@mdanalysis

A python library to analyze and manipulate molecular dynamics trajectories

mdanalysis.org
Joined February 2014
  • Tweets361
  • Following40
  • Followers5.3K
65Media
MDAnalysis @mdanalysis.bsky.social retweeted
Brady Johnston@bradyajohnston17 Jul 2024
I have been working like absolute crazy over the past two months for this - #MolecularNodes 4.2 is now released for #b3d 4.2 A huge number of new features - which I will cover some here. - Selections using @mdanalysis selection language are updated live.
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MDAnalysis @mdanalysis.bsky.social retweeted
NumFOCUS
@NumFOCUS11 Jul 2024
Catch up on another round of the latest updates from our projects: June 2024 edition! hubs.la/Q02GgpkP0
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MDAnalysis @mdanalysis.bsky.social retweeted
Lily Wang@lilyminium27 Sep 2023
Replying to @HighSpeedMode
@HighSpeedMode digs into the health of the project in the State of the Union at the first @mdanalysis UGM
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MDAnalysis @mdanalysis.bsky.social retweeted
Soumith Chintala
@soumithchintala18 May 2023
Are you familiar with @NumFOCUS? It's a non-profit that sponsors numpy, pandas, jupyter, Julia, scikit, matplotlib, and more. They've had decreased funding this year, let's help. Donate to @NumFOCUS today, and I will match all donations up to $10,000 within the next 48 hours!
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MDAnalysis @mdanalysis.bsky.social retweeted
NumFOCUS
@NumFOCUS11 Apr 2023
Are you looking to advance your career & work for a great organization like NumFOCUS 😄?! We're currently hiring for an Open Source Science Program Manager. Learn more about the position, its requirements & how to apply in this blog post: bit.ly/3KoToYe! #openscource

Now Hiring!

Open Source Science Program Manager

numfocus.medium.com
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MDAnalysis @mdanalysis.bsky.social retweeted
Fiona Naughton@ExplainedByCats18 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 !
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MDAnalysis @mdanalysis.bsky.social retweeted
Orion Archer Cohen@orionarcher_20 Aug 2022
Panel #1 of my #ACSFall2022 poster, my first conference of grad school! Come see the rest and learn how solvation-analysis makes understanding solvation in MD simulation easy. Sci-Mix and PHYS poster sessions
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MDAnalysis @mdanalysis.bsky.social retweeted
Lily Wang@lilyminium22 Jun 2022
Replying to @sangyoung123go1
Yes! IIRC you should be able to load something with `mda.Universe(my_topology_file, my_numpy_array)`, or use `u.load_new` like here: userguide.mdanalysis.org/sta…
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MDAnalysis @mdanalysis.bsky.social retweeted
Antonia Mey@ppxasjsm10 Mar 2022
Check out this year's @ccpbiosim conference (June 6-8th in Edinburgh) speakers! And if you want to learn more about MDAnalysis and how to get started with ML for biomolecular simulations stay for the workshop (9th-10th June) Registration is now open 👉 bit.ly/3hRC4gE
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MDAnalysis @mdanalysis.bsky.social retweeted
biohub
@biohub31 Aug 2021
🚨#OpenSource tools are the invisible foundation of biomedicine. That’s why we’re continuing to support open source software projects essential for scientists. Learn more about our grantees czi.co/3kH2Hpr

New Grants Support Software Tools and Diversity in Open Source

CZI awards $16 million for foundational open source software tools that are essential to biomedicine

chanzuckerberg.com
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MDAnalysis @mdanalysis.bsky.social retweeted
Julien Michel is also on Mastodon@julienmich8023 Aug 2021
Are you using OpenMM-based apps in your research, or developing new ones ? Are you using or developing Quantum Machine Learning potentials ? Please take 5 min to fill a quick survey and help the OpenMM consortium plan software dev efforts ! @openmm_toolkit forms.gle/9uwxnReYe7nkxZYk8

OpenMM research community survey

Collecting feedback from the community of users and developers of OpenMM

docs.google.com
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MDAnalysis @mdanalysis.bsky.social retweeted
Irfan Alibay@HighSpeedMode20 Mar 2021
I'm trying to get insight on how useful @mdanalysis is (if at all) outside academia. Are there any folks in industry that can testify to it being used in production anywhere? #compchem #moleculardynamics #opensource
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MDAnalysis @mdanalysis.bsky.social retweeted
Irfan Alibay@HighSpeedMode9 Mar 2021
Come take part in @gsoc with us 🙂 You can either work on one of our project ideas or propose your own! If you are interested, please do get in touch early so there's enough time to discuss project ideas
MDAnalysis @mdanalysis.bsky.social@mdanalysis9 Mar 2021
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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MDAnalysis @mdanalysis.bsky.social retweeted
Cédric Bouysset@cedricbouysset9 Mar 2021
Had a fantastic experience with @mdanalysis during @gsoc last summer, so if you want to improve your coding skills, be part of a supportive community, and contribute to #compchem projects, consider applying! 👍
MDAnalysis @mdanalysis.bsky.social@mdanalysis9 Mar 2021
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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MDAnalysis @mdanalysis.bsky.social retweeted
Hugo MacDermott-Opeskin@HugoMacdermott10 Mar 2021
@gsoc with @mdanalysis was an amazing experience last year. Contribute to a skilled and supportive open source community while growing your programming skills! Lots of great projects on offer so get in touch early! #compchem
MDAnalysis @mdanalysis.bsky.social@mdanalysis9 Mar 2021
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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MDAnalysis @mdanalysis.bsky.social retweeted
Lily Wang@lilyminium6 Mar 2021
Would anyone have an old Tripos user manual, or otherwise a complete list of SYBYL atom types lying around? Having this publically available would help @mdanalysis and others make a more robust mol2 writer format. @davidlmobley #compchem
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MDAnalysis @mdanalysis.bsky.social retweeted
Cédric Bouysset@cedricbouysset26 Oct 2020
My presentation at this year's RDKit UGM is now available online! If you want to catch up on what I've been doing during my Google Summer of Code project with @mdanalysis, this is a great start. If you just want the code demos, the slides are online too github.com/rdkit/UGM_2020/tr…
RDKit@RDKit_org26 Oct 2020
The individual videos from the 2020 RDKit Virtual UGM are online. Now's a great time to catch up on anything you missed! youtube.com/playlist?list=PL… #RDKitUGM2020

2020 RDKit Virtual UGM

PDFs of presentations and posters from the UGM are available in the Github repo: https://github.com/rdkit/UGM_2020

youtube.com
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MDAnalysis @mdanalysis.bsky.social retweeted
Cédric Bouysset@cedricbouysset1 Sep 2020
The latest blog post to conclude my GSoC adventure with @mdanalysis is here🏁 I present some new features for descriptors and fingerprints calculation, and the main takeaways from my experience cedric.bouysset.net/blog/202…

Conclusion of my GSoC adventure

After 3 months of hard work, I’ve reached the end of my journey as a Google Summer of Code student with MDAnalysis.

cedric.bouysset.net
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MDAnalysis @mdanalysis.bsky.social retweeted
Cédric Bouysset@cedricbouysset7 Aug 2020
Not a lot of time yet some quite interesting features for this week's Google Summer of Code blog post: bringing MD trajectories to @RDKit_org, adding SMARTS selection to @mdanalysis and improving the converters API 🚀 cbouy.github.io/blog/2020/08…

Adding new features to MDAnalysis

This week I’ve been attending my first ever virtual meeting, the International Symposium on Olfaction and Taste (ISOT for short). While technically this means I didn’t have a lot of time to implement...

cedric.bouysset.net
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MDAnalysis @mdanalysis.bsky.social retweeted
Cédric Bouysset@cedricbouysset4 Jun 2020
I've finally started working on my Google Summer of Code project with the @mdanalysis team 🎉 Here are some more details about how I'll tackle the interoperability with @RDKit_org: cbouy.github.io/blog/2020/06… I'll be posting regular updates on my blog too!
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