Apple pie @applepie@social.cleverlibre.org

Let's follow up yesterday's post with another from my archive, this time a guide to #HighPerformanceComputing!

I wrote this as a cheat sheet to remind myself of a few things when I was new to using a #ClusterComputer, and it turned into a resource I often point new students to. It runs through connecting via SSH, installing Python and using SLURM.

Maybe some of you here on #ScienceMastodon might get some use out of it too!

https://www.steventhomson.co.uk/post/hpc_guide/

#HPC #computing #cluster #slurm #Python

#introduction I’m a Royal Society research fellow at UCL where my lab uses computational biology to study how mutations cause disease, with a special interest in #aging and #cancer!

Our research covers multiple scales- how mutations change proteins to trigger disease, how genes coordinate to control cell behaviour, and how cells compete and interact in the tissue to cause disease! Check out my lab website for more info https://www.hall-lab.com/ #sciencemastodon

*Incredible* {ggplot2} ↔Observable interactive explainer by @allison_horst !!!!!

https://observablehq.com/@observablehq/plot-from-ggplot2

Deadline 16 November: #postdoc position for someone interested in #microbiomes and #bioinformatics! Be part of a large team and compare a clinical #IBD cohort with a large general population cohort.

https://www.jobbnorge.no/en/available-jobs/job/231369/postdoctoral-fellow-in-bioinformatics-and-the-human-intestinal-microbiome?s=09

Very cool preprint from Bin Wu's lab.
They found bursting behavior of #translation by #SingleMolecule #mRNA #imaging in live cells, which is modulated by 5'UTR.
@biorxivpreprint

https://www.biorxiv.org/content/10.1101/2022.11.07.515520v1

Never thought Elon Musk would do so much for the adoption of a decentralised infrastructure…

Please Elon, can you buy Elsevier ?

I will give a talk today (15:30 CET) about

✨ How to improve research quality through Research Software Engineering #RSEng and #OpenScience ✨

Event infos: https://www.helmholtz-hirse.de/events/2022_11_10-seminar_8.html
(send and email to sign up 📧 anyone can join)

Slides: https://docs.google.com/presentation/d/1xTneE2vsrXDCO9bN-yJK4xgQqAV1CjoTUMMdKoLPzyk/edit?usp=sharing

Have just realised that #academics can use @ORCID_Org to
#verify themselves.

Just include your full mastodon link (like this: https://mas.to/@marekmcgann) in the "Websites and Social Links" section in ORCID, then include link to your ORCID record in your Mastodon profile.

Hurray for distributed digital identities!

I spent a very valuable hour tonight talking on the phone with a good friend in #Biomanufacturing. Her research is in #Upstream process development for fancy #AAV #GeneTherapy stuff. Her work is all very much "If we figure this out it will massively change the lives of millions of people someday! Unless it doesn't work and my research ends up as a footnote..."

BUT WAIT...most good #Science is built on footnotes! Footnotes are actually the bones of the researchers who found out their ideas didn't work. They did it right, but they were wrong. Most science is TOTALLY the future. Right up until the moment it's NOT...

It's important to remember that none of the people in footnotes were failures.

Long ago I did frontier research and I know the rewards of that life. I also know the feeling of seeing data from the international community CRUSH YOU because your paradigm was proven false. That's life in science. No one figures anything out alone.

In contrast to my friend, my work is as a #GMP #Downstream #QualityControl analyst in #Biomanufacturing. My job is to make sure we make the known science work. We make it work EVERY TIME.

I'm results-focused because the comparatively mundane #biotherapeutics I help produce go in patients every day. Therapeutic #Proteins like the ones that combat #Autoimmune #Disease are a massive benefit to society. I didn't develop any of these therapies but I make sure no one dies because of a mistake at the factory.

So I don't push any boundaries as a scientist. I very much make sure to NEVER push boundaries. NEVER EVER. Pushing boundaries is a problem. I'm here to execute.

So all I can leave you with is this: Is science a series of questions, or a series of answers?

What do we really need more? I've always struggled with this. I still don't know.

If you're honest and remember reading Kuhn, you know science has never proven anything. But wow we've had some results.

Go out.
Never settle.
Demand results.

If you download your Twitter archive it arrives wrapped as a static HTML page, which is not very useful for doing anything with, and worse: it requires the original account to be still active to do useful things like enlarge the images since they use t.co links.

So here's a Python script to convert a Twitter archive to markdown or other formats: https://github.com/timhutton/twitter-archive-parser

Now you can archive your tweets in any way you want.

Just a reminder about Mastodon.

Try not to directly upload videos here.
You have to remember that these videos have to be stored on the server that you're hosted on.

This would also eat up on available bandwidth, storage and memory resources of said servers and slow them down. Which would force server hosts to upgrade at a substantial cost.

Suggested idea...

Upload to YouTube, Vimeo or other video streaming services and share the link to the video here instead.

Hello #MassSpec and #proteomics friends:

What tutorial are you missing to analyse your MS and/or quantitative proteomics data?

📢 📢 Exciting chance to come join us on a #rotation-based, 4 year, international #PhDStudentship- include our #TubulinCode project! Closing date: 9th January 2023. #imaging #cytoskeleton #cilia #ciliopathies #GenomeSurgery #RareDisease Message me, if you want to hear more! 📢 📢

More info: https://www.ed.ac.uk/mrc-human-genetics-unit/graduate-research-and-training/four-yr-international-prog-human-genetics-genomic

In patients with advanced head and neck squamous cell carcinoma.
#Immunotherapy #TumorImmunology #Preprint

"Through a combination of single-cell analyses by mass cytometry (CyTOF), single-cell RNA-sequencing and TCR- sequencing (sc-RNA+TCR-seq), single cell RNA- and protein-sequencing (CITE-Seq), and multiplexed ion beam imaging (MIBI), we examined CD8+ T cells across tissues from patients treated with surgery as standard of care as well as patients treated with perioperative anti-PD-L1 ICB (atezolizumab)"

https://www.biorxiv.org/content/10.1101/2022.11.08.513062v1

New #preprint from our lab:

kegg_pull: a Software Package for the RESTful Access and Pulling from The Kyoto Encyclopedia of Gene and Genomes

https://www.biorxiv.org/content/10.1101/2022.11.03.515120v1.full

Staff scientist Eric Huckvale's first project has been to write a new #python 📦 to query KEGG's REST API (prelude to other work we want to do w/ KEGG data).

Other stuff we found didn't provide the options we wanted, so you all get to benefit too!

#bioinformatics #metabolomics

My students often struggle with selection bias and measurement error bias in linear regression models. So I have made a couple of Shiny apps to help visualize these concepts.
Selection bias: https://apps.biostat.au.dk/stefan/selection/
Measurement error: https://apps.biostat.au.dk/stefan/measurementerror/

Feel free to use them in your teaching #rstats #datascience #stats

Code is available at my GitHub.

First post here, so be nice

#introduction #sciencemastodon #twittermigration #virology

I'm a Staff Scientist at Seattle Children's. I develop highly accurate long-read #sequencing approaches to understand host-pathogen interactions through the lens of #genomics. Currently working on projects related to viral evolution, transcriptional regulation, and mutational profiling. Originally from Argentina, but now a US West Coaster. Will also post about photography, music, social justice, entrepreneurship, and biotech.

#bioinformatics #introduction Hello Tooters! I’m George, I head up bioinformatics at the MRC LMS. Reformed immunologist, retro/virologist, repetitive elements, genomes, *seq, #nextflow. Let’s see what Mastodon can do for us all!

Hey everyone !

Time for my #science #introduction

I am the PI of the @cellcommlab @ the UKE in Hamburg, Germany. We use #microscopy & #imageanalysis to study how cells move & communicate.

I am from #Chile, where I did my #PhD at PUC, then moved to Paris to work at the Institut Curie and IPGG.

After quite some years in #science (20 since I started my BSc !) I keep my fascination to observe how cells do things, like these migrating leukocytes.

#scicomm #sciencemastodon #nomoa

@5uie1 @mttaggart @cruzin

About using #Emacs #orgroam on the go: I found the android app Orgzly on Fdroid, a note taker that produces #orgmode files which can be imported to org-roam. The import is necessary as the mobile cannot know what node id's to use — I have the same trouble importing my LinkedIn posts, I could transform them or orgmode, but then had to script a load-and-save on each file to integrate with my graph.