#Bioinformatics

Metabolic exchanges are ubiquitous in natural microbial communities
https://doi.org/10.1038/s41564-023-01511-x
#microbiology #bioinformatics

Machine learning for microbiologists
https://doi.org/10.1038/s41579-023-00984-1
#microbiology #bioinformatics

Alignment-based Protein Mutational Landscape Prediction: Doing More with Less
https://doi.org/10.1093/gbe/evad201
#microbiology #bioinformatics

Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems
https://doi.org/10.1038/s43705-023-00333-6
#microbiology #bioinformatics

Data Scientist (LLM and semantic data engineer) position at @SIB https://apply.refline.ch/499599/0305/pub/1/index.html #LLM #bioinformatics #job

#kerblam is viable! I'll make the first beta release tonight.

If you do #datascience, #bioinformatics or any sort of data processing that needs to be reproducible, perhaps kerblam will be useful to you!

Let me know of any problems or thoughts that you can think of! I'd greatly appreciate any feedback.
(github stars also make my day if you want to leave one thanks luv you)

https://github.com/MrHedmad/kerblam

We run #apprenticeships for #LabScience and #Bioinformatics so we have an interest in the #FestivalOfGenomics, is anyone from here going?

https://festivalofgenomics.com/london/en/page/home

PhD position in viral evolution and diversity @foaylward

Virginia Tech

Funded PhD positions in the Aylward Lab to study the #evolution and #genomics of giant #viruses. Both computational and wet-lab projects available.

See the full job description on jobRxiv: https://jobrxiv.org/job/virginia-tech-27778-funded-phd-position/?feed_id=67074

#bioinformatics #evolution #genomics #metagenomics #virology...
https://jobrxiv.org/job/virginia-tech-27778-funded-phd-position/?feed_id=67074

Postdoc in biostatistics or bioinformatics

Icahn School of Medicine at Mount Sinai

#bioinformatics postdoc opportunity in #NYC working on rare diseases

See the full job description on jobRxiv: https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postdoc-in-biostatistics-or-bioinformatics/?feed_id=67067

#genetics #genomics #human_disease #human_g...
https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postdoc-in-biostatistics-or-bioinformatics/?feed_id=67067

10 years ago today, I successfully defended my thesis and became, Dr. Simon P. Skinner.

🔗 https://scholarlypublications.universiteitleiden.nl/access/item%3A2936021/download

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

#biochemistry #bioinformatics #biology #biophysics #chemistry #CompChem #metabolomics #NMR #NMRChat #NMROnline #physics #StructuralBiology

We are looking for a colleague! Assistant/associate professor machine learning in bioinformatics at Wageningen University https://www.wur.nl/en/vacancy/assistantassociate-professor-machine-learning-in-bioinformatics.htm
#Bioinformatics #MachineLearning #WUR #AssistantProfessor #AssociateProfessor

Postdoctoral Fellow Position in Computational Biology

National Cancer Institute

Come join us at the #NCI as a #bioinformatics postdoc

See the full job description on jobRxiv: https://jobrxiv.org/job/national-cancer-institute-27778-postdoctoral-fellow-position-in-computational-biology/?feed_id=66980

#ScienceJobs #hiring #research
Bethesda #UnitedStatesUS #Bioinfor...
https://jobrxiv.org/job/national-cancer-institute-27778-postdoctoral-fellow-position-in-computational-biology/?feed_id=66980

For scRNA-seq and scATAC-seq, have people been using "reads" as the important measurement instead of "fragments" for the past few years? Because this paper seems to suggest people have been unintentionally over-inflating the variance in their data by counting "reads"

https://www.nature.com/articles/s41592-023-02112-6/figures/1

I thought we we figured this out a long time ago with the whole "RPKM vs FPKM vs TPM" debate in bulk RNA-seq years ago.

#single_cell #rnaseq #atacseq #compBio #bioinformatics

❤I share my Medium Stories with yoy ! There are 33 stories with topics about networkscience, open source tools, neuroscience, gephi tutorials,
among others.

👉https://medium.com/@vespinozag

#Gephi #NodeXL #networkscience #DataVisualization #postdoc #MachineLearning #DataScience #Bioinformatics #PhD

I am very happy to see the publication of WOMBAT-P is finally out, which is based on the @elixir_europe #proteomics implementation study. If you want to #benchmark #bioinformatics tools in proteomics, have a look!
Thanks to all the authors!

https://doi.org/10.1021/acs.jproteome.3c00636

Pensez à vous inscrire et à soumettre vos présentations (jeunes chercheurs/chercheuses bienvenues ! !). Pour assister dans une ambiance chaleureuse et bienveillante à ALPHY 2024 alphy2024.sciencesconf.org
#PopGen #bioinformatics

🔍 Want a swift way to sift through a VCF file's data lines without wading through the meta-info jungle? Simplify with `sed` and pipe it into `head` or `more`.

Check out the full post here 🔗 https://lpembleton.rbind.io/ramblings/bash/#extract-data-lines-from-a-vcf-file

#Bioinformatics

Unix: Files are great, let's use them for everything.
Linux: File systems are great, let's use them for everything.
#Bioinformatics: File formats are great, let's use them for everything.

HN: Movi: a fast and cache-efficient full-text pangenome index https://news.ycombinator.com/item?id=38485293 & co. #bioinformatics #genomics

@bioconductor As I gave the Voyager presentation again, I feel like the Bioconductor conference is the most enjoyable due to the social aspects. I like the walking tour and dinner, keynote from the patient's perspective, and talks and discussions on the community such as translating documentation. The table configuration this year also made it less daunting to talk to others and I had dinner with these new friends. Not all comp-bio conferences have those. #academia #bioinformatics

Recommended reading for all researchers
Data Management for Researchers By Dr Kristin Briney
https://www.amazon.com.au/Data-Management-Researchers-Kristin-Briney/dp/1784270113
#Genomics #bioinformatics

If anyone is looking for the WGCNA tutorials while the Horvath's lab website has been down for a while, there's a Dropbox link with all the tutorials here: https://bioinformatics.stackexchange.com/a/21886

#bioinformatics

The #GraphicDesign phase of an awesome external #NMR project is complete!

Even more exciting news soon… 😎

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

#biochemistry #bioinformatics #biology #biophysics #chemistry #CompChem #metabolomics #NMRChat #NMROnline #physics #SoftwareDevelopment #SoftwareEngineering #StructuralBiology #WebDev

Computational Post-doctoral position in San Diego, CA

University of California San Diego (UCSD)

#bioinformatics postdoc #UCSD

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-california-san-diego-ucsd-27778-computational-post-doctoral-position-in-san-diego-ca-3/?feed_id=66573

#ScienceJobs #hiring #research
San Diego #U...
https://jobrxiv.org/job/university-of-california-san-diego-ucsd-27778-computational-post-doctoral-position-in-san-diego-ca-3/?feed_id=66573

How do people feel about short reads alignment accuracy for minimap2? I'm primarily working long reads with minimap2 anyway, so maybe I should consolidate instead of switching between bwa and minimap2.
Just talking within microbial/phage genome contexts.

#bioinformatics

#AI under the #microscope: The #algorithms powering the search for cells:
https://www.nature.com/articles/d41586-023-03722-y #ML #MachineLearning #bioinformatics #microscopy #imaging

Noticed my old #introduction was a bit outdated, so here's a new one.

I'm a computer scientist, bioinformatician and sometimes applied mathematician, using and developing machine learning methods for biology and health care. I mostly work on genomics data, but also on small organic molecules and electronic health records.

ME/CFS is affecting every area of my life, including how much I work and go out of my home.

#bioinformatics #machineLearning #genomics

1/2

@cyrilpedia nice study that. IL1-RA often forgotten as a regulatory element. I see it come up often in transcriptomic data, often with proinflammatory cytokines - often wondered if that's an inbuilt counter regulatory homeostatic mechanism. #immunology #bioinformatics

I just stumbled over TFlink which is a type of aggregator of databases of transcription factor targets. I will be using this for pathway analysis to understand RNA expression and chromatin modifications #Genomics #Epigenetics #bioinformatics
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9480832/

Two new bioinformatics jobs currently open at WEHI:

Casual Biostatistician/Statistical Bioinformatician
https://wehi.wd3.myworkdayjobs.com/en-US/WEHI/job/Parkville-Victoria-Australia/Casual-Biostatistician-Statistical-Bioinformatician_JR2296-1

and

Bioinformatics Research Officer or Research Assistant—Parental Leave Replacement.
https://wehi.wd3.myworkdayjobs.com/en-US/WEHI/details/Bioinformatics-Research-Officer-or-Research-Assistant-Parental-Leave-Replacement_JR2328-1

#bioinformatics #getfedihired #jobs

#Bioinformatics
#Genomics
#Hivemind

Any votes for favorite method for de novo transcript assembly? I don't need genome-wide. There's just one locus that was the target of Cas9 in an experiment we're helping analyze. Bulk transfection for knockout with no clone selection. Supposedly the western showed no protein. But the RNA-Seq shows absolutely no difference in transcript levels. Trying to figure out if the target triggered isoform switching rather than out of frame for all transcripts.

At my workplace, we're looking into how we can support the processing of very large datasets in R. It would be wonderful if some bioinformaticians could answer a couple of questions to direct us to the problem points.

We're hoping that we can publish something out of this that will be helpful to everyone in the field: https://forms.office.com/r/jNd2cbEZkh

#rstats #bioinformatics

`kerblam run` (mostly) works!

With it, you can dynamically run different makefiles with different input data based on profiles, so you can break down different aspects of your #bioinformatics or #datascience analysis and run them with ease.

I'll iron out the bits that don't work tomorrow.

I'll post more "ads" for kerblam as I develop it. Mute #kerblam if you don't want to see them!

https://github.com/MrHedmad/kerblam

3 years ago today, we began Tweeting updates about our little #NMR hobby project.

It's hard to believe that what started as a lockdown activity, has grown to where we are now.

Life changing.

Thank you for following our journey, and get ready to GO ELECTRO (and more) in 2024!

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

#biochemistry #bioinformatics #biology #biophysics #chemistry #CompChem #metabolomics #NMRChat #NMROnline #physics #StructuralBiology

According to some random guy on the internet #bioinformatics is only for biologists. Guess, I'm doing it wrong. 🤷‍♂️

https://www.reddit.com/r/bioinformatics/comments/182y9ul/dont_do_bioinformatics_if_you_are_not_biologist

I made a dumb little meme to try & prompt a bit of conversation about how to bridge the #skillsgap with #Apprenticeships

I really want to connect with #UK folk who need #DataScientists (including #Bioinformatics & #ComputationalBiology) #LabScientists #SeniorLeaders #DigitalMarketers & #Managers

I hear a lot about #skills shortages, but see less action to address them.

I've got access to a big part of the puzzle, but I need exceptional partners to work with on it.

#openai adalah salah satu start-up paling fenomenal di dunia ini, dengan produk andalannya yaitu #chatgpt 💪 . Namun, perkembangan perusahaan tersebut memasuki trajectory menarik ketika Sam Altman, CEO perusahaan tersebut, diberhentikan dewan komisarisnya pada tanggal 17 November kemarin 😳 .Apakah yang terjadi? Siapakah yang diuntungkan dengan kejadian tersebut? Kemudian, bagaimana #openai kedepannya? Mari kita simak sajian berikut ini! 😉 #bioinformatics #AI https://www.akurat.co/dunia/1303319733/drama-manajerial-openai-sebagai-dialektika-antara-idealisme-dan-pragmatisme

Just FYI, as announced earlier this week, we've stopped using X/Twitter (both our OBF account and BOSC) https://www.open-bio.org/2023/11/20/leaving-x/ - Mastodon users can follow us here or @BOSC for our annual #Bioinformatics #OpenSource conference specifically.

A lethal fungus with unprecedented abilities to evade the immune system:

Read the latest study led by Philippe Hauser (CHUV Lausanne), with SIB's Marco Pagni in charge of the #bioinformatics analyses, revealing a new molecular mechanism of #antigenic variation.

Link here: https://www.sib.swiss/news/a-lethal-fungus-with-unprecedented-abilities-to-evade-the-human-immune-system

#fungi #pathogen #ImmuneEvasion #immunology #pneumocystis #immunocompromised

Come work with us! I have a PhD position available to help understand which mutations in the non-coding parts of coding transcripts have functional consequences in Stem Cells.

We will using genome wide mesaurement of the effect of variation in miRNA binding sites to address when vairation causes changes in regulation and when it doesn't.

Mixed wetlab, bioinformatics and statistics project.

https://www.findaphd.com/phds/project/white-rose-bbsrc-dtp-how-can-we-identify-variants-in-untranslated-rna-that-affect-stem-cells/?p160958

#phdPosition #PhD #bioinformatics #UTR #miRNA #genetics

PhD Position in Systems Medicine of host-microbiome interactions

Heidelberg University, Medical Faculty

Come join us in #Heidelberg as a PhD student in an international collaboration to study host-microbiome interactions in the gut using #bioinformatics.

See the full job description on jobRxiv: https://jobrxiv.org/job/heidelberg-university-med...
https://jobrxiv.org/job/heidelberg-university-medical-faculty-27778-phd-position-in-systems-medicine-of-host-microbiome-interactions/?feed_id=66016

hey so the prof gave us this stupid fucking task

we have a pdb file that has the HELIX and SHEET entries

and we are supposed to compare the first and last residues of the sheets and helixes

to the same file with the whole header cut off, so like, comparing to whatever pymol autogenerates

"well how are we supposed to do this, manually try to select the residues to match up with the secondary structures shown by pymol?"
"yeah that's probably the easiest way"

and thus, I really want to automate this because fuck no I am not manually finding 30 residues that line up with the secondary structure

the closest thing I found is this but it doesn't fucking work https://pymol-users.narkive.com/pi4Jp9uI/pymol-how-to-export-secondary-structure-information-from-a-pdb-using-pymol#post2

I'm now trying to find any API docs for fucking pymol, because you can run python code in the console right?

but trying to find what the fuck chempy.Atom or chempy.models.Indexed are is just fucking impossible

these do not exist in the docs of chempy

unless pymol has it's own package different from the shit on pypi and gives zero fucks about the name collision

but I couldn't find any documentation implying that either

I am losing my fucking mind rn

#bioinformatics

The F in #bioinformatics stands for file format conversions.

I am very excited to announce the interactive paper for my "langevitour" widget is now published in The R Journal. Langevitour is a Javascript widget for touring 2D projections of high-D data, which I demonstrate using #scrnaseq data. It's a scatter-plot with a statistical physics engine. The figures in the paper move and are interactive, and can also be controlled using buttons in the text itself.
#rstats #javascript #dataviz #bioinformatics

https://journal.r-project.org/articles/RJ-2023-046/

Opinion

Heatmaps are better than cladograms.

#bioinformatics #phylogenetics

I’ve an exciting week teaching #bioinformatics to Genetics undergraduates. We begin with the 2 classic pillars of bioinformatics: Intro to the Unix command line, and Wrangling Miscellaneous Sequence Files. We’re then looking at 16S community data of human arms and legs that @domino_joyce & students generated on a minION last week. Cool stuff

As the 4th year panic of doctoral studies comes in, I’m beginning the early stages of probing jobs…seems like a lot of tech research postings are exclusively looking for experience in Python/ML. Any insights on the market for people with expert level #r / #rstats programming and strong knowledge working in #c ? Is it worth going back to Python for some pet projects to make my resume more industry-friendly? #jobs #jobtalk #bioinformatics #compsci #research #industry

Computational Post-doctoral position in San Diego, CA

University of California San Diego (UCSD)

#bioinformatics postdoc #UCSD

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-california-san-diego-ucsd-27778-computational-post-doctoral-position-in-san-diego-ca-3/?feed_id=64074

#ScienceJobs #hiring #research
San Diego #U...
https://jobrxiv.org/job/university-of-california-san-diego-ucsd-27778-computational-post-doctoral-position-in-san-diego-ca-3/?feed_id=64074

Second edition of the R Bioinformatics Cookbook Functional programming in R with purrr, working with the latest tools in tidyverse, ggplot2, RNAseq, genomics workflows, work with reproducible environments and use ChatGPT in R #Bioinformatics #datascience packt.link/5jWrC

We are looking for a postdoc to work on mechanisms of DNA damage and repair at regulatory elements in neurodegenerative disease. Needs to be capable in both computation and lab. Because of this, better than average salary (for UK postdocs) available.

https://www.jobs.ac.uk/job/DDN708/research-associate-in-genomic-stability

#academicchatter #bioinformatics #jobs #postdoc

Passionate about #opensource and #openaccess? Consider joining JOSS as an editor!

See this link:
https://fosstodon.org/@arfon/111205009417828311

We could use help in many domains, including #bioinformatics, #biomedical engineering, and #MaterialScience

Sowas liebe ich ja. EULA Abfragen wenn man seine Skripte headless laufen lassen will auf dem Cluster. 🙄

#Bioinformatik
#Snakemake
#bioinformatics

Today's learning resource

Understanding the difference between #ComputationalBiology & #Bioinformatics
and what each is used for.

https://graduate.northeastern.edu/resources/computational-biology-vs-bioinformatics/

#STEM #science #education #computerScience #biology #lifelongLearning
--------------------------------
For Students/Researchers :

Have you tried the CRISPR-based map that ties every human gene to its job function?

https://news.mit.edu/2022/crispr-based-map-ties-every-human-gene-to-its-function-0609

https://gwps.wi.mit.edu/

#STEM #edtech #biology #genetics #genomics #fediscience #ScienceMastodon

I can finally communicate about it! Here is my last preprint: https://www.biorxiv.org/content/10.1101/2023.10.23.563600v1
It is part of a collaborative project between my official lab from Tel-Aviv and my host lab in Montpellier. #SexDet #TransposableElements #stem #bioinformatics

@elan Here's a #bioinformatics one https://github.com/Emiller88/Mastodon-Bioinformatics

https://nathanlesage.github.io/academics-on-mastodon/

Our recent review article "The five pillars of computational reproducibility: bioinformatics and beyond" has just been published 😀
I'm very thankful to everyone who contributed suggestions and critiques of our work including my colleagues, twitter friends and peer-reviewers 🙏
https://academic.oup.com/bib/article/24/6/bbad375/7326135
#Genomics
#Bioinformatics

Finally!
#excel #gene #names #data #bioinformatics
https://www.theverge.com/2023/10/21/23926585/microsoft-excel-misreading-dates-human-genes-conversion-fixed

I am looking for a new position in computational biology/bioinformatics preferably in #academia in the #USA.

I am an experienced Computational Biologist with eight years of post-PhD experience in applying computational methods across diverse domains, from molecular modeling to #highdimensional and #machinelearning based single-cell flow/mass cytometry and serum proteomics data analysis.

Any leads would be helpful.

#computationalbiology #bioinformatics #jobsearch #lookingforwork

OMG! I was literally adding a homebrew version of this
command by Stephen Turner
to all my dev environments.

📌 corner: Print the top left corner of a data frame.

Fellow bioinformaticians🧬🧪how often are you doing a glance check of your large genotype matrixes?
#Bioinformatics #Rstats
https://github.com/stephenturner/Tmisc

Bioinformatics position in Atlanta GA (USA CDC, citizens only).
Applications are being accepted for a bioinformatics position in the USA CDC's "Polio and Picornavirus Laboratory Branch". US citizens only. Starting at $104K/year.
https://www.usajobs.gov/job/753178900
#bioinformatics #job #publichealth

Just sent out the latest @OpenBio newsletter. You can also read it here: https://github.com/OBF/newsletter/blob/master/newsletters/2023-09.md #opensource #bioinformatics

#transposons #bioinformatics people: how do you find TEs in genomic reads directly? Just count k-mers and take the most abundant ones? I can't find any obvious choice in the TE-from-reads-software out there

@MrHedmad I think #snakemake is one of the most important #bioinformatics projects, maybe @johanneskoester would like a hand?

Any #openscience projects that need a hand in coding? I want to contribute to some projects (on Github, preferably) but I feel a bit intimidated, and I'm not sure where to start.

I'm fluent in #python and #rlang.

#bioinformatics

30 years ago today, ExPASy.org put online 3D protein structures from PDB, for the first time ever. From the good bye lecture of Amos Bairoch, retiring from his professor position at UNIGE (he's continuing as @SIB group leader). #otd #bioinformatics #pdb #expasy

I'm looking for a new job (remote or #PDX), please boost!

I am a research software engineer with 11 years experience developing interdisciplinary scientific software that is robust, #accessible, and user-friendly.

I have experience in population genetics, #BioInformatics, #ReproducibleResearch, and #PublicHealth. My main language is #RStats, but I can also speak #Python, #JavaScript, #Lua, #C, #XML, etc.

#GetFediHired #RSEng

The following thread describes why you want me on your team

1/

Anyone work at a company they like that's hiring #PhD #research interns for summer 2024? Interested in roles related to #ComputerScience #DataVisualization #ExplainableAI #Genomics #Bioinformatics #SoftwareEngineering #ML #interpretability #EDA #DataAnalytics

I'm a third year PhD student in Computer Science at an R1 university (completed MS coursework), and a dual citizen USA/EU :) Thanks for boosting! #GetFediHired

📢 Calling #Bioconductor community!

Our Social Media Working Group is evaluating Bioconductor presence on Twitter/X. We value your opinion! Please complete our short survey (< 5 mins) by **Tuesday, 3rd October** to help shape our communication strategies.

🔗 https://t.maze.co/187240083

#Bioinformatics #RStats #CommunityFeedback

Another new job at WEHI, this time for a Research Software Engineer in my team! https://wehi.wd3.myworkdayjobs.com/en-US/WEHI/job/Research-Computing-Engineer--Large-data-analytics-_JR2188-3

#Bioinformatics #FediHired #GetFediHired #Hiring #RSE #RStats

Final paper from Marine Duhamel's PhD and second installment of our project on the causes and consequences of #recombination suppression in #sex determining #Chromosomes

The dynamics of #transposable #elements accumulation in non-recombining regions

Fully formatted, #peer reviewed and #openaccess at
https://www.nature.com/articles/s41467-023-41413-4

#seXYevol #EvolutionaryBiology #bioinformatics #FungiFriday #Genomics

📢 Exciting News! 🚀 Don't miss out on this opportunity!

There are still a few seats left for our October courses. Ready to boost your data analysis skills? Join us now: https://physalia-courses.org/courses-workshops/ 💪📊

#DataAnalysis #Rstats #Genomics #Bioinformatics #Python #DataScience

Lessons learned:

1. Blogs can still be a useful source of info
2. Some topics remain useful for a very long time (even #bioinformatics explainers!)
3. Maintaining a blog is a really good way to improve your writing skills

#blogging #sciencewriting #sciencecommunication

Any bioinformaticians help me out?

I'm looking for a server/program/whatever that, given 2 protein sequences from organism X, will go away and hunt down a few hundred equivalent sequences from other organisms, and then look at evolutionary covariance (at an amino acid level) between the two proteins.

I'm looking to see if there is something out there that already does what I need, before going in. I'm certain there should be, but I can't find it yet.
#Bioinformatics

Are you interested in #metagenomics and #bioinformatics? Here is your chance to move to beautiful Ghent, Belgium for #FAIR science!

https://jobs.vib.be/j/61679/postdoctoral-scientist-meta-genomics-bioinformatics

Hi there!

I am a biologist working in the University of Antioquia, in Medellín, Colombia. I am mostly involved in #ComputationalBiology and #Bioinformatics, but I enjoy and work in other subjects too:

- Molecular Biology
- Genetics
- Dynamical systems (ODEs)
- Systems Biology
- Microbiology

I believe in #OpenScience and I could say that #Linux and free software changed my life.

Currently I am promoting the field of Computational Biology in Colombia: https://biologia-computacional.github.io/

#introduction

crosshap from my former PhD student Jacob Marsh is now out in Bioinformatics!

It's an R-based tool that visualises phenotype-haplotype-associations in a region of interest. We used it to explore population diversity around specific candidate genes; follow-up papers are under peer review.

Paper: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad518/7247532
Repo: https://jacobimarsh.github.io/crosshap/

#bioinformatics #genomics

I can see a lot of crossover potential here

#bioinformatics

@maxkennerly Ugh, I've got colleagues who do work on molecular tumor boards. What they can do is so constrained by this sort of methodolatry. It goes so far as to use the oncologist's recommendation as ground truth, regardless of the rigor of the #bioinformatics analysis, some old dude's gut takes precedence.

I am a chemist working in biology on the domains of #cheminformatics and #bioinformatics (currently) on questions in the fields of #drugDiscovery, #metabolomics, and #toxicology I strongly support #openScience

Yesterday I recorded a much-improved lecture on the rationale and methods of Label-Free Quantitation in LC-MS/MS #proteomics. I hope you enjoy it!
#bioinformatics #biostatistics
https://www.youtube.com/watch?v=AQchAPIfkGA

#trivia #bioinformatics

#SIB course:
"#Biodiversity #bioinformatics: from large-scale #phylogenomics to gene families and functions"
30.08-1.09 Lausanne #UNIL.
- key evolutionary concepts
- methodological approaches
- hands-on in comparative genomic analyses, protein-coding gene evolution and function across animal genomes, from model and non model species; using e.g. #OrthoDB, #BUSCO, #OMA @bgeedb
Trainers: @rmwaterhouse, N Glover, C Dessimoz, & me https://www.sib.swiss/training/course/20230830_COMGE #MolecularEvolution #Genomics #training

@scipy2023

Enjoying this year's SciPy Conference? Join the SciPy 2023 Group just by following @scipy2023

Folks who follow the chirp.social account & mention it in a post will get their post automatically boosted!

#SciPy #ScientificPython #Science #Python #MachineLearning #Astronomy #Physics #Bioinformatics #Biology #Neuroscience #Ocean #Geo #Atmospheric #DataScience #MaterialScience #Chemistry #OpenSource #FOSS

@SciPyConf @dillonniederhut @melissawm @sirhc @joshmoore @crazy4pi314 @ivanov

Announcing #SIB Comparative genomics course, taught by Christophe Dessimoz, Natasha Glover, @rmwaterhouse and myself, 30 August - 01 September in Lausanne #UNIL
• Introduction to molecular evolution & phylogenetics
• Orthology-focused arthropod comparative genomics
• Duplication of genes and genomes, expression
with #SIB resources #OMA, #Orthodb #BUSCO and @bgeedb #ortholog #orthologs #paralog #duplication #MolecularEvolution #Genomics #bioinformatics #training @P_Palagi https://www.sib.swiss/training/course/20230830_COMGE

Hi folx! It's been a minute since I did one of my #ConnectionList #Introduction #TwitterMigration posts, where I hand-pick accounts that you might like to follow, using my reach to more richly connect the #Fediverse :fediverse:

Dr @josephguillaume is a #researcher at the @ANUFennerSchool where he specialises in #model-based #science and #decision support. Joseph was a key contributor to the @AlgFuturesLab series of workshops 👋 🇦🇺

@ANUResearch is a new arrival to #Mastodon - great to see #ANU have an official presence here! This account posts about #research and #TechnologyTransfer and #ResearchTranslation 👋 🇦🇺

Dr @michealaxelsen is a Senior Lecturer in #InformationSystems at UQ #UniQueensland 👋 🇦🇺

Prof Janet Vertesi @cyberlyra is a #professor of #sociology at #Princeton @princeton specialising in #STS 👋 🇺🇸

@erici is a #soil #science student in #Naarm / #Melbourne, who is interested in #Microbiology and #BioInformatics 👋 🇦🇺

Professor Anne Pasek @Aepasek is a Professor at #TrentUniversity where she specialises in #ClimateChange, #DigitalInfrastructure and #EnergyPolitics 👋 🇨🇦

Dr @katrinagrant is an #ArtHistorian and #DigitalHumanities #researcher at #ANU, interested in #maps, #GLAM, #landscapes, #gardens and #museums 👋 🇦🇺

@datasociety is the non-profit #research institute that studies the social implications of #data-centric technologies and #automation #STS 👋

That's all for today!

Announcing my new #rstats package!

🐶 hlabud: HLA analysis in R

· Fetch data from IMGT and cache it locally
· Return convenient matrices for analysis

In the thread below, learn more about HLA and see examples of how to use #hlabud

#bioinformatics #immunology #genetics

https://github.com/slowkow/hlabud

I never thought I would be working in research of COVID but here I am working in the EPIVINF project, lead by IrsiCaixa (https://www.irsicaixa.es), I'll be working in HIV, COVID and epigenetic regulation, in the #DataManagement, #multiomics and #Bioinformatics with #rstats
More info: https://www.epivinf.eu/

📣 We're redesigning the #Bioconductor website and we need YOUR input!

Whether you're a wet lab biologist, expert developer or other, your perspectives will shape Bioconductor's future. Takes 5-10 minutes. Closes Friday June 23.

➡️https://t.maze.co/169169456

#Bioinformatics #rstats

Occasionally, I think about how to work effectively with #rstats. Currently, I am teaching my #bioinformatics courses with #RKWard again. I try to do most of it with packages from the base installation. #datatable is an exception. But otherwise, I like to use #within (very fast) instead of #mutate.
But there are more approaches, which are often simpler/faster/stable:

- https://github.com/matloff/TidyverseSkeptic/blob/master/RDesign.pdf
- https://davidhughjones.medium.com/dont-forget-non-tidyverse-solutions-979c870c7f3e

It's a while since I've written an #Introduction #Introductions #Connections #TwitterMigration post, where I use my large follower count to more richly connect the :fediverse:

So, please meet:

@alyssa - Alyssa is a #Linux hacker who works with #graphics drivers (THANK YOU!) and who is doing amazing things with #GPU stuff on Macs.

@adam42smith is Sebastian Karcher works in #qualitative #data at #Syracuse, and works closely with the @zotero project (also THANK YOU!)

@rachelcoldicutt researches #innovation and alternative #infrastructures, and helps build intentional #communities

@ed is Stefano Maffulli, the current Executive Director of the #OpenSource Initiative - @osi

@DianaOfPortland is Diana Larasen, and she works in #Leadership #Agility

@photocyte is Dr Tim Fallon, who is a #biologist, #biochemist and #genomics and #bioinformatics #postdoc at #UCSD

@bridgetbarrett is an incoming Assistant #Professor at CU Boulder in #Advertising - working in #MediaStudies and #SocialIdentity and #SocialMedia

Please share your own #ConnectionList - and help us create a strong and connected #Fediverse :fediverse: ❤️