MelBioInf, to bioinformatics
@MelBioInf@genomic.social avatar

A final reminder: we are currently advertising three jobs! Applications close on 15 May. Details and links in the thread ⬇️ https://genomic.social/@MelBioInf/112295817677021230

sotneStatue, to bioinformatics
@sotneStatue@fosstodon.org avatar

Today I'll be using #R for RNAseq analysis for the first time, wish me luck

#bioinformatics

bffo, to bioinformatics
@bffo@mastodon.social avatar

You do in ? Elsewhere in the world? You lead a group? Maybe invite your students be volunteers at the largest International Bioinformatics Conference?

https://www.iscb.org/ismb2024/general-info/apply-to-be-event-staff

bffo, to bioinformatics
@bffo@mastodon.social avatar

Remembering the first Canadian Workshop: … we used to use mouse pads back then! This was a useful one for those didn’t know their standard genetic code by heart

necrosis, to science German
@necrosis@chaos.social avatar

Leute. Ich hab sooooooooooo was geiles entdeckt.

Kennt ihr schon https://www.olivetin.app/ ?

Damit kann man Tools eine verpassen. 😍

Ok, das würde sich auch mit von umsetzen lassen. Aber dennoch.

Für unsere Beschäftigten, die eher Windows gewohnt sind kann ich so Shell Tools leichter zugänglich machen. Das ist so toll. 😍

Für sicher auch einen Blick wert. :3


rmflight, to bioinformatics
@rmflight@mastodon.social avatar

What RNA-Seq datasets are everyone using for RNA-Seq differential analysis workshops, using {DESeq2} or {limma} ?

Two or three categories, and ideally a good (4 or 5+) number of replicates, human or mouse?

We have some new methods in ontology enrichment, and we really could use some more datasets to try them on.

I've found the {airways} dataset, and lung adenocarcinoma from {recount3} (as an easy pull). Looking for others. TIA.

davelunt, to bioinformatics
@davelunt@genomic.social avatar

If anyone would like to chat to me about applying for a MSCA fellowship please get in touch #bioinformatics #molecular_evolution #genomics #polyploidy #transposons #population_genomics
https://marie-sklodowska-curie-actions.ec.europa.eu/actions/postdoctoral-fellowships?

MelBioInf, to bioinformatics
@MelBioInf@genomic.social avatar

We are hiring! Melbourne Bioinformatics is expanding our team by recruiting into three new positions. This is your chance to become part of a dynamic team of expert bioinformaticians who are at the forefront of Australian training, outreach, and research.

All three roles are full-time, continuing positions based at the University of Melbourne's Parkville campus. Applications close 15 May 2024. For more information, including application instructions, follow the links below.

thatdnaguy, to linux
@thatdnaguy@genomic.social avatar

If you work on the command-line in Linux a lot, find + exec is your friend.

"I have many copies of MYFILE because my project got sloppy over time. Are they different?"

find . -type f -readable -name "MYFILE*" -exec md5sum {} ;

Also handy for if temporary files get out of control and rm chokes.

find . -type f -readable -name "*.temp" -exec rm {} ;




computingnature, to bioinformatics
@computingnature@neuromatch.social avatar

Despite all their hype in AI, we found that Transformers do not outperform for cellular segmentation tasks: https://www.biorxiv.org/content/10.1101/2024.04.06.587952v1

Cellpose outperforms winner of Neurips challenge (Ma et al 2024) on test set images. We show example images from the test set with Cellpose segmentations overlaid in yellow.

lambdamoses, to python
@lambdamoses@fosstodon.org avatar

I'm thrilled to announce a new preprint from our lab, with in depth analyses showing that Seurat and Scanpy give drastically different results for ostensibly the same data analysis tasks: https://www.biorxiv.org/content/10.1101/2024.04.04.588111v1

BOSC, to opensource
@BOSC@genomic.social avatar

TWO WEEKS LEFT to submit your abstract to BOSC! The deadline is April 19 by the end of the day Anywhere on Earth. (Sorry, no extensions.) We welcome submissions on all aspects of and

If you are hoping for a talk, please submit a 2-page pdf; if you only want a poster, we only need a short (250-word) abstract. Please see https://www.open-bio.org/events/bosc-2024/submit/ for more information and a button for submitting.

F2erron, to bioinformatics French
@F2erron@fediscience.org avatar

Hello sugar people of the :fediverse: . My former collegue Bernard Henrissat now in 🇩🇰 is looking for a student in a Marie Sklodowska-Curie 🇪🇺 training network to work with him at the Technical University of Denmark. More info:
https://euraxess.ec.europa.eu/jobs/201030
The deadline for application is May 31st, 2024 and the job will start in November.

Skills desired: , general biology (++ ) and fluency in 🇬🇧.
Eligibility: the candidate should not have worked in 🇩🇰 before.

xgrau, to bioinformatics Catalan
@xgrau@ecoevo.social avatar

We have two open positions to work on the bioinformatics team of the Biodiversity Cell Atlas initiative, at CRG (Barcelona).

Please contact Arnau Sebé if you're interested, as the deadline is next week — 10th of April!

Both positions are funded by the Moore Foundation.

naturepoker, to bioinformatics
@naturepoker@genomic.social avatar

Yikes - this looks like a pretty serious issue. Especially considering high chance that the original author of the package might have been behind the backdoor attempt.

I know quite a few #bioinformatics packages also need xz for compilation. Hate that we need to worry about stuff like this more from now on.

https://arstechnica.com/security/2024/03/backdoor-found-in-widely-used-linux-utility-breaks-encrypted-ssh-connections/

persagen, to llm
@persagen@mastodon.social avatar

Bioinformatics and Biomedical Informatics with ChatGPT: Year One Review
https://arxiv.org/abs/2403.15274

... covering omics, genetics, biomedical text mining, drug discovery, biomedical image understanding, bioinformatics programming, and bioinformatics education ...

#LLM #ChatGPT #NLP #AI #bioinformatics #biomedical

lwpembleton, to programming
@lwpembleton@genomic.social avatar

pyOpenSci, to random
@pyOpenSci@fosstodon.org avatar

Accepted into the pyOpenSci ecosystem in 2021, OpenOmics from Jonny Tran is a #Python library that helps with the integration of heterogeneous multi-omics #bioinformatics data through both an API and web interface.

OpenOmics supports:
🧬 Genomics, Transcriptomics, Proteomics, and Clinical data.
〰️ Harmonization with 20+ popular annotation, interaction, and disease-association databases, such as GENCODE, Ensembl, RNA Central, BioGRID, and DisGeNet

📄Docs: https://openomics.readthedocs.io/en/latest/

lunareclipse, to bioinformatics

anyone know some simple software for extracting tables from scientific papers (pdfs)?

#bioinformatics

bioconductor, to bioinformatics
@bioconductor@genomic.social avatar

✍️ Check out our blog post about the recent launch of the redesigned Bioconductor website: https://buff.ly/4bYFJEb

#BioconductorCommunity #Bioinformatics #RStats

hexylena, to bioinformatics
@hexylena@galaxians.garden avatar

waking up to horrors well within my comprehension

i know so many viral annotation/phylogeny colleagues who would’ve loved this.

bigcat_UM, to bioinformatics
@bigcat_UM@social.edu.nl avatar

hi, we're the #bioinformatics group BiGCaT at Maastricht University in The Netherlands, led by Prof. dr Chris Evelo (chair), Dr Susan Steinbusch-Coort, Dr Lars Eijssen, Dr Egon Willighagen, and Dr Friederike Ehrhart. More information on our homepage at http://www.bigcat.unimaas.nl/ #introduction

modrak_m, to bioinformatics
@modrak_m@bayes.club avatar

A nice little paper arguing that Chord diagrams are generally harder to understand than Sankney plots for the same data. Relevant for when people will next request the "nice circular diagrams" for a bioinformatics analysis: https://dl.acm.org/doi/fullHtml/10.1145/3544548.3581119

A Sankney plot showing the flow of loans and debts between a few nations.

nmronline, to bioinformatics
@nmronline@mstdn.science avatar

looks fun!

We hope everybody is having a great time, whilst building up their networks and strengthening their portfolios!

@bioinformatics @biophysics @chemistry @compchem @nmrchat @physics @strucbio

tyx, to bioinformatics

The most annoying things in data analysis:

  • R package/lib hell
  • basic Python API instability
  • conda solving envos for hours
  • lustre (all about it)
  • each R package having it's own class for genetic/trees/geospatial data storage.

I have freaking bingo of hitting all of them today at once.

Are there any I missed?

#rstats #conda #lustre #dllHell #PackageHell #DependencyHell
#geospatial #bioinformatics #hpc

  • All
  • Subscribed
  • Moderated
  • Favorites
  • •
  • provamag3
  • thenastyranch
  • DreamBathrooms
  • InstantRegret
  • magazineikmin
  • everett
  • Youngstown
  • ngwrru68w68
  • slotface
  • ethstaker
  • rosin
  • khanakhh
  • kavyap
  • tacticalgear
  • JUstTest
  • cisconetworking
  • mdbf
  • Leos
  • Durango
  • osvaldo12
  • tester
  • GTA5RPClips
  • cubers
  • anitta
  • megavids
  • normalnudes
  • modclub
  • lostlight
  • All magazines
    •