RSE @ OMSF (biomol MD, free energy calcs, etc...), @MDAnalysis and @openfreeenergy core developer | he/him - views are my own
England, United Kingdom
Joined June 2009
- Tweets823
- Following320
- Followers433
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Irfan Alibay retweeted
Are you a new or prospective MDAnalysis user?
Join us for our online training workshop for a basic introduction to MDAnalysis and hands-on tutorials!
🗓️ October 25, 15:00 UTC
🔗 Apply by September 30: eventbrite.com/e/68163176796…
Irfan Alibay retweeted
The 2024 edition of the Free Energy Workshop will take place in Leiden, Netherlands, 13-15th May, 2024!
We have not yet opened registration, but you can already book the dates in your calendars.
Keep an eye on the wiki for further information: alchemistry.org/wiki/2024_Wo…
#alchemy2024
Awesome work by @mikehenry42, alongside his previous push for py3.11 we can finally unblock a lot of the downstream ecosystem!
Happy to announce @ambermdprog Ambertools 23 now has an osx-arm64 build on @condaforge 🚀
Now you can install ambertools without having to use Rosetta 2 emulation 🎉
Big thanks to @mwt_dev @jaime_rgp @ghutchis @hainm_comp @isuru_f for all of their help! 🙌
A few details 🧵
Irfan Alibay retweeted
🔥off the Arxiv press: SILVR a generative diffusion model for molecule generation from X-ray fragment data: arxiv.org/abs/2304.10905
✅ Conditioning for X-ray fragments
✅ Linking and merging X-ray fragments
✅ Molecules fit in binding site
❌ No retraining needed
Irfan Alibay retweeted
My team is recruiting an organic chemistry postdoc at LANL. Feel free to contact me directly.
Irfan Alibay retweeted
MDAnalysis will participate in #GSOC 2023! If you have some experience with #MD or other simulations at the molecular scale and if you like #coding to solve problems in #physics #chemistry #compchem #biochemistry #materialsscience is your thing: read mdanalysis.org/2023/02/22/gs…
ALT Google Summer of Code 2023 with MDAnalysis.
Please come by for a chat! I'll be there during breaks throughout the day too!
Last year, @MDAnlaysis released a whitepaper outlining our proposed "MDAKits" -> github.com/MDAnalysis/MDAKit…
For those at #bps2023, hear more at @HighSpeedMode's poster(B446) on MDA today
But first, let's take a quick walk through MDAKits+the idea behind them- with some cute cats!
Link to the poster if you don't happen to be at #bps2023 github.com/IAlibay/MDAnalysi…
Irfan Alibay retweeted
Attending #BPS2023 and want to become the proud owner of a shiny new @mdanalysis sticker or fridge magnet? Come find me (look for the blue hair 😜 ), @HighSpeedMode, @lilyminium or @orbeckst !
Irfan Alibay retweeted
I'm still interviewing for some postdocs, especially those with some software and/or stats/ML background. lanl.jobs/search/jobdetails/…
Irfan Alibay retweeted
Dear #compchem folks, please consider applying for the community manager position with @openmsf if you have a passion for open science, improving research tools and practices, and most importantly, finding better ways to support researchers in molecular sciences.
Please RT!
We are looking for a community manager to help us build efficient information flows for #opensource projects in molecular sciences, and herd cats in real and virtual spaces!🐱
Read the job description: omsf.io/about/careers/#commu…
Apply here: forms.gle/wMUu6eU82vzpnJPx9
Please RT!
Irfan Alibay retweeted
Anyone know folks at/working with Google Scholar? We're having some problems with how LiveCoMS journal articles appear in Google Scholar (many articles get collapsed into a single entry) and it would help if we can talk with a human about what we can do to improve the situation.
Irfan Alibay retweeted
Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale #cheminformatics
pubs.acs.org/doi/10.1021/acs…
@joshhorton93 @Yoshanuikabundi @dotsdl @rvkrishnan30 @davidlmobley @jchodera @cressetgroup @ColeGroupNCL
#vol62 #issue22 #JCIM #compchem
Irfan Alibay retweeted
Our preprint on OpenFold, our trainable reproduction of AlphaFold2, is finally up (biorxiv.org/cgi/content/shor…)! Since we open-sourced parameters in June, we've trained the model to high accuracy more than 50 times, on a variety of datasets. Here's what we learned (a lot) -> (1/19)
Irfan Alibay retweeted
We are excited to be awarded another CZI EOSS grant to expand our mentoring, teaching and community engagement efforts. We will be hiring a full time project manager, for more details:
mdanalysis.org/2022/11/10/CZ…
Apply by Dec 15th
We’re announcing 40 new grants to some of the most widely-used scientific #OpenSource software tools that are essential to science chanzuckerberg.com/eoss/prop…
Irfan Alibay retweeted
Hello #compchem! We want to change the license of @MDAnalysis from GPLv2+ to LGPLv3+. This means that you'll have more freedom in choosing your own license when you develop code that uses MDAnalysis. We want to get your thoughts! Details below 👇 #opensource #FOSS
Irfan Alibay retweeted
I'm at my first in-person event after a 3-year hiatus and I'm happy that it is #cziopensci 2022 event -- great to be at a place surrounded by so many people doing cool #openscience stuff.
Thanks to the #CZI team for organizing and inviting me on behalf of @openmsf!
With our recent revamping of our deployment infrastructure, 2.3.0 is the first of our releases on ~ 3 monthly schedule. Smaller updates, but with critical fixes delivered more timely.
MDAnalysis 2.3.0 is now out!
Updates include; improvements to PDB reading / writing (improved CONECT record handling and formal charges), a new RDF norm keyword, improved Universe serialization, and initial work on Cythonizing core MDAnalysis objects.
mdanalysis.org/blog/#mdanaly…