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.
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)
PhD position in viral evolution and diversity @foaylward
See the full job description on jobRxiv: 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
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
10 years ago today, I successfully defended my thesis and became, Dr. Simon P. Skinner.
Postdoctoral Fellow Position in Computational Biology
National Cancer Institute
See the full job description on jobRxiv: 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"
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.
🔍 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
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.
@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
Even more exciting news soon… 😎
Computational Post-doctoral position in San Diego, CA
University of California San Diego (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
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.
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.
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
Two new bioinformatics jobs currently open at WEHI:
Casual Biostatistician/Statistical Bioinformatician
Bioinformatics Research Officer or Research Assistant—Parental Leave Replacement.
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
`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!
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.
Thank you for following our journey, and get ready to GO ELECTRO (and more) in 2024!
According to some random guy on the internet #bioinformatics is only for biologists. Guess, I'm doing it wrong. 🤷♂️
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
A lethal fungus with unprecedented abilities to evade the immune system:
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.
PhD Position in Systems Medicine of host-microbiome interactions
Heidelberg University, Medical Faculty
See the full job description on jobRxiv: https://jobrxiv.org/job/heidelberg-university-med...
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
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)
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
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.
Today's learning resource
Have you tried the CRISPR-based map that ties every human gene to its job function?
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
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 🙏
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.
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.
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
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.
The following thread describes why you want me on your team
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.
Fully formatted, #peer reviewed and #openaccess at
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.
- Molecular Biology
- Dynamical systems (ODEs)
- Systems Biology
Currently I am promoting the field of Computational Biology in Colombia: https://biologia-computacional.github.io/
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.
@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.
"#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
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
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 👋 🇦🇺
That's all for today!
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/
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:
So, please meet: