Lightnews — Scholar-powered news

Jochem Smit @jhsmit.bsky.social · Sep 9

"Microfluidics is a field that studies and songs the movement of very small amounts of liquids in miniature channels, often as thin as a human hair."

Seems pretty accurate! 😆

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Jochem Smit @jhsmit.bsky.social · Sep 1

Still, it looks like a powerful use case. How does it compare to `dataview`?

I was using a plugin for a while to generate notes with YAML properties from Zotero, but I think it disappeared with Zotero 7. Perhaps zotero-actions-tags can do it?

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Jochem Smit @jhsmit.bsky.social · Jul 16

Just updated my hikemap with our Ardennes hikes!🗺️🥾
One of the perks of living in Belgium: epic trails basically in your backyard 🇧🇪🌳

There are a couple of cool two-day hikes here as well which were (rather painful😅) training sessions for our Norway adventure 🇳🇴🏔️

jhsmit.org/hikes/hikema...

#hiking

Map of hiking routes in the Belgian Ardennes, with markers and trails highlighting hikes.

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Jochem Smit @jhsmit.bsky.social · May 20

Such a pleasure to define HDX-MS states directly in VS code!

#solara #hdxms-datasets

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Jochem Smit @jhsmit.bsky.social · May 17

Here in sunny Belgium the tomatos are doing really well this year - they are facing south on the balcony and I invested in some serious pottery

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Jochem Smit @jhsmit.bsky.social · May 2

You can make animations in molviewspec and then if you set 'keepSnapshotCamera' to `true` it comes pretty close to a trajectory

I have an example in pycafe using ipymolstar here:
bsky.app/profile/jhsm...

Jochem Smit @jhsmit.bsky.social · Apr 29

Having some fun with 3DPGA & kingdon (GA library for python) in ipymolstar!

Geometric Algebra feels like magic 🪄; I don't understand it but surely its very powerful 💪

Live example on pycafe: py.cafe/jhsmit/ipymo...

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Jochem Smit @jhsmit.bsky.social · Apr 29

Having some fun with 3DPGA & kingdon (GA library for python) in ipymolstar!

Geometric Algebra feels like magic 🪄; I don't understand it but surely its very powerful 💪

Live example on pycafe: py.cafe/jhsmit/ipymo...

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Jochem Smit @jhsmit.bsky.social · Apr 10

New release for #ipymolstar: I've added a widget for the amazing and very powerful MolViewSpec. This allows you to control the camera📷from python🐍, as well as all other molviewspec features 🎉

ipymolstar repo: github.com/jhsmit/ipymo...
Molviewspec: molstar.org/mol-view-spec/

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Reposted by Jochem Smit

Jörg Enderlein @joergenderlein.bsky.social · Mar 23

I was invited, for July, to a scienctific meeting in Telluride (Colorado). I was told it is a wonderful place for a conference, and I was very much looking forward to an exciting meeting in a fantastic environment. I have just canceled my participation, despite having booked already everything.

French scientist denied US entry after phone messages critical of Trump found

France’s research minister said the scientist was traveling to Houston for a conference when his phone was searched

www.theguardian.com

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Reposted by Jochem Smit

Eve Seuntjens @eveseuntjens.bsky.social · Feb 19

Hi folks, I would like to know which EU universities are willing or planning to organise #standupforscience activities in solidarity with US scientists Please contact me if you are. Thanks for reposting!

Eve Seuntjens @eveseuntjens.bsky.social · Feb 18

What if we would organise a solidarity action at our universities all across the world? Who would be in? I am tossing this idea on the next council meeting for international affairs at KU Leuven, Belgium. Please spread #standupforscience

Stand Up for Science! @standupforscience.bsky.social · Feb 12

Welcome to the Bluesky account for Stand Up for Science 2025!

Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!

#scienceforall #sciencenotsilence

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Reposted by Jochem Smit

Pekka Kallioniemi @vatniksoup.bsky.social · Feb 18

In today’s Vatnik Soup, I’ll introduce how the Elon Musk’s Election Interference Machine™ (EIM) works. Since Musk and his broligarch allies won the presidency for Trump, they’ve now harnessed the machine to interfere in European elections, including the ones in Germany and Romania.

1/23

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Jochem Smit @jhsmit.bsky.social · Jan 27

Only caught 💩 so far ('chicken curry'); looking forward to the next milestone!

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Jochem Smit @jhsmit.bsky.social · Jan 8

Speed? Although now that mamba solver is default for conda maybe that's not such an issue I think? There are also smaller differences like envs being project based instead of global which helps me remember which env goes with which project. And there is no base env (which you shouldn't use)

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Jochem Smit @jhsmit.bsky.social · Jan 8

pixi add cudatoolkit 🙂

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Jochem Smit @jhsmit.bsky.social · Jan 8

ah yes that makes sense, generally no for non-python, you can install pytorch-cuda wheels with uv though

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Jochem Smit @jhsmit.bsky.social · Jan 8

I also got vague emails from them some time ago

But since uv works so well I havent felt the need to use conda for anymore. Are there use cases left for conda?

I went pip > conda > miniconda> mamba> (poetry) > uv
since pip install would not resolve sometimes but uv just works

docs.astral.sh/uv/

uv

docs.astral.sh

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Jochem Smit @jhsmit.bsky.social · Jan 6

I have some exciting news to share!!

A cute little boy arrived in our lives early december
Mom & dad are very tired but happy 😃

birth card illustration by Tintenbaum
tintenbaum.com

illustration of a baby boy riding a rhino into the sunset

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Jochem Smit @jhsmit.bsky.social · Dec 6

You can try it on Huggingface: huggingface.co/spaces/Jhsmi...

The data is only encoded in the link and not stored so you can use it to share unpublished data*

(at your own risk, no warranty, links might stop working)

Ipymolstar Annotate Colors - a Hugging Face Space by Jhsmit

Annotate protein structural models with colors

huggingface.co

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Jochem Smit @jhsmit.bsky.social · Dec 6

Here's a neat way to share you protein-annotated data 🚀🧪

Upload your .csv with residue/value data, select data column, colormap and norm to interactively color your protein model.

Then, add title/description and click the button to open a shareable view with url-encoded data and settings.

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Jochem Smit @jhsmit.bsky.social · Dec 6

Here is the monomer/dimer/tetramer version:
py.cafe/jhsmit/tetra...

PyCafe - Solara - Tetramerization Kinetics Analysis

Create & Share Streamlit, Dash and Python Apps Online.

py.cafe

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Jochem Smit @jhsmit.bsky.social · Dec 6

This looks like a nice to leave a link to a PyCafé app on monomer/dimer kinetics:

I made this a while a go to answer the question 'if your 10x above kD how much dimer is there'
py.cafe/jhsmit/dimer...

PyCafe - Solara - Protein Binding Equilibrium Simulator using Solara

Create & Share Streamlit, Dash and Python Apps Online.

py.cafe

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Jochem Smit @jhsmit.bsky.social · Nov 29

#ipymolstar v0.0.9: Added click interactions

try it on pycafé: py.cafe/jhsmit/ipymo...

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Jochem Smit @jhsmit.bsky.social · Nov 20

"er kan nog veel meer geld worden weggehaald" 😆

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Jochem Smit @jhsmit.bsky.social · Nov 7

Two-way tertiary/primary structure hover and highlight with #ipymolstar and #altair

Try it on pycafe: py.cafe/jhsmit/ipymo...

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Reposted by Jochem Smit

Thiago Carvalho @cyrilpedia.bsky.social · Oct 29

"In the Netherlands — where the Party for Freedom (PVV), led by the anti-Islam firebrand Geert Wilders, entered a coalition government in July — researchers are bracing for €1 billion (US$1.1 billion) in cuts to the budget, the worst in decades."

Far-right governments seek to cut billions of euros from research in Europe

Anti-immigration parties are pushing policies that are hostile or indifferent towards science.

www.nature.com

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