Jochen Weile @jweile@qoto.org

TIL: GitHub supports callout boxes in their markdown rendering 🙌

https://github.com/orgs/community/discussions/16925

BioRxiv has joined forces with Company of Biologists to expand our presence on Mastodon.

Mastodon accounts now available for every subject category https://connect.biorxiv.org/news/2023/09/27/biorxiv_expands_on_social_platforms

“In a large study published in September 2022 ..researchers developed a tool that’s essentially a library of every conceivable change to the N-protein over time. They used deep mutational scanning to predict how each of those changes would affect the ability of 17 antibodies used in 11 commercially available rapid tests to latch onto the virus… can cross-reference changes in each new variant of the virus to quickly assess whether a given test will still work. “

https://www.cell.com/cell/fulltext/S0092-8674(22)01044-3

Our new #git #cheatsheet is ready for use, thanks to @SciCompAalto: https://aaltoscicomp.github.io/cheatsheets/git-the-way-you-need-it-cheatsheet.pdf

It's designed for beginners/intermediates to introduce things slowly, recognizing that most use is simple, and grouping advanced uses together how they are used. It'll be used in our workshop next week. #RSEng #HPC #teaching

For all the folks starting their #PhD (or their master thesis) today - a reminder why your PhD advisor can solve a problem so "easily" ...

#astrodon #academia #AcademiChatter #research

Deep mutational scanning reveals the functional constraints and evolutionary potential of the influenza A virus PB1 protein http://biorxiv.org/cgi/content/short/2023.08.27.554986v1?rss=1

Docking With AlphaFold Structures: Oops | Science | AAAS

#StructuralBiology #Alphafold @strucbio
https://www.science.org/content/blog-post/docking-alphafold-structures-oops

Writing or reviewing a manuscript? Watch out for these ten common statistical mistakes ⬇️ 6/n
#AcademicChatter #Writing #Academia #PhDlife #PhD #ECR #SciComm #ScholComm #Reproducibility #DataScience #DataAnalysis #Data #Research #Statistics
https://elifesciences.org/articles/48175?utm_source=mastodon&utm_medium=social&utm_campaign=organic

Code sharing increases citations but remains uncommon

https://doi.org/10.21203/rs.3.rs-3222221/v1

'We examine temporal trends in code sharing in ecology and evolution publications since 2010.

We find that scientists are overwhelmingly (95%) failing to publish their code.

We also find code sharing can considerably improve citations.'

#openscience #code #ecopubs

My favorite paper that I've read this year — a look at how confusion between inferential uncertainty and outcome variability creates all sorts of problems — is now out in PNAS.

Here's the paper: https://www.pnas.org/doi/abs/10.1073/pnas.2302491120

Here's the thread I wrote about the preprint last April: https://fediscience.org/@ct_bergstrom/110267907188002904

Optimizing #RShiny applications with webR is a game-changer 🤯 By leveraging browser-based computation, we witness a significant reduction in server load and enhanced responsiveness.

Dive deeper into the technical insights: https://appsilon.com/bringing-webr-into-shiny/

#webR #RStats

alright #rstats , no cheating -- without running it beforehand, what would you expect this code to do?

add <- function(a, b) {
a + b
} / 2

add(2, 4)

Just discovered there is an extension of #Inkscape to quickly edit scientific figures (change axis ratio, font sizes, etc) 🤩

https://github.com/burghoff/Scientific-Inkscape

The approach itself is implemented in multidms software package, which is available at https://github.com/matsengrp/multidms

We think it should also be useful to other labs performing deep mutational scanning across protein variants or selection conditions.

In new study, we develop rigorous method to jointly analyze deep mutational scanning of different protein homologs or conditions

We use it to identify mutations w effects on spike-mediated viral entry that differ by >1,000-fold among #SARSCoV2 strains.

https://www.biorxiv.org/content/10.1101/2023.07.31.551037v1

Is it left handed or this some sort of optical illusion? 🧐
---
RT @hajirasouliha
A DNA double helix molecule made of drones! #AGBT23
https://twitter.com/hajirasouliha/status/1623107978613211140

Announcing papertooter. Papertooter is a simple script that takes the URL of a biorxiv preprint, and posts the title and link to the paper on Mastodon using the Mastodon Python API. It also posts a unique hashtag it generates from the paper's DOI.

Feature requests and bug reports welcome.

https://github.com/idoerg/papertooter