going on right now, and some are more… experimental than others, but most of it’s not very polished. A lot of it is about rewriting the boring, backend, server-y code to be more flexible and support more tools and applications.

We’ll write more about that in the coming month!

Southeast Asia Hands-on Phage Workshop, by Phages for Global Health

by Donna May Papa

In this article Donna writes about her experiences with the Hands-on Phage Workshop by Tobi’s Phages for Global Health, which usually runs in Africa. This time they made a detour to Southeast Asia! I was surprised to learn how much nitty-gritty bioinformatics they learned, including setting up their own Linux environments. Honestly, I’d love to take the Phage Workshop (as a non-microbiologist) myself, to get my hands wet in the wet lab.

Evergreen 2023: Looking Back

by Jan Zheng

We were going to post about the highlights, photos, and learning from Evergreen right after Evergreen happened, but we had too many guest posts that needed to go out! We finally got around to posting the Evergreen recap this month. Evergreen was such a treat, with so many mini-fires burning in the background… but eventually turned out great! Take a look at just a few of the many pictures we took (and read about how we got stuck at Mt. Rainier until midnight…).

ChatGPT tips for lab work

by Jan Zheng and Jessica Sacher

In this article, Jessica and I wrote about experiences using ChatGPT for lab work and data work. This served mostly as an introduction / overview for all the articles we wanted to write, and we wrote it as a baseline. We got some emails saying “our use cases were pretty obvious” but you’d be surprised how few people turn to ChatGPT for help. When we’re used to doing math by hand, it can be sometimes be hard to remember to pull up the calculator — and ChatGPT is merely a calculator for words!

C&T Throwback!

I wanted to highlight our Slack Channel this time, which Sayde Perry wrote about in Issue 166 from the C&T archive! I’m calling it out because Jess has been asking a lot of production and “what machine to get” kind of questions — and getting a ton of helpful responses from other phage folks. Read Sayde’s archived guide to the Slack community. The community is now retired; read the notice.