@ExplainedByCats

Computational biochemist. Postdoc @ UCSF in the Grabe lab. @MDAnalysis core developer. Believes everything can be explained using cats.

Joined February 2017
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Read about our #MDAKits approach in our @SciPyConf paper "MDAKits: A Framework for FAIR-Compliant Molecular Simulation Analysis" conference.scipy.org/proceed… by @HighSpeedMode @lilyminium @ExplainedByCats @ianmkenney and funded by @czi . Create your MDAKit at mdakits.mdanalysis.org/
Schematic showing how MDAKits are part of process involving a registry, continuous integration and review, documentation, and publication.

ALT Schematic showing how MDAKits are part of process involving a registry, continuous integration and review, documentation, and publication.

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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…
Google Summer of Code 2023 with MDAnalysis.

ALT Google Summer of Code 2023 with MDAnalysis.

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Fiona Naughton retweeted
Irfan Alibay@HighSpeedMode21 Feb 2023
Please come by for a chat! I'll be there during breaks throughout the day too!
Fiona Naughton@ExplainedByCats21 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!
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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
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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…
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MDAnalysis is working to create a sustainable ecosystem of MDAKits, packages that use MDAnalysis. We've created a whitepaper outlining our plan; read more on our blog post here: mdanalysis.org/2022/08/24/md… We'd love to hear any feedback!
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MDAnalysis is hiring a #SoftwareDeveloper to help improve our teaching materials! Flexible contract: 1month FTE, $24/hour, $3,600. info + apply here: bit.ly/3Q0zfJP Deadline Sept 1st #compchem
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We are excited to announce the release of MDAnalysis 2.1.0! Updates include a new dielectric constant analysis module, parsing RDKit R/S chirality, improved H5MD support, Gromacs 2021 TPR support, and many more including several bug fixes mdanalysis.org/blog/#mdanaly…
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New to open source? Want to be mentored by experienced MDAnalysis developers? Work with us in #GSoC 2022 (Google Summer of Code by @GoogleOSS ) : read mdanalysis.org/2022/03/07/gs… to learn how to apply and get in touch!
Google Summer of Code logo

ALT Google Summer of Code logo

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Fiona Naughton retweeted
Irfan Alibay@HighSpeedMode17 Jan 2022
New preprint out on chemrxiv: chemrxiv.org/engage/chemrxiv… with @philbiggin @aniket_magarkar @SeeligerDaniel Feedback very much welcome!
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MDAnalysis is excited to be awarded a @cziscience EOSS4 grant for our proposal “MDAnalysis: Faster, extensible molecular analysis for reproducible science”. Read about our plan to improve performance and expand analyses into MDAKits in our blog post: mdanalysis.org/2021/08/31/CZ…
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Fiona Naughton retweeted
Irfan Alibay@HighSpeedMode24 Aug 2021
In virtual sci-mix row 6 if you want to come along for a chat - here's a copy of our poster (GitHub for now, zenodo later): github.com/IAlibay/MDAnalysi…
Irfan Alibay@HighSpeedMode22 Aug 2021
And it's now available! Lots of fun stuff in this release, if you're at #ACSFall2021 I'll be giving a COMP talk tomorrow at 5.40 pm EST on MDAnalysis 2.0 and the future. If you're attending a better talk (can't blame you 😜), I'll be in the virtual sci-mix Row 6 tomorrow.
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Replying to @HighSpeedMode
@HighSpeedMode is presenting in just under one hour (5.40 pm EST) in zoom room 10 (COMP molecular mechanics session). Otherwise find him during the virtual sci-mix session 8-10 pm. #ACSFall2021 #compchem #OpenSource
Irfan Alibay@HighSpeedMode22 Aug 2021
And it's now available! Lots of fun stuff in this release, if you're at #ACSFall2021 I'll be giving a COMP talk tomorrow at 5.40 pm EST on MDAnalysis 2.0 and the future. If you're attending a better talk (can't blame you 😜), I'll be in the virtual sci-mix Row 6 tomorrow.
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We are very excited to announce our two @gsoc 2021 students and their projects mdanalysis.org/2021/05/19/gs… : @ebojeda (curvature analysis of biological membranes) and @orion__archer (solvation analysis). #gsoc #compchem #moleculardynamics #OpenSource
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MDAnalysis version 1.1.1 is now out! The version 1 branch of MDAnalysis brings along a lot of fixes, changes, deprecations and enhancements. It will be followed by MDAnalysis 2.0 which will be python 3.6+ only. See our blog post for more details: mdanalysis.org/2021/05/02/re…
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If your project uses MDAnalysis, you can now let your users know with our shiny new "Powered by MDAnalysis" badge. See mdanalysis.org/pages/citatio… for code. Read more in the blog mdanalysis.org/2021/04/11/po…
Powered by MDAnalysis

ALT Powered by MDAnalysis

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We are excited to announce that @mdanalysis was selected to be a @gsoc organization again this year! Please see here fore more details, including possible projects: mdanalysis.org/2021/03/09/gs… The application deadline is April 13, if you are interested please get in touch early!
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Congratulations to our 3 #GSoC2020 students Yuxuan Zhuang, @cedricbouysset, @HugoMacdermott who sucessfully completed their #GSOC projects summerofcode.withgoogle.com/… . Read more about them in our blog mdanalysis.org/2020/09/10/gs…
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The final report for my GSoC project is here 😃 mdanalysis.org/2020/08/29/gs… It's a recap of the whole interoperability project between @mdanalysis and @RDKit_org with a demo of (existing and) upcoming features that I will detail next week in a blog post.
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Fiona Naughton retweeted
Irfan Alibay@HighSpeedMode22 Jun 2020
Today after ~ 2 years of contributions, my 50th PR for @mdanalysis was merged. It has been, and continues to be, a really fun project to contribute to 😀 Special thanks to @richardjgowers, @orbeckst, @lilyminium, @RoccoMeli, and @ExplainedByCats for all the help and reviews.
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