Cute. Our abstract submission for a conf was rejected because we have a preprint already up with essentially an identical abstract.

The conf wanted "original, unpublished research". But they ran it against iThenticate, and didn't check "where" it was published (I don't agree, but most places don't count preprints as official publication).

Whatever. I have even less time now to worry about a sub-omics specific pres than I thought when we submitted the abstract.

I'm having a blast testing out Phold from @GB13Faithless - new preprint available here:

https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1

Protein language model & structural alignment aided annotation. It immediately picked out some interesting replication genes from a prophage region I've been wrecking my head over for a while now.

https://github.com/gbouras13/phold

Worth checking out!

Interested to learn about how to run your own Loculus (the database code behind @pathoplexus )?

Sign up for the Loculus Tutorial on Mon 8 Sept at BC2 Conference (by @SIB ) in Basel, run by @chaoranchen & Anya Parker!

Register: https://www.bc2.ch/registration-info

I would love to see a scientific journal that focusses on computational reproducibility, where authors submit data and Jupyter/Rmarkdown notebook scripts. Only after those reports are compiled, does the work actually go for peer review.

Our primary instance is shutting down and Elly is no longer in the system so we're going to repurpose this account as our system account as we have neither the energy or time to look for a new instance [this is copied from old, and will be edited over time until we've established] #introduction - Updated: 2024-10-08

We're The Weather System (Athena's Realm System), We're Trans fem, and we're an officially diagnosed autistic, bipolar and dissociative identity disorder system, we a collection of various leftist, and believe strongly in queer, and neurodiversity rights movements, we view plurality in general as neurodivergence

Our pronouns are Su/Sudo/Suselves, however She/Her/Herselves, and They/Them/Theirselves

We are most likely to toot about #Medicine, with focus on #Genetics, #Epigenetics, #Bioinformatics, and #Neuroscience giving our focus back in uni was Genetics of Human Disease, and Neuroscience but we are likely to talk about a whole range of medical topics, besides medicine we are likely to toot about #meteorology and #geology, with specific interests in #SynopticMeteorology #TropicalCyclones / #Hurricanes / #Typhoons / #TropicalStorms, #ExtratropicalCyclones, #SubtropicalCyclones, and #Tornadoes, among other topic, and we may toot about #Geology, #Minerals, and #Vulcanology, and what ever else is on our mind, we collected #MyLittlePony and are a fan of every generation of MLP, also we collect #WildManes and Radioactive stuff and play #EliteDangerous

See attached thread for System Information, System Membership 58+

Our system name is subject to change, it was previously the Athena's Realm System, however only one member, arguably two members made that decision on behalf of the entire system, without consulting us, so we're in the process of trying out system names to see which fits us best, but for the time being we will display both "Athena's Realm" and the current trialing system name so it is less confusing for those who know us by our old system name

#ucsc We are pleased to announce the release of a new Public Hub, UniversalEPI ENCODE for hg38. This track hub displays normalized #atacseq and #HiC interaction predictions based on ENCODE data and generated using UniversalEPI. UniversalEPI is an attention-based deep ensemble model that predicts enhancer–promoter interactions (EPIs) up to 2 Mb apart using only DNA sequence and chromatin accessibility (ATAC-seq) data.

https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://boevalab.inf.ethz.ch/resources/universalepi_pred_encode/ucsc_track_hub/hub.txt&genome=hg38&position=lastDbPos

Looking for a reviewer!
Journal of Open Source Software got this interesting submission:
https://github.com/openjournals/joss-reviews/issues/6892

If you're into #metabolomics #bioinformatics #rstats #programming #omics and you want to check out a new software, contact me or write directly in the linked GitHub issue.
Reviewing for JOSS is public, and you get a checklist (https://joss.readthedocs.io/en/latest/reviewer_guidelines.html) - try it out!

Honoured to be part of a video series by Instituto Todos Pela Saúde about Bioinformatics! It's been wonderful to see more & more women come into Bioinf, as such an important & wide-ranging field - full of awesome & impactful projects!
#womeninstem #bioinformatics

https://www.linkedin.com/posts/instituto-todos-pela-sa%C3%BAde-itps_mulheresnaciencia-bioinformatica-cienciaparatodos-activity-7357119328208486401-RzTp?utm_source=share&utm_medium=member_ios&rcm=ACoAACUv8AQBjrI7k1bQZ-x4yQ4zxFcdjeMWSag

cool new work by the San Francisco @wikipathways team!

https://fosstodon.org/@wikipathways/114977968168380876

New release of PFOCR! Over 6,500 new pathway figures added for a total of 116,972. These include 147,974 unique genes across hundreds of species (18,775 human), 7,855 unique ChEBI, and 748 unique disease DOIDs.

https://pfocr.wikipathways.org

Using the search tool, you can specify a gene, keyword and year, e.g., all the pathway figures from 2025 so far that mention APOE4: https://pfocr.wikipathways.org/search.html?query=APOE4%202025

Today marks 10 years since the very first @multiqc commit!

What started as a simple tool for QC reports has grown into something used by labs worldwide. It's become a foundational tool in the fabric of #bioinformatics and it's a joy to see it play a part in research

I'm so grateful for the amazing community that's contributed, given feedback, and helped shape it into what it is today. A true testament to the power of #openscience

Here's to the next decade of making QC beautiful!

NIST finalizes first full Digital Identity Guidelines update since 2017

https://www.biometricupdate.com/202508/nist-finalizes-first-full-digital-identity-guidelines-update-since-2017

A short video recap of ISMB/ECCB 2025, covering the current trends and latest surprises in bioinformatics.
https://youtube.com/shorts/QVCU8zkGFxQ?feature=share
#ISMBECCB2025 #ISMB #ECCB #bioinformatics #artificialintelligence #quantumcomputing

Got sent a request to review Friday morning. Kinda looks in my wheelhouse, but I'm currently kinda slammed with analyses, figure I'll take a closer look tomorrow, you know, when I'm back at work.

Get a reminder tonight. I get it, it's already Monday there, but seriously. Almost makes me want to stop reviewing there.

I've had 1 working day with the request (Friday), and I've got a reminder before I actually start work on what will be day 2.

Is anyone planning on going to ISMB in Washington DC next year?
I suspect Europeans will prioritize ECCB, Canadians and many others may avoid the US too, and my friends in the US may not have the funding to go. I cannot help but worry for the conference.
#bioinformatics #compbio

Fun new tool from Heng Li. Thinking maybe I can use this to help find plasmid replication gene correlated repeat regions - though he specifically mentions it's not for tandem repeat regions. Hmm.

#bioinformatics

https://github.com/lh3/longdust

yeah, that's cool

"Now, researchers have found a way to image the sugars at a resolution of just 9 Ångström — 0.9 nanometres — using an off-the-shelf light microscope." https://doi.org/10.1038/d41586-025-02376-2 and https://doi.org/10.1038/s41565-025-01966-5

Job - Alert

Wissenschaftliche Leitung (w/m/d) für das Sachgebiet Datenwissenschaft Biodiversität  

Deadline: 2025-08-31 
Location: Germany, Hamburg

https://www.academiceurope.com/ads/wissenschaftliche-leitung-w-m-d-fur-das-sachgebiet-datenwissenschaft-biodiversitat/

DDoS-атака
1. Одна человеческая клетка содержит 75Мб генетической информации
2. Один сперматозоид содержит 37.5Мб.
3. В одном миллилитре содержится около 100 млн сперматозоидов.
4. В среднем, эякуляция длится 5 секунд и составляет 2.25 мл спермы.
5. Таким образом, пропускная способность мужского члена будет равна:
(37.5Мб x 100M x 2.25)/5 = (37 500 000 байт/сперматозоид x 100 000 000 сперматозоид/мл x 2.25 мл) / 5 секунд = 1 687 500 000 000 000 байт/секунду = 1 687.5 Терабайт/с
Получается что женская яйцеклетка выдерживает эту DDoS-атаку на полтора терабайта в секунду, пропуская только один выбранный пакет данных и является самым офигенным в мире хардварным фаерволом...
Но тот один пакет, который она пропускает, кладёт систему на 9 месяцев...

Sure! Here's the English version of your post with categories and hashtags:
DDoS vs. Biology
**The human egg is the world’s most advanced hardware firewall.**
Incoming data stream: **1.7 TB/sec**,
Only **one packet** gets through — and it **crashes the system for 9 months.**
Categories:
#Cybersecurity
#Biotech
#InfoSec
#Science
#DDoS
#TechHumor
#Bioinformatics
#Genetics
#Engineering
#NerdJokes
Let me know if you'd like it turned into a visual card, carousel, or meme graphic!