Little blog post, preprint included, re: spatial/image Bioc hackathon on a little Venetian island — Thank you @wkhuber.bsky.social and especially @davi1893.bsky.social (and Elena!) for organizing and securing this 🤩 location 🤩 — Let’s do it again!

Bioconductor@bioconductor.bsky.social · 2mo ago

🧬 Earlier this year, members of the Bioconductor community met on San Servolo Island, Italy, for a 3-day hackathon on spatial omics and bioimaging. The event produced a collaborative preprint to strengthen spatial omics support across Bioconductor. 📖 Learn more: bit.ly/43C5pDM

Registration is now open! See: csama2026.bioconductor.eu/registration...

CSAMA 2026 Biological Data Science

csama2026.bioconductor.eu

Davide Risso@davi1893.bsky.social · 8mo ago

This year's CSAMA Biological Data Science Summer School in Brixen takes place 24-29 May 2026. Topics: single-cell and spatial omics, statistics, multi-omics, ML/AI, all very hands-on using R / Bioconductor! More info: csama2026.bioconductor.eu Registration: 1 Feb 2026! @bioconductor.bsky.social

This year's CSAMA Biological Data Science Summer School in Brixen takes place 24-29 May 2026. Topics: single-cell and spatial omics, statistics, multi-omics, ML/AI, all very hands-on using R / Bioconductor! More info: csama2026.bioconductor.eu Registration: 1 Feb 2026! @bioconductor.bsky.social

CSAMA 2026 Biological Data Science – CSAMA 2026 Biological Data Science

22nd Edition Bressanone-Brixen, Italy 24-29 May 2026

csama2026.bioconductor.eu

EuroBioC2025 is in full swing here in Barcelona! Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow! #EuroBioC2025 #Bioconductor #OpenScience #Community

📣 Late-breaking poster call for #EuroBioC2025 is now open! Submit by July 11 to present your work in Barcelona this September. 🔗 forms.gle/ewTGdKzB2xyE... 📅 Notifications by July 15 #Bioconductor #Bioinformatics

EuroBioC2025 late-breaking poster abstract submission

Please fill the form below before the end of Friday July 11th, 2025, to submit an abstract for a poster to be considered for presentation at EuroBioC2025 in Barcelona on September 17-19, 2025…

forms.gle

🤔Could quality control create more harm than good? We explore this question in the context of #SRT. SpotSweeper is developed to combat implicit selection bias. Led by fellow rising star @mictott.bsky.social and collab with amazing mentor @stephaniehicks.bsky.social 👉: bsky.app/profile/mict...

Nature Methods@natmethods.nature.com · last yr.

Quality control matters in spatial transcriptomics. Check out this paper from Guo and colleagues on SpotSweeper that corrects for both local and regional artifacts across diverse technologies. www.nature.com/articles/s41...

Everyone involved in trying to pass off that ChatGPT-extruded disinformation manifesto as a scientific report should be, at the very least, barred from public office for life. The MAHA report is dangerous criminal misconduct and an offence to the process of science.

Mehdi Hasan@mehdirhasan.bsky.social · last yr.

This is what happens when you put internet conspiracy theorists in charge of major government departments.

The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.

THREAD 🧵 Internal State Department records show that months of warnings have become a reality: The Trump administration’s sudden withdrawal of foreign humanitarian aid has brought about death, violence and unrest. 1/

22 years ago I pivoted from working on antibiotic resistance to pandemic viruses. Since then, I've argued that if we care about saving US lives in expectation, advance capacity for producing bird flu vaccine offers by far the greatest expected return on investment. ... We were so goddamn close.

Trump administration cancels plans to develop a bird flu vaccine

The Department of Health and Human Services is ending a $766 million contract with the vaccine company Moderna to develop an mRNA vaccine for flu strains with pandemic potential, including bird flu.

npr.org

This is terrible news, HMMER & Infernal are at the heart of DBs like Pfam, Rfam & Dfam. And vital pipelines such as AlphaFold.

Sean Eddy@cryptogenomicon.bsky.social · last yr.

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

I appreciate the offers from other scientists to help Harvard (students, labs, etc) through this attack, but what would be most helpful is for you to use your position to contact your elected representatives and make it clear this fight isn't just Harvard, it will affect you, and their districts too

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"): www.biomedcentral.com/collections/...

Fascinating talk by @andganna.bsky.social at #ds4hb A lot of food for thought on efficient data collection and fairness in AI for health!

Science is under threat in the US. @elife.bsky.social have commissioned a series of articles discussing the implications and what we can do. The first three articles are now live. More to follow: elifesciences.org/articles/106... elifesciences.org/articles/106... elifesciences.org/articles/106...

Science Under Threat in the United States: How scientists and institutions should respond

Individual researchers and university leaders need to make the case for science to their elected representatives and to the public at large.

elifesciences.org

Would you like to spend a #postdoctoral fellowship in the beautiful Italian Alps doing great science? Apply for a MSCA Postdoctoral fellowship with us on #stats #biostats #genomics #epidemiology Many infos here 👇 🧵 #StatsSky #rstats #popgen #nephsky 1/n

📣📣Are you looking for a postdoc? 📣📣 Does a EU or Horizon Europe assoc country (eg UK, S Korea) seem like a good destination? These fellowships a great funding option for anyone in the 🌎 👀 Check them out - next call opens 8 May 🧪 👨‍🔬👩‍🔬 marie-sklodowska-curie-actions.ec.europa.eu/actions/post...

Abstract submissions are now open for the European Bioconductor Conference (EuroBioC2025), 17-19 September 2025 in Barcelona. This event will bring together the Bioconductor community in Europe to advance bioinformatics, data science, and open-source software. eurobioc2025.bioconductor.org

🎨 Reminder that EuroBioC2025 Sticker Contest is still open! Deadline Mar 10. Don't miss out on the chance to have your design featured at the conference and win free registration ✨ Submit buff.ly/42JiCLN Abstracts are open for submission too! #EuroBioC2025 #RStats #Bioinformatics #StickerContest

"Your AI can’t see gorillas!" A few years ago we found that students are more likely to see the gorilla in their data if they are not also asked to test a specific hypothesis. In his blog Chiraag Gohel now shows that Chat-GPT can’t help you to find it either. chiraaggohel.com/posts/llms-e...

In two weeks (10th March) John Burn-Murdoch will be holding a Conversation at the San Giobbe campus, Room 6A (2pm). Everyone is very welcome to join (and thanks @crisvarin.bsky.social for making this happen)!

New #rstats pkg gander is now on CRAN! gander is a coding assistant that knows how describe the objects in your global R environment. So, when you're working with data, LLMs will know the names, types, and distributions of data columns, resulting in much more effective completions.

📣 EuroBioC2025: Abstract Submissions Open! Join us in Barcelona, Spain 🇪🇸, Sep 17-19, 2025, for the European Bioconductor Conference! Submit your abstract for a short talk, workshop, or poster by Apr 24. ➡️ Submit https://buff.ly/3EN9w6P #EuroBioC2025 #Bioinformatics #RStats #DataScience

European Bioconductor Conference 2025

EuroBioC2025 is the European edition of the Bioconductor conference that will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor…

buff.ly

The sgdGMF #rstats package is now officially on CRAN: cran.r-project.org/package=sgdGMF Please give it a try and let us know if you have any feedback!

sgdGMF: Estimation of Generalized Matrix Factorization Models via Stochastic Gradient Descent

Efficient framework to estimate high-dimensional generalized matrix factorization models using penalized maximum likelihood under a dispersion exponential family specification. Either deterministic an...

cran.r-project.org

Davide Risso@davi1893.bsky.social · 2y ago

This is long overdue, but over the winter break we were finally able to write up our sgdGMF paper: arxiv.org/abs/2412.20509 We present a stochastic gradient descent method that allows to efficiently and very quickly estimate latent factors for, e.g., dimensionality reduction of single-cell data

🎨 EuroBioC2025 Sticker Contest! Unleash your creativity for the European Bioconductor Conference in Barcelona! The winning sticker will be featured on our website and handed out at the event. 🗓 Deadline: Mar 10, 2025 🏆 Prize: Free reg to EuroBioC2025 for winning design! Abstract call coming soon!

Trump & Musk are making massive cuts to the National Institutes of Health. I know there is a lot going on right now, but this is one of worst things they have done so far, will affect cancer research and trials, the search for cures, innovation and competitiveness, our universities. Your lives.

Modern-Day Oracles or Bullshit Machines? Jevin West (@jevinwest.bsky.social) and I have spent the last eight months developing the course on large language models (LLMs) that we think every college freshman needs to take. thebullshitmachines.com

INTRODUCTION

thebullshitmachines.com

8. It is difficult to overstate what a catastrophe this will be for the US research and education systems, particular in biomedical fields. It is deliberate and wanton devastation entirely out of scale with any concern about DEI activities on campuses. The goal is destroy US universities.

1. Today the NIH director issued a new directive slashing overhead rates to 15%. I want to provide some context on what that means and why it matters. grants.nih.gov/grants/guide...