#bioinformatic — Public Fediverse posts

📣 Le blog se réveille après une trop longue hibernation 😪
La semaine dernière, l'ami Mathurin nous a fait part de la façon dont il a vécu le passage du monde académique 🎓 au monde de l'entreprise 🏢 Une délicate étape qui concerne bon nombre d'entre nous 👀
https://bioinfo-fr.net/le-changement-de-mentalite-en-passant-en-rd
#bioinfofr #stem #bioinformatic

📣 Le blog se réveille après une trop longue hibernation 😪
La semaine dernière, l'ami Mathurin nous a fait part de la façon dont il a vécu le passage du monde académique 🎓 au monde de l'entreprise 🏢 Une délicate étape qui concerne bon nombre d'entre nous 👀
https://bioinfo-fr.net/le-changement-de-mentalite-en-passant-en-rd
#bioinfofr #stem #bioinformatic

📣 Le blog se réveille après une trop longue hibernation 😪
La semaine dernière, l'ami Mathurin nous a fait part de la façon dont il a vécu le passage du monde académique 🎓 au monde de l'entreprise 🏢 Une délicate étape qui concerne bon nombre d'entre nous 👀
https://bioinfo-fr.net/le-changement-de-mentalite-en-passant-en-rd
#bioinfofr #stem #bioinformatic

Do you perform analysis on #metagenomics, #metataxonomics #metatranscriptomics #metaproteomics datasets?

Would you like to find out how to make your #bioinformatic analysis more efficient, scalable, and reproducible?

Join us on December 10th for an online ‘Meta-*omics #Nextflow #pipeline community exhibition day’, for an intro and hands-on tutorial directly from the developers!

Interested? Please register your interest with this link: https://tally.so/r/31qJyQ !

Do you perform analysis on #metagenomics, #metataxonomics #metatranscriptomics #metaproteomics datasets?

Would you like to find out how to make your #bioinformatic analysis more efficient, scalable, and reproducible?

Join us on December 10th for an online ‘Meta-*omics #Nextflow #pipeline community exhibition day’, for an intro and hands-on tutorial directly from the developers!

Interested? Please register your interest with this link: https://tally.so/r/31qJyQ !

Do you perform analysis on #metagenomics, #metataxonomics #metatranscriptomics #metaproteomics datasets?

Would you like to find out how to make your #bioinformatic analysis more efficient, scalable, and reproducible?

Join us on December 10th for an online ‘Meta-*omics #Nextflow #pipeline community exhibition day’, for an intro and hands-on tutorial directly from the developers!

Interested? Please register your interest with this link: https://tally.so/r/31qJyQ !

Do you perform analysis on #metagenomics, #metataxonomics #metatranscriptomics #metaproteomics datasets?

Would you like to find out how to make your #bioinformatic analysis more efficient, scalable, and reproducible?

Join us on December 10th for an online ‘Meta-*omics #Nextflow #pipeline community exhibition day’, for an intro and hands-on tutorial directly from the developers!

Interested? Please register your interest with this link: https://tally.so/r/31qJyQ !

Do you perform analysis on #metagenomics, #metataxonomics #metatranscriptomics #metaproteomics datasets?

Would you like to find out how to make your #bioinformatic analysis more efficient, scalable, and reproducible?

Join us on December 10th for an online ‘Meta-*omics #Nextflow #pipeline community exhibition day’, for an intro and hands-on tutorial directly from the developers!

Interested? Please register your interest with this link: https://tally.so/r/31qJyQ !

Google Deepmind: "AlphaGenome: #AI for better understanding the #genome"

#bioinformatic #science

https://deepmind.google/discover/blog/alphagenome-ai-for-better-understanding-the-genome/

Google Deepmind: "AlphaGenome: #AI for better understanding the #genome"

#bioinformatic #science

https://deepmind.google/discover/blog/alphagenome-ai-for-better-understanding-the-genome/

I had hoped that DIA-NN 2.02 could be accelerated by either ATI or nVidia GPUs, but I have tried with both types of cards to no avail.
#bioinformatic #proteomics #OpenCL #CUDA

I had hoped that DIA-NN 2.02 could be accelerated by either ATI or nVidia GPUs, but I have tried with both types of cards to no avail.
#bioinformatic #proteomics #OpenCL #CUDA

Seems like gmap does this sort of thing and will output into a gff3 format 👍 It was published in 2005 - goes to show that #bioinformatic tools don’t always need to be replaced with new tools.

https://academic.oup.com/bioinformatics/article/21/9/1859/409207

Seems like gmap does this sort of thing and will output into a gff3 format 👍 It was published in 2005 - goes to show that #bioinformatic tools don’t always need to be replaced with new tools.

https://academic.oup.com/bioinformatics/article/21/9/1859/409207

Today, I don’t know what happened, but ChatGPT did not work. It was weird at the beginning to code without it, but I have to say that copying and pasting is not the best way to learn. It is true that it took me longer to finish what I was doing, but I have the sensation that I control better what I am doing. So I will try to code by myself more and just ask more specific questions to ChatGPT. #bioinformatic

Benchmarking #bioinformatic #virus identification tools using real-world #metagenomic data across biomes

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03236-4

Benchmarking #bioinformatic #virus identification tools using real-world #metagenomic data across biomes

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03236-4

We wonder if anyone is up for the challenge of figuring out how to repurpose the new NPU chips for simulating DNA structures and other interlinked bioinformatics simulation tasks instead of "AI" LLMs...

#dna #bioinformatics #bioinformatic #transhumanism #technology #tech #science #npu #simulation #freedomofform #opensource #gnugpl #gplv2 #biohacking

I was thinking 🤔 recently about common hurdles 🚧 with #dev, #datascience and #bioinformatic setups. Do you think they stem mainly from general workplace IT limitations, costs, personal preference, etc. Orrrr are there larger, broader issues at play? 🤔

For example, if you were given say $5k to $10k to upgrade your setup (hardware, software, home office, hey could even throw in a coffee machine), would it solve most of your current woes or would the core problem still persist?
#programming

I was thinking 🤔 recently about common hurdles 🚧 with #dev, #datascience and #bioinformatic setups. Do you think they stem mainly from general workplace IT limitations, costs, personal preference, etc. Orrrr are there larger, broader issues at play? 🤔

For example, if you were given say $5k to $10k to upgrade your setup (hardware, software, home office, hey could even throw in a coffee machine), would it solve most of your current woes or would the core problem still persist?
#programming

PhD or Postdocs in computational disease biology & biomedical data science

UMass Lowell, Department of Biology & Center of Biomedical and Health Research in Data Sciences

Come join our lab at @UMLResearch using #datascience and #bioinformatic for discoveries in cancer and Alzheimers...
https://jobrxiv.org/job/umass-lowell-department-of-biology-center-of-biomedical-and-health-research-in-data-sciences-27778-phd-or-postdocs-in-computational-disease-biology-biomedical-data-science/?feed_id=70378

PhD or Postdocs in computational disease biology & biomedical data science

UMass Lowell, Department of Biology & Center of Biomedical and Health Research in Data Sciences

Come join our lab at @UMLResearch using #datascience and #bioinformatic for discoveries in cancer and Alzheimers...
https://jobrxiv.org/job/umass-lowell-department-of-biology-center-of-biomedical-and-health-research-in-data-sciences-27778-phd-or-postdocs-in-computational-disease-biology-biomedical-data-science/?feed_id=70378

PhD or Postdocs in computational disease biology & biomedical data science

UMass Lowell, Department of Biology & Center of Biomedical and Health Research in Data Sciences

Come join our lab at @UMLResearch using #datascience and #bioinformatic for discoveries in cancer and Alzheimers...
https://jobrxiv.org/job/umass-lowell-department-of-biology-center-of-biomedical-and-health-research-in-data-sciences-27778-phd-or-postdocs-in-computational-disease-biology-biomedical-data-science/?feed_id=68044

PhD or Postdocs in computational disease biology & biomedical data science

UMass Lowell, Department of Biology & Center of Biomedical and Health Research in Data Sciences

Come join our lab at @UMLResearch using #datascience and #bioinformatic for discoveries in cancer and Alzheimers...
https://jobrxiv.org/job/umass-lowell-department-of-biology-center-of-biomedical-and-health-research-in-data-sciences-27778-phd-or-postdocs-in-computational-disease-biology-biomedical-data-science/?feed_id=68044

PhD or Postdocs in computational disease biology & biomedical data science

UMass Lowell, Department of Biology & Center of Biomedical and Health Research in Data Sciences

Come join our lab at @UMLResearch using #datascience and #bioinformatic for discoveries in cancer and Alzheimers...
https://jobrxiv.org/job/umass-lowell-department-of-biology-center-of-biomedical-and-health-research-in-data-sciences-27778-phd-or-postdocs-in-computational-disease-biology-biomedical-data-science/?feed_id=67900

PhD or Postdocs in computational disease biology & biomedical data science

UMass Lowell, Department of Biology & Center of Biomedical and Health Research in Data Sciences

Come join our lab at @UMLResearch using #datascience and #bioinformatic for discoveries in cancer and Alzheimers...
https://jobrxiv.org/job/umass-lowell-department-of-biology-center-of-biomedical-and-health-research-in-data-sciences-27778-phd-or-postdocs-in-computational-disease-biology-biomedical-data-science/?feed_id=67900

To get a comprehensive list of #neuropeptides, we combined #bioinformatic screening and mass spectrometry in collaboration with Amanda Kieswetter and Liesbet Temmerman at KU Leuven. We found 15 new proneuropeptides and confirmed the endogenous processing (cleavage, amidation etc) of many of them. #Nematostella has at least 33 neuropeptide precursors.
#cnidaria #neuroscience

And finally, some skills that will be helpful: #bioinformatic and #statistical skills: population genetics/#genomics, quantitative genetics, #RNAseq, #ATACseq, integration of #multi_omics data; willingness to get involved in data generation (wet lab) is a plus.

A lot of software can provide genotype likelihood for a #WGS #NGS sample, only one I know provide the likelihood of ALL 10 genotypes for a site, i.e. ANGSD.

Anyone knows any software that calculate all allele likelihood for a site? So I wanna know the probability of observing allele A, C, G, and T in a site. The ones I found only provide probability of one allele (consensus/random).

#Genomics #genomic #PopulationGenomics #bioinformatic #compBio

:boost_ok: :boost_requested: :mastoread:

A lot of software can provide genotype likelihood for a #WGS #NGS sample, only one I know provide the likelihood of ALL 10 genotypes for a site, i.e. ANGSD.

Anyone knows any software that calculate all allele likelihood for a site? So I wanna know the probability of observing allele A, C, G, and T in a site. The ones I found only provide probability of one allele (consensus/random).

#Genomics #genomic #PopulationGenomics #bioinformatic #compBio

:boost_ok: :boost_requested: :mastoread:

👉
Last week our colleagues hosted #scientists from the State Scientific Research Institute of Laboratory Diagnostics and Veterinary and Sanitary Expertise in #Ukraine.

A productive week full of #training in serological methods for the detection of #antibodies against Crimean-Congo haemorrhagic fever virus and #bioinformatic tools as part of the German Biosecurity Programme, funded by the German Federal Foreign Office, lies behind the scientists. @AuswaertigesAmt

👉
Last week our colleagues hosted #scientists from the State Scientific Research Institute of Laboratory Diagnostics and Veterinary and Sanitary Expertise in #Ukraine.

A productive week full of #training in serological methods for the detection of #antibodies against Crimean-Congo haemorrhagic fever virus and #bioinformatic tools as part of the German Biosecurity Programme, funded by the German Federal Foreign Office, lies behind the scientists. @AuswaertigesAmt

Hello #ScienceMastodon #AcademicMastodon !

#introduction: My name is Selene Fernández, an I'm a researcher interested in all things #RNA in particular #lncRNAs and their #evolutionarydynamics. My group, the #RegRNALab focuses on studying #lncRNAs in plants 🌱 and animals (flies, 🦎, humans) using #genomic and #bioinformatic approaches.

Other interests include promoting #WomenInSTEM , #reading , #dancing , #scuba_diving and #languages (🇫🇷, 🇬🇧, 🇪🇸, 🇵🇹, 🇯🇵)

Curious to see how this community evolves 😉

Hello #ScienceMastodon #AcademicMastodon !

#introduction: My name is Selene Fernández, an I'm a researcher interested in all things #RNA in particular #lncRNAs and their #evolutionarydynamics. My group, the #RegRNALab focuses on studying #lncRNAs in plants 🌱 and animals (flies, 🦎, humans) using #genomic and #bioinformatic approaches.

Other interests include promoting #WomenInSTEM , #reading , #dancing , #scuba_diving and #languages (🇫🇷, 🇬🇧, 🇪🇸, 🇵🇹, 🇯🇵)

Curious to see how this community evolves 😉

Hello #ScienceMastodon #AcademicMastodon !

#introduction: My name is Selene Fernández, an I'm a researcher interested in all things #RNA in particular #lncRNAs and their #evolutionarydynamics. My group, the #RegRNALab focuses on studying #lncRNAs in plants 🌱 and animals (flies, 🦎, humans) using #genomic and #bioinformatic approaches.

Other interests include promoting #WomenInSTEM , #reading , #dancing , #scuba_diving and #languages (🇫🇷, 🇬🇧, 🇪🇸, 🇵🇹, 🇯🇵)

Curious to see how this community evolves 😉

Hello #ScienceMastodon #AcademicMastodon !

#introduction: My name is Selene Fernández, an I'm a researcher interested in all things #RNA in particular #lncRNAs and their #evolutionarydynamics. My group, the #RegRNALab focuses on studying #lncRNAs in plants 🌱 and animals (flies, 🦎, humans) using #genomic and #bioinformatic approaches.

Other interests include promoting #WomenInSTEM , #reading , #dancing , #scuba_diving and #languages (🇫🇷, 🇬🇧, 🇪🇸, 🇵🇹, 🇯🇵)

Curious to see how this community evolves 😉

Hello #ScienceMastodon #AcademicMastodon !

#introduction: My name is Selene Fernández an I'm a researcher interested in all things #RNA , in particular #lncRNAs and their #evolutionarydynamics. My group, the #RegRNALab focuses on studying #lncRNAs in plants 🌱 and animals (flies, 🦎, humans) using #genomic and #bioinformatic approaches.

Other interests include promoting #WomenInSTEM , #reading , #dancing , #scuba_diving and #languages (🇫🇷, 🇬🇧, 🇪🇸, 🇵🇹, 🇯🇵)

Curious to see how this community evolves 😉

Hello #ScienceMastodon #AcademicMastodon !

#introduction: My name is Selene Fernández an I'm a researcher interested in all things #RNA , in particular #lncRNAs and their #evolutionarydynamics. My group, the #RegRNALab focuses on studying #lncRNAs in plants 🌱 and animals (flies, 🦎, humans) using #genomic and #bioinformatic approaches.

Other interests include promoting #WomenInSTEM , #reading , #dancing , #scuba_diving and #languages (🇫🇷, 🇬🇧, 🇪🇸, 🇵🇹, 🇯🇵)

Curious to see how this community evolves 😉

Hello #ScienceMastodon #AcademicMastodon !

#introduction: My name is Selene Fernández an I'm a researcher interested in all things #RNA , in particular #lncRNAs and their #evolutionarydynamics. My group, the #RegRNALab focuses on studying #lncRNAs in plants 🌱 and animals (flies, 🦎, humans) using #genomic and #bioinformatic approaches.

Other interests include promoting #WomenInSTEM , #reading , #dancing , #scuba_diving and #languages (🇫🇷, 🇬🇧, 🇪🇸, 🇵🇹, 🇯🇵)

Curious to see how this community evolves 😉

Hello #ScienceMastodon #AcademicMastodon !

#introduction: My name is Selene Fernández an I'm a researcher interested in all things #RNA , in particular #lncRNAs and their #evolutionarydynamics. My group, the #RegRNALab focuses on studying #lncRNAs in plants 🌱 and animals (flies, 🦎, humans) using #genomic and #bioinformatic approaches.

Other interests include promoting #WomenInSTEM , #reading , #dancing , #scuba_diving and #languages (🇫🇷, 🇬🇧, 🇪🇸, 🇵🇹, 🇯🇵)

Curious to see how this community evolves 😉

@caterpillar_coevolution Sorry for becoming the bearer of bad news but the dopamine hit stops that moment you got that zero exit code along with empty output files.

#bioinformatic #hpc #Genomics

#Introduction

My name is Rory and I am a #molecular #microbiology researcher from the UK. My field of study is #epidemiology and #genomics of #AMR #bacteria from different niches around the world using #WGS #bioinformatic analysis.