Fiona Naughton

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

[Fiona Naughton @ExplainedByCats]

As of last week, I'm finally done with all corrections I'll ever have to make to my DPhil thesis.

Among my favourite changes was the creation and inclusion of this cat-based graphical summary. Don't let anyone say you can't represent 3+ years of research entirely using cats!

[Fiona Naughton @ExplainedByCats]

What are these cats saying about my work with sugar transporters? Come to poster B374 today at #bps2024 to find out 😺(and maybe take one home in sticker form - while supplies last!)

[Fiona Naughton @ExplainedByCats]

Any @mdanalysis users at #BPS2024 - come find me to get your hands on some shiny MDAnalysis stickers - now featuring a small selection of cat-based stickers! Look for the pink hair, or come by my poster B374 on Tuesday and also hear about my work with sugar transporters

[MDAnalysis @mdanalysis.bsky.social @mdanalysis]

Read about our #MDAKits approach in our @SciPyConf paper "MDAKits: A Framework for FAIR-Compliant Molecular Simulation Analysis" https://t.co/k5FRKA5afI by @HighSpeedMode @lilyminium @ExplainedByCats @ianmkenney and funded by @czi . Create your MDAKit at https://t.co/TvjYqz9Kv5

[Fiona Naughton @ExplainedByCats]

@mdanalysis @SciPyConf @HighSpeedMode @lilyminium @ianmkenney @czi Want an overview of our #MDAKits rationale and framework, conveyed via some cute kitties? Here's a thread from earlier this year, featuring just that! https://t.co/ifem2EXx2n

[Fiona Naughton @ExplainedByCats]

1. Like a cat, good code needs continual care: food (maintenance), checkups (tests), guide for interaction (docs), etc.

However, scientists often lack time/expertise for this. Code is abandoned+stops working, or is difficult to find, leading to effort duplication.

[MDAnalysis @mdanalysis.bsky.social @mdanalysis]

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 https://t.co/fgoFpOPJJ4

[Fiona Naughton @ExplainedByCats]

What do these cats have to do with @WestpaSoftware, and what am I using WESTPA for in my research?

Come to my poster today at #BPS2023 (B341) to hear about my work on the transport cycle of SGLT sugar transporters!

[Irfan Alibay @HighSpeedMode]

Please come by for a chat! I'll be there during breaks throughout the day too!

[Fiona Naughton @ExplainedByCats]

The cookie cutter is already available here: https://t.co/nNL9LOlhi1

The registry isn't available for external submissions yet, but can be found here https://t.co/NNBLa581cm

[Fiona Naughton @ExplainedByCats]

Last year, @MDAnlaysis released a whitepaper outlining our proposed "MDAKits" -> https://t.co/G6YDjjjHPa

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!

[Fiona Naughton @ExplainedByCats]

4. The MDAKit Framework
-Creation
-Registration via PR w/ metadata file containing Kit name, code location, etc. There are some minimal best practice-requirements
-Going forward, badges will show compatibility w/ latest MDA+can be awarded for improvements like more test coverage

[Fiona Naughton @ExplainedByCats]

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 !

[MDAnalysis @mdanalysis.bsky.social @mdanalysis]

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

[MDAnalysis @mdanalysis.bsky.social @mdanalysis]

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.

https://t.co/sDNngV9TMr

[Fiona Naughton @ExplainedByCats]

What's making this MDAnalysis cat so sad, and what are we doing to help? Come to @lilyminium's talk on @mdanalysis toolkits (MDAKits) and you might find out! #ACSFall2022

[MDAnalysis @mdanalysis.bsky.social @mdanalysis]

For those at #ACSFall2022, @lilyminium will be presenting on this later today #PHYS, room S404a @4.15. Hope to see people there!

[MDAnalysis @mdanalysis.bsky.social @mdanalysis]

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: https://t.co/XyPy6cqjkm

We'd love to hear any feedback!

[Fiona Naughton @ExplainedByCats]

I'm a day late for #InternationalCatDay, but here's a demonstration of cat-herding I drew as part of a cat-based explanation of @WestpaSoftware

[MDAnalysis @mdanalysis.bsky.social @mdanalysis]

MDAnalysis is hiring a #SoftwareDeveloper to help improve our teaching materials!

Flexible contract: 1month FTE, $24/hour, $3,600.

info + apply here:
https://t.co/GvINSUfcXG
Deadline Sept 1st

#compchem