RSE @ OMSF (biomol MD, free energy calcs, etc...), @MDAnalysis and @openfreeenergy core developer | he/him - views are my own
Joined June 2009
- Tweets 825
- Following 322
- Followers 435
- Likes 2,144
59 Photos and videos
Pinned Tweet
24 Aug 2022
@mdanalysis #shiny sticker travelling journey: attending @orbeckst' COMP talk at s401d
23 Aug 2022
Love a sticker that has travelled more than I have 😂
2
6
Irfan Alibay retweeted
11 Aug 2023
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…
4
74
243
21,704
Irfan Alibay retweeted
4 Jul 2023
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
1
22
82
14,031
27 Jun 2023
Awesome work by @mikehenry42, alongside his previous push for py3.11 we can finally unblock a lot of the downstream ecosystem!
27 Jun 2023
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 🧵
2
218
Irfan Alibay retweeted
24 Apr 2023
🔥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
1
8
24
2,950
Irfan Alibay retweeted
7 Apr 2023
My team is recruiting an organic chemistry postdoc at LANL. Feel free to contact me directly.
2
13
12
5,159
Irfan Alibay retweeted
22 Feb 2023
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.
2
28
71
8,001
21 Feb 2023
Please come by for a chat! I'll be there during breaks throughout the day too!
21 Feb 2023
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!
2
3
13
1,604
21 Feb 2023
Link to the poster if you don't happen to be at #bps2023 github.com/IAlibay/MDAnalysi…
1
141
Irfan Alibay retweeted
18 Feb 2023
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 !
6
5
91
7,553
Irfan Alibay retweeted
30 Jan 2023
I'm still interviewing for some postdocs, especially those with some software and/or stats/ML background. lanl.jobs/search/jobdetails/…
6
7
1,906
Irfan Alibay retweeted
17 Jan 2023
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!
23 Nov 2022
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!
1
6
7
2,063
Irfan Alibay retweeted
13 Jan 2023
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.
1
8
19
8,057
Irfan Alibay retweeted
26 Dec 2022
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
8
36
4,819
Irfan Alibay retweeted
23 Nov 2022
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)
15
221
936
Irfan Alibay retweeted
10 Nov 2022
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…
1
7
23
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
2
19
63
Irfan Alibay retweeted
19 Sep 2022
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!
1
3
6
4 Sep 2022
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…
1
2
5
4 Sep 2022
As such, here is our planned release schedule:
Dec 2022 - v2.4.0
March 2023 - v2.5.0
June 2023 - v2.6.0
September 2023 - v3.0.0 (major API breaking changes)
1
1