Hey everyone,
Welcome to the last issue of 2023!
What a whirlwind of a year it’s been – I feel like it was only yesterday when we were all trapped on that mountain at Evergreen 😒. Compared to the Covid years, these couple of years in Australia completely flew by.
Proudest Moments
For us, 2023 has been filled with deep phage work and coding and AI deep dives.
Jessica’s spent much of her time working on phage production and purification — and learned to use the AKTA Flux and AKTA Pure to purify phages. She’s then developed dozens of SOPs and logs for data collection, and has written about her lab techniques and learnings throughout Capsid. Between her and Steph (who handles everything upstream of production) they’ve been able to identify, produce, and purify phages for one patient per month (and in one month, three patients!!). Oh, and she’s also found time to host many lab visits, present her work at 5 (or 6?) conferences, help co-organize Evergreen, and learn how to code on Replit’s 100 days of Code.
As for me, I’ve spent a lot of the year working in the background, cooking together data streams like our REDCap electronic data capture system for our clinical data, setting up tools like Cloudflare R2 for data backups and versioning, experimented with building data-crunching and UI-generating “agents” with GPT-4, and other prototypes like Instill.xyz, a simplified commenting / forum system) and blogalog.net, a system for hosting simple blog pages on top of Notion. I’m SUPER proud of how Evergreen turned out, from the signup, registration, and payment process itself to the actual event (massive shoutout to Ria!). I’m also proud of Capsid & Tail’s articles this year, as I took over much of the article writing, editorial, and begging for guest posts 😉 work. I’m also happy I was able to convince to turn Capsid’s tone to lean more conversational!
Biggest Surprises
The biggest surprise of the year is that phage work is getting more funding! And that phage therapy collectives like Phage-UK, UK Phage Therapy, Phage Canada are getting together to pave the regulatory pathway like at the UK Parliament. There’s also an uptick in new phage startups, and whispers of more funding for fundamental phage research towards better understanding the mechanisms of phage therapy.
On a personal note, Jess is surprised that people love to nerd out about her technical lab articles, and happily email her about her writing! (💡 tip: want others to nerd out YOUR lab work? Write for Capsid & Tail to find collaborators!)
For me, the (obvious) surprise of the year is the rise of AI and large language models (LLMs). They bring capabilities (like text extraction, recommendation, and ranking) that were previously only available to organizations with deep pockets and armies of ML researchers. For me, this meant having to rethink how to build a lab inventory and data processing system for an AI-centric future. I’ve been writing a lot about phage and lab data, and using AI to process it. The advent of LLMs means biology will get even more computational… for better or worse!
Favorite Capsid Articles
Here’s a selection of our favorite articles from this year. Every article is my favorite because I planned, scheduled them (and wrote many of them!) this year. But if we had to choose…
Jessica: I like the S. aureus article we published last week, by David Sáez and Lorenzo Corsini, because we need more articles digging into what doesn’t work with phages, and this one did a great job highlighting that.
I’m cheating and picked two articles — one by Thomas Hunt on learning to code and building lab automations in the lab, and one by Jessica about using AI to discover coding. Learning to code used to be very hard, because sometimes you’d get stuck on a hard problem for days (or weeks!), and you had to pour through textbooks and manuals. Nowadays, it’s a couple queries away from GPT-4. (Heck, I used cursor.sh to write much of the code for me)
What we look forward to
We’re moving back to the US!
And we have our sights set on moving to the heart of AI and biotech (the Bay Area), and work with the amazing phage labs, biotechs, and AI startups there.
I’m keen to use all my experience I gained from working with Phage Directory and Phage Australia to work on AI-centric tools that make lab work and lab informatics easier — and this might mean joining a phage lab, a biotech or “tech-bio” startup, or even an AI company. I’ll still be working on the biobank lab inventory and data system (codenamed Atlas), which will continue as labspace.ai.
Jessica is excited about completing handover of phage work to the new, rapidly expanding team here, and being on call for support as they scale up — while being on the same continent as her family again, and reuniting with her horse!
We’re spending the next few weeks to think about where we can go next and be most of value. For me, that’s exploring more AI projects, and for Jessica, that could be to phage companies, phage research labs, phage therapy centers, or even beyond phage…
The next chapter of Phage Directory
Just because we’re moving back to the US doesn’t mean Phage Directory will go anywhere!
We’re planning to simplify it and take it back to its roots: Capsid & Tail, helping the community, improving the Directory, and Phage Alerts.
I have lots of plans to rebuild and redesign Phage Directory, integrate some of the new AI and data tools. We also have more plans to experiment with Capsid & Tail (we’d love if you wrote for us! 😉), and I really hope to expand the phage and phage host directories with expanded details like synergy/antagonism, citations, receptors, etc. — with the help of AI. I’m also excited to rebuild the Lab and Member directories with editable profiles, but also…
We will also launch Phage Directory Profiles, which gives everyone a CV site like janzheng.com, jess.bio, Atif Khan’s site, and for labs and organizations like ivom.phage.directory, Phages for Global Health: Online, PhageBiotics, womeninphage.phage.directory.
Because we’re moving, we’re taking a break with Capsid & Tail in January, and publishing fewer articles February.
In 2024, we’re looking forward to bring both Phage Directory (and ourselves) back to our roots!
Happy Holidays!
~ Jan & Jessica <>-{
