Recent searches
Search options
#bioinformatics
:mega: April 2025 WikiPathways release: 454 edits by 10 contributors and 9 new pathways.
Accessible via #webservices, #rstats, Pathvisio, and Cytoscape. Supported by AWSOpen https://www.wikipathways.org/download.html
A few images from yesterdays first #HoloDeck presentation at Prof. Varshneys #lab at the #Indian Institute of #Science (#IISc) in #Bangalore (#India), where people enjoyed 'playing molecules'.
Holodeck, also known as the Rechenkraft.net #Molecular #AR Environment is our #OpenSource approach - based on the @tiltfive hardware - to visualize molecular #structures in #3D for #education & #research & #development purposes.
gen 
it seems I just released my first Pypi package every.
pyBacting 2.14 with Bacting 1.0.5 is now out: https://pypi.org/project/pybacting/0.2.14/
This gives you access in Python to (some of) the functionality of the Chemistry Development Kit, OPSIN, ChemSpider, PubChem, InChI, Excel files, BridgeDb, and BioJava
Cloud computing: where you're not just a bioinformatician, you’re also the finance manager, compliance officer, and IT support, all while carrying a hefty dose of mental fatigue. I miss those PhD days with a inhouse HPC when all you had to do was sbatch every parameter combo under the sun to test your research question… then complain about queue times and who was clogging the damn cluster with their BLAST jobs 
#bioinformatics
#Genetic data repo #OpenSNP to self-destruct before authoritarians weaponize it
The reason, according to #bioinformatics researcher Bastian Greshake Tzovaras, one of the founders of the project, is the dissolution of genetic testing biz #23andMe and the potential weaponization of genetic data by #farright #authoritarian regimes.
https://www.theregister.com/2025/04/01/opensnp_shutdown/
#Genomics
#Bioinformatics
#Academia
Beware US academic coders. If you have collaborators contributing code from a sanctioned region, your repos may be locked.
See https://mastodon.social/@organicmaps/114155428924741370
The kicker is that the US is leaning authoritarian and all in on censorship. If Canada or Mexico become sanction targets and you have code pushes from there, Microsoft will lock you out of your GitHub accounts.
Does anyone have any posts or past toots they could reshare about how they have setup or are working within a team in #bioinformatics, #genomics, #research etc. things that how worked or haven’t worked, organising and sharing projects and code, notes and documentation, collaboration and communication, software, network and local or cloud compute arrangement. Always find reading others experiences insightful and beneficial.
How does everyone organise all their projects on #GitHub within their teams, like projects into groups or topics? naming schemes or have you switched to #GitLab for this feature?
#research #genomics #bioinformatics
I like to remind people, if you want less of my human rights, future, open science, and other opiniatied posts, follow my #cheminformatics and #bioinformatics account at @egonw@social.edu.nl
Of course, I love you to stay here too, because I honestly believe in a better future and am hopeful. But hoping is not enough, hence my posts here.
very exciting Google Summer of Code project idea around @wikipathways for a great student with a lot of enthusiasm and drive to learn a lot of new things and get things done! https://github.com/nrnb/GoogleSummerOfCode/issues/264
Creating #Python tools for biological sequence analysis? #EuroSciPy2025 is seeking proposals on genomic data parsing, phylogenetics, and structural #bioinformatics.
Show us how you're decoding life's data! #ComputationalBiology
Or you don't feel like going to USA you might prefer to come to #Barcelona on September for #rstats and #bioinformatics at #EuroBioc2025: also with time for abstract submissions https://eurobioc2025.bioconductor.org/
The weather is still sunny and hot on September 
#rstats Bioconductor conference is with Galaxy #bioinformatics. There is still some time for early registration (and abstract submission). https://gbcc2025.bioconductor.org/
As I face the prospect of analyzing a dataset with 3 variables: time (3 time points), temperature (2), exposure to chemical (2); but only 2 biological replicates, please, people, consult a biostatistician before doing your experiments.
Please, please, please, talk to someone in data analysis *before* running these kinds of experiments. If there isn't enough money for *more samples*, drop one of the factors so there are more "N" for the remaining ones.
Scolary helps you find the best scientific software tools for your workflow:
It includes 170 tools for searching for information:
https://scolary.com/category/exploring/searching
It includes 21 tools related to machine learning:
https://scolary.com/search?q=machine%20learning
March 2025 WikiPathways release: 1,297 edits by 6 contributors and 1 new pathway
Accessible via #webservices, #rstats, Pathvisio, and Cytoscape. Supported by AWSOpen https://www.wikipathways.org/download.html
@BenjaminHCCarr I'm obviously biased, but I couldn't agree more!
That's why we offer #Degree level #apprenticeship programmes covering #softwareengineering #network engineering and #datascience (for which we offer both generalised #data science and #bioinformatics routes).
https://www.aru.ac.uk/study/degree-apprenticeships/employer/our-courses
@faassen
Thanks for this! Great post.
3/8 
For the first time (or do update us), we've modelled dynamic, plant gene circuits with absolute units for both RNA and protein copies per cell.
You can compare our mathematical models directly to your biochemical data. Over time, both approaches should benefit! #SystemsBiology
4/8 
Those absolute units mean that we can predict the DNA-binding dissociation constants (Kd) of our clock transcription factors in vivo, for example.
After some tricky calibration, we estimated comparable Kd values in vitro from our earlier data and the literature, extending the method to any promoter sequence (more on this later).
So, did they match?