Jochem Smit

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

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

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

#solara #hdxms-datasets

5 tomato plants in pots on a balcony

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

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...

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...

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/

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

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.

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!

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

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

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)

pixi add cudatoolkit 🙂

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

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/

illustration of a baby boy riding a rhino into the sunset

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

Ipymolstar Annotate Colors - a Hugging Face Space by Jhsmit Annotate protein structural models with colors

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)

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.

PyCafe - Solara - Tetramerization Kinetics Analysis Create & Share Streamlit, Dash and Python Apps Online.

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

PyCafe - Solara - Protein Binding Equilibrium Simulator using Solara Create & Share Streamlit, Dash and Python Apps Online.

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...

#ipymolstar v0.0.9: Added click interactions

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

"er kan nog veel meer geld worden weggehaald" 😆

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

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

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.

"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."

PyCafe - Solara - Tetramerization Kinetics Analysis PyCafe: get your daily fix of Python!

By popular demand: How much monomer/dimer/tetramer are formed at steady-state given the two kds and the total concentration of protomer? 🧐

py.cafe/jhsmit/tetra...

A screenshot of the solarafold result viewer showing SecA2:SecB4 complex with plddt residue colors

I've created this #solara app where you can drag & drop your #alphafold3 .zip file and switch between chain color or plddt colors. Includes 'spin' and theme toggle for maximal viewing pleasure. The screenshot below shows the elusive SecA2/SecB4 complex.
huggingface.co/spaces/Jhsmi...

A screenshot of jupyter lab showing a code cell where a local .bcif file is loaded and passed to `PBDeMolstar`. The output is a 3D render of nCov spike protein.

New in #ipymolstar version 0.0.4: directly load your local data files

`pip install "ipymolstar==0.0.4"`
github.com/Jhsmit/ipymo...

Dit is en blijft racisme. Iemand uit Afrika mag geen mening hebben over het Fries en komt gewoon geld graaien.

Ik vind het ontluisterend dat dit op tv is en blijft.

demo of ipymolstar in a solara app ipymolstar source: https://github.com/Jhsmit/ipymolstar example app source and live demo: https://github.com/Jhsmit/ploomber-solara-ipymolstar ipymolstar

I've created my first widget with #anywidget! Its called `ipymolstar` and allows visualization of proteins or molecules interactively from python.

check out the video below or try it live on ploomber:
youtu.be/Syra-DCtQkA

Render of MBP cryoEM structure in ipymolstar with residues coloured by HDX-MS gibbs free energies

Nice! I've updated the structure reference in our HDX-MS database, here it is rendered in ipymolstar (beta) and colored by HDX-MS Gibbs free energy (blue = rigid, yellow = more flexible)

Interested in the mechanisms driving subcellular organization in bacteria? The Vecchiarelli lab has a postdoc position available!

docs.google.com/document/d/1...

Plz RT!