Issue 248
C&T Round Up for November 2023!
Round up time! This month Jan released Open Phage Data Sheet (google sheet full of phage tools/links/resources, open to all to contribute!) and shared a walkthrough on using ChatGPT for data work. And Libby Duignan wrote about her recent Australian phage adventure!
Community digest1alert5updates3jobs6posts
Phage alert
Urgent need for Staphylococcus epidermidis phages for a patient in the UK
We are urgently seeking Staphylococcus epidermidis phages for a patient in the UK.
Ways to help at this stage:
- By sending your phages for testing on the patient's strains
- By receiving the patient's strain and testing your phages
- By helping spread the word about this request
- By providing us with names/email addresses of labs you think we should contact
Please email staff@phage.directory if you can help in any way, or if you would like further details/clarification.
Let’s make a difference, Phage Directory
Updates
Oxford Silk Phage Technology, in collaboration with the University of Exeter and the University of Hertfordshire, has been awarded 2 million British pounds via a new Collaborative Innovate UK Biomedical Catalyst grant. The funds will accelerate pre-clinical development of OSPT’s first product, aimed at reducing patients’ risk of surgical site infections.
Fagofarma, a Czech microbiological and pharmaceutical company, has been authorized by the Czech State Institute for Drug Control to produce GMP phages for clinical use, making it the second Czech company to do so.
Justin Boeckman (Center for Phage Technology, Texas) and colleagues published a protocol detailing methods for phage DNA extraction, genome assembly, and genome closure.
Erez Yirmiya (Weizmann Institute of Science, Israel) and colleagues analyzed groups of closely related Bacillus phages that showed differential sensitivity to bacterial defense systems, and discovered four distinct families of anti-defense proteins that inhibit the Gabija, Thoeris, and Hachiman systems.
Rachel Samson (National Collection of Industrial Microorganisms, India) and colleagues wrote a new review on the status quo and emerging trends of phages in a One Health context.
Jobs
Vetophage (Lyon, France) is hiring a director of development to help commercialize its first diagnostic phage products.
The Le Roux lab at the Université de Montréal is hiring a postdoc in Microbial Genomics to investigate Vibrio phage-bacteria coevolution and phage satellites.
Tim Blower (Durham University) and Jay Hinton (University of Liverpool) have an opening for a PhD student funded by BBSRC NLD Doctoral Training Partnership to study cyclic nucleotide signalling and BREX phage defence.
Community board
Phage Research Progress Assessment for Collective Funding Application
Dear Phage Research Community,
We invite you to participate in this brief survey to assess the current state of phage research in various labs. Your valuable insights will help us understand the progress and challenges in the field with the ultimate goal of knowing the state of phage research in Africa. Please take a few minutes to provide information about the stage of your phage work, collaborations, challenges, and future plans. Your responses will contribute to a comprehensive overview of phage research, supporting collaborative efforts and funding applications.
Thank you for your participation and contribution to advancing phage research.
Sincerely,
Africa Phage Forum team
Abstract submissions are OPEN for #VoM2024 Meeting in Cairns, Australia! Join us July 15-19, 2024 to explore the expanding frontiers in virology. Check the website for details & to submit an abstract, & watch the video invitation to get even more excited!.
Call for Organizers: VoM 2026! The ISVM invites enthusiastic members to organize the Viruses of Microbes 2026 conference, #VoM2026. Submit your application by April 30, 2024, to board@isvm.org. Be at the forefront of this exciting conference!
iVoM Season 3, the ISVM’s webinar series, kicks off this December with its first session on "Ecological & Functional Roles of Viruses in Contrasting Environments." Mark your calendars: Dec 12, 2023, 8 PM CET.
Phage Oxford 2024, the longest running phage conferences series in Europe, and the second longest running phage conference globally, will be held on 02-03 September 2024 as a ‘virtual/in-person’ hybrid event at St Edmund Hall, Oxford, UK.
The Sustainable Microbiology journal has a themed collection focused on phage diversity and contributions to improving animal, environmental, and human health. Submit your research by January 1, 2024.
Happy Turkey Day, everyone!
As everyone’s crunching for grant deadlines going into the winter (or summer!) break, it’s been a quiet month of guest posts. This means I can write more posts on data engineering and GPT-4 experiments!
We have one phage post from Libby, who visited our Phage Australia lab from the UK, and spent a week exchanging phage manufacturing notes with Jess.
The other two posts are both by me: the first one is the launch of a shared, publicly-editable, work-in-progress Google Sheets of phage resources; the second is a post on all my AI and GPT-4-assisted experiments to extract and work with data.
If you’re using GPT-4 for any kind of lab or data work, I highly recommend you read through this one — it’s full of examples of what GPT-4 does well and poorly!
For this article, I got to launch an initiative I’d always wanted in the phage world — a completely open, publicly editable spreadsheet of all kinds of phage resources. This could be grants, clinical trials, and bioinformatics tools, all sourced and collected into a single place for everyone to find. The difference between this and Phage Directory is that Phage Directory’s more curated, whereas this is 100% community sourced. So far I’ve filled in some 400+ bioinformatics tools (with the help of AI), and I’ve yet to clean them all up. I’m also going to incrementally fill the other tabs over the next several weeks as I find time.
This article is filled with examples of using ChatGPT for real data engineering and data extraction work. This could be things like extracting text from screenshots or photos using GPT-Vision, processing CSVs, graphs, and tables using GPT-4, trying to read handwriting or QR codes, counting plaques, running FASTA files with GPT-4 Data Analysis, and a ton more. I write about what worked, didn’t work, and what surprised me. The main takeaway is that GPT-4 is very powerful and great for 60% of the work, but lacks a lot of necessary tools to do the rest. In the future we’ll cover “custom actions” and how you can connect GPT-4 to custom tools, code, and servers to go the rest of the way. Exciting times!
We were lucky enough to have University of Liverpool postdoc Libby Duignan visit us here at Phage Australia recently, ostensibly to ‘learn from us’ — really, we learned from her! She flew over from the UK and she and Jess spent days in the lab talking phage production and purification, sharing notes and lab hacks, and ripping Jess’ protocols to shreds. It was extremely productive, and we now highly recommend everyone orchestrating their own week-with-a-phage-buddy to help evaluate whether their methods are really as bulletproof and reproducible as they hope. Libby then sadly left us to return to her homeland, but at least she wrote up a nice blog piece on her visit! Super excited to watch what she does next (she will be joining a company in the UK to bring phage manufacturing to life over there!).