Jochem Smit
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jhsmit.bsky.social
Jochem Smit
@jhsmit.bsky.social
Biophysics; protein dynamics/folding using smFRET and HDX-MS.

https://jhsmit.org/
"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! 😆
September 9, 2025 at 2:50 PM
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?
September 1, 2025 at 9:31 AM
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
May 17, 2025 at 4:54 PM
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...
May 2, 2025 at 9:52 AM
Only caught 💩 so far ('chicken curry'); looking forward to the next milestone!
January 27, 2025 at 4:26 PM
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)
January 8, 2025 at 8:31 PM
pixi add cudatoolkit 🙂
January 8, 2025 at 3:42 PM
ah yes that makes sense, generally no for non-python, you can install pytorch-cuda wheels with uv though
January 8, 2025 at 2:52 PM
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
January 8, 2025 at 12:31 PM
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The data is only encoded in the link and not stored so you can use it to share unpublished data*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
December 6, 2024 at 3:17 PM
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
December 6, 2024 at 2:51 PM
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
December 6, 2024 at 2:51 PM
"er kan nog veel meer geld worden weggehaald" 😆
November 20, 2024 at 11:47 AM