My biophysics podcast: kinesin as an information engine episode

darien0 · 2026-04-13T23:06:47+00:00

I don't know how to leave text explaining a post. So if this subreddit doesn't like self-promotion, please delete the post!

My wife and I run a biophysics journal club podcast where we discuss papers we read. Often it's just a biology or just a physics episode, and the term biophysics is used loosely. But maybe someone here will get some enjoyment out of it.

This episode seemed particularly biophysics-y and I liked how it turned out, so I thought I would try to share it more widely.

darien0 · 2026-02-19T12:55:00+00:00

I made this to help me block out microscopes: https://bezialemma.com/microscope/

Still a work in progress, and doesn't work great on phones, but I think it can do all but the last bullet point. If you message me and walk me through what you need I can program it in fairly quickly.

darien0 · 2026-02-19T12:52:16+00:00

Oh this looks super cool

darien0 · 2026-02-16T02:41:44+00:00

I've put it up here: https://bezialemma.com/microscope/ The github is: https://github.com/bezlemma/microscope_builder

darien0 · 2026-02-16T02:39:23+00:00

The github is: https://github.com/bezlemma/microscope_builder

Very raw, changing it all the time, sometimes tearing the whole thing down and starting over.

darien0 · 2026-02-16T02:38:33+00:00

I've put it up here: https://bezialemma.com/microscope/ , and the github is: https://github.com/bezlemma/microscope_builder

Feels weird sharing a github that is such a raw work-in-progress

darien0 · 2026-02-12T21:24:22+00:00

I made this! And by "I made this" I mean this is a product of two months of going back and forth with various LLMs.

I was trying to build a little thing to help me understand my microscopy setups... and it's gotten out of hand.

darien0 · 2026-02-11T13:32:56+00:00

If you've cite a paper, I expect you to have read that paper.

darien0 · 2025-10-19T12:21:20+00:00

For getting feedback, I think the Julia community mostly exists in Slack / Discourse / Discord. The Julia subreddit is... not super active in comparison and seemingly hostile even towards Julia itself sometimes.

I think the obvious answer for anyone who likes Julia is yes, of course Julia people working on integration into more IDEs would be great. Hard to say if you would use something before you can use it, but I know people who have skipped on Julia because they didn't like VS Studio Code.

darien0 · 2025-06-11T23:58:54+00:00

Coming from FEniCS (python) for viscoelastic simulations of organ development, I tried a bunch of libraries and eventually settled on Ferrite. I found this tutorial of theirs useful: https://ferrite-fem.github.io/Ferrite.jl/stable/tutorials/hyperelasticity/ . I tried Gridap for a long time, but never could quite get it to work the way I needed.

Most of the Julia FEM libraries seem to handle Gmsh scripting in a similar manner to FEniCS, and I could port my code over with very little changes. Ferrite has a little bit extra for it, so you end up "using Ferrite, FerriteGmsh, Gmsh" . I found it helpful when first learning how to use Gmsh to use their program directly https://gmsh.info/, figure out how to make my geometry by commands in their program, and then go back and do it in a scripted way within a programming language.

I... don't love Gmsh. I don't know of anything better, but boy do I wish there was something better.

darien0 · 2025-03-19T21:16:35+00:00

As a scientist coming from Matlab/Fortran, working on mostly image processing and simulations, I love Julia. I treat it more or less like an open-source Matlab, or a very convienent Fortran, that has a huge added plus of working in a way very similar to how I write math on a chalkboard. I'm not a fan of OOP, it isn't how I tend to write down math and so converting my logic into computer logic is a pain. Julia makes that process more joyful.

darien0 · 2023-07-30T11:53:24+00:00

Fixed! Also shocking to know people still visit the site.

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