Was great to chat to the Aberystwyth Science Cafe last night about all things #Parasites in canine faeces. #Worms 🪱Thanks @amandaclare.bsky.social for the invite. Loved every minute of it! @aberdlsagb.bsky.social @bchcaber.bsky.social
Great talk! If anyone is looking for a science speaker who is entertaining and expert about parasites, invite Russ! And you get to learn about the consequences of dog poo in the environment. And he brings along things in jars to hand around the audience.
Llongyfarchiadau i'r myfyrwyr AberCompSci a gyflwynodd bosteri yn y @bcswomenlovelace.bsky.social yng Nghaerfaddon y mis hwn!
Congratulations to the AberCompSci students who presented posters at the BCSWomen Lovelace Colloquium in Bath this month!
Each publication in a #Microbio26 journal helps fund 4 student travel grants. Please publish with us if you can!
May I interest you in £10k for humanities or social science research? Our small grants scheme is open. Apply by 3rd June.
We allocate through partial randomisation - awarding randomly between all applications that meet our quality threshold
www.thebritishacademy.ac.uk/funding/sche...
I posted a while ago about doing DNA analysis in a single day of a lab course for non science majors. For many reasons we are looking into LAMP assays for various bacteria. If anyone out there has experience w/ LAMP especially in undergraduate courses, I would love pointers/ comments.
the astronauts are on the dark side quick everyone hide
Amanda on a train with a tube of posters. Aberystwyth train station can be seen through the window.
I’ve set off from Aberystwyth with a poster tube full of @aberuni.bsky.social @abercompsci.bsky.social posters for the Lovelace Colloquium @bcswomenlovelace.bsky.social in Bath. Looking forward to hearing some great keynote speakers: Sarah Winmill and Edafe Onerhime.
Two new bioinformatics internships available in @johnlees.bacpop.org group at EMBL-EBI: 1) testing and developing ML methods for identification of bacterial promoter regions; 2) Applying innovations in protein structure prediction to search massive datasets. Apply here: www.bacpop.org/jobs/
https://coursesandconferences.wellcomeconnectingscience.org/event/scalable-genomics-and-pangenomics-20261011/
Do you plan to analyse lots of genomes? Or few that are large? One or multiple species? Join us for the course on analysing data at scale! (and yes, it will involve a lot of k-mers!). With @katiejenike.bsky.social and others...
@sangerinstitute.bsky.social @connectingscience.bsky.social
This. A thousand times this.
Diff where some code was moved out of f to a helper function g. The diff highlights parts of both functions without matching delimiters.
Diff where the same code was moved out of f to a helper function g. Difftastic does a better job of highlighting the whole definition of f, and just the name and left arrow defining g. No unmatched delimiters!
Native git diff for a function that got a new argument and whose definition is now on multiple lines because it got too long to fit on one line of 80 characters. Git highlights all the lines as changed.
Difftastic diff for a function that got a new argument and whose definition is now on multiple lines because it got too long to fit on one line of 80 characters. Difftastic only highlights the line with the new argument and the comma on the line before that.
New post! Better Git diff with difftastic
A diffing tool that understands syntax and can
- ignore formatting changes
- match delimiters in wrappers
- ...
masalmon.eu/2026/03/30/d...
#RStats
📣 Still time to apply to this bioinformatics postdoc position with us! If you have any questions, please DM me here or send me an email. Deadline 3 April.
"If a researcher used an LLM to generate their peer review, instructions hidden in the watermark prompted the LLM to include telltale phrases in the review text. The presence of these phrases revealed that an AI model had been used to generate the review."
www.nature.com/articles/d41...
New paper in mSystems! 🧵 - how much of your metagenome is actually bacterial/archaeal DNA? For many samples, nobody knows.
We built SingleM prokaryotic_fraction (SPF) to answer this, then ran it on >100,000 public metagenomes. 🧬🖥️🦠
Here's what we found 👇
doi.org/10.1128/msystems.01062-25
'recently, the EPSRC announced a funding competition for a foundational AI research lab....the call gave applicants “less than four weeks to apply, so it’s going to go to an existing hub”. Logically, Hall said, “another £40m of [funding for] important foundational AI work is going to men”.' 3/3
I just had that conversation earlier this week. The college dean is deciding if they will (dis)continue the bioinformatics training program for grad students. An argument for discontinuation is that students will use GenAI to help them code, so they don’t need to learn bioinformatics.
Data Organization in Spreadsheets Karl W. Broman & Kara H. Woo Pages 2-10 | Received 01 Jun 2017, Accepted author version posted online: 29 Sep 2017, Published online: 24 Apr 2018 1. Introduction 2. Be Consistent 3. Choose Good Names for Things 4. Write Dates as YYYY-MM-DD 5. No Empty Cells 6. Put Just One Thing in a Cell 7. Make it a Rectangle 8. Create a Data Dictionary 9. No Calculations in the Raw Data Files 10. Do Not Use Font Color or Highlighting as Data 11. Make Backups 12. Use Data Validation to Avoid Errors 13. Save the Data in Plain Text Files ABSTRACT Spreadsheets are widely used software tools for data entry, storage, analysis, and visualization. Focusing on the data entry and storage aspects, this article offers practical recommendations for organizing spreadsheet data to reduce errors and ease later analyses. The basic principles are: be consistent, write dates like YYYY-MM-DD, do not leave any cells empty, put just one thing in a cell, organize the data as a single rectangle (with subjects as rows and variables as columns, and with a single header row), create a data dictionary, do not include calculations in the raw data files, do not use font color or highlighting as data, choose good names for things, make backups, use data validation to avoid data entry errors, and save the data in plain text files.
Every day is a good day for sharing one of the most useful papers about research data ever written. PLEASE get your people to understand and follow this advice.
www.tandfonline.com/doi/full/10....
📣 The Whelan lab is hiring a bioinformatics postdoc 📣
Together with @fabricejpierre.bsky.social, we are offering a 1-year bioinformatic PDRA position in comparative genomics of Pseudomonas aeruginosa. To find out more please visit whelanlab.co.uk/contact/. Applications close 3 April 2026!
I have to give a big shout out to Aberystwyth University library for emailing us students with the message:
Don't like/trust/approve of AI?
Don't feel pressured into using it. You're not missing out if you don't. It's potentially wasting your time and eroding your confidence with false flattery.
Haven’t the shires gone electric yet?
If you want to join a team making pathogen sequencing and analysis for public health, surveillance, and research more accessible, more equitable and more ✨awesome✨ - look no further - come join us on this mission at ARTIC!
#openscience #opendata #opensource
How often an appropriate choice of benchmark is absent from a paper announcing a new technique or approach, and it takes papers like this to make the comparisons ;)
New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/
www.biorxiv.org/content/10.6...
New post, on whether I could get Claude Code to complete a data task that had taken me AGES a decade ago…
kucharski.substack.com/p/how-much-t...
AI has huge promise for genomics -- but it has consistently failed at microbiome-based prediction.
My new post on why simple models keep winning, where deep learning actually earns its place, and where the field is headed
blekhman.substack.com/p/ai-keeps-f...
Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...
1/ LLMs are great at text extraction, but sometimes they hallucinate. A simple way to catch hallucinations is to check if the extracted text actually exists in the source. Turns out this is harder than it sounds. (new paper with Aaron Streets)
www.biorxiv.org/content/10.6...
This article is now published! academic.oup.com/nargab/artic...
We’ve added a few new analyses. First off, we show that, while gene presence absence variation (PAV) scales with evolutionary distance in both plants and animals, the base level and rate of accrual are both twice as high in plants.
