Dr Frames Catherine White
(She/her)
PhD.
Working on biology cell simulations.
Engineering, ML, Constrained Optimization, Modelling, JuliaLang, AutoDiff, Programming
This is my professional bsky.
- Something I have been thinking about on and off is about the annotation of function primatives with properties, like nilpotent, associative, commutative, etc, then using (type) inference to infer this about functions built in them. Then using that for automatic parallelism and other optimisations.
- Reposted by Dr Frames Catherine WhiteI accidentally turned on AI completion in VS-Code yesterday. And I though "_fine_, I will finally try this thing" and I am really not liking having my tab completion lie to me? I just have to check it when it doesn't work, then look up the right way. When I could have just immediately looked it up
- Reposted by Dr Frames Catherine White
I've just created a #JuliaLang package BlueskyClient.jl github.com/AtelierArith... . You can post text, images with ALT text, GIFs, and MP4 videos from the package. Give it a try! - this is a really cool page on all the tricks you can use to express different ideas in terms of (Mixed Integer) linear programming. Cos the whole thing is very tricky. Like the trick of splitting variables so you can have L1 regularisation which is nonlinear in naive implementation
- I have spent far too much time dealing with flakey tests and nondeterministic failures today
- the amount of hatred i have for good tests that were marked "skip" because they are too slow that have bit rotted, is only exceeded by my hatred for good tests that were marked "skip" that are still good and would have caught bugs had they not been set to skip
- does python 3 have an abstract base class for strings? I feel like it should. because for data-structures like a rope you want the string API, but you definately do not want to store it like a string, so inheriting from str is no good. en.wikipedia.org/wiki/Rope_(d...
- I wanted to see if I was part of the Anthropic settlement class: ✅ Book on LibGen before 2021 ✅ Book has ISBN ❎ were registered with the United States Copyright Office Alas, I am not. While my rights have obviously been violated, it is not in a way that is covered by this court case.
- So we had a model incorporating thermodynamic constrains called a ThermoModel. And another model with enzyme constraints called a GeckoModel. (Gecko = Genome-scale model Enzyme Constraints, using Kinetics and Omics.) And we were making a model to combine them. Some kind of ThermoGecko.
- I need to set julia to always run with bounds checks enabled. I have done this before. The big virtue is no more redoing precompilation between running normally and running tests. Since julia makes seperate compliation caches for the 3 different settings for bounds checks. +tests always have them on
- I made an OpenSCAD library for engraving emoji into 3D prints. github.com/oxinabox/ope...
- Pretty happy with this for something I designed and printed all in one day, while doing other things. It snugly fits the brace on the back of mirrors. Which has a funny bumpy shape. No more bracelets scattered over my dressing table.
- Reposted by Dr Frames Catherine White🚨 Breaking news 🚨 Two epic tutorials announced for #JuliaCon Local Paris 2025: one about Pluto notebooks and one about using JuMP for optimization. Be sure to get your tickets this week, otherwise the early bird pricing will be gone 🦜 @juliacon.bsky.social @julialang.org @pydataparis.bsky.social
- I ordered a 3D printer. I haven't had access to one since I left uni in 2018. And that one was ancient and temperamental.
- I should implement the same design o want to 3D print in OpenSCAD, Descartes.jl, ConstructiveGeometry.jl, ImplicitCAD and a few other programatic CADs. Then compare and contrast
- One julia thing I am coming around to after using python for a bit is explicit imports. I used to be moderately hard against it. Working out where something is from is a tooling problem that is kinda solved. But when jumping into a codebase where you are unfamiliar with the whole ecosystem...
- The 1 module per file pattern is not idiomatic Julia. I am dubious of its success in python where it is built in and required. You end up with a hell of avoiding circular dependencies. And trying to match API organisation (external) to development organisation (internal) is just messy. Long files.
- Sometimes it's fun to pick up random open source repos and contribute to them. Yesterday I picked up ConstructiveGeometry.jl Which is a Julia based OpenSCAD alternative. It's a 1 person effort not touched in 4 years, and I got it working with latest releases of its dependencies etc. and made a PR
- DataStructures.jl v0.19 has been released.. Our first breaking release in 5 years. It shouldn't be too breaking if you kept up with removing deprecated calls. (For reference 0.18 has 22 patch releases which was an annoying amount of backporting to do. Might be a record for backporting) #julialang
- I actually quite like SQL. Nice language to express things in. Though how different versions of the same query will perform is mysterious
- Biology be like: So 1 gene encodes for 1 protein right? It's 1-1. Well no, some genes are no coding. Ok so it's 1-0/1 Well no, each AA can come from multiple different codons so two different genes can technically make the same protein. Ok so many-0/1. (It gets worse though)
- Something i just said seriously at work: "How different is a human from yeast anyway? Probably not that different."
- What database normalisation rule is broken by having redundant information For example have a column for middle name and another column for middle initial. It clearly breaks some rule as they could be updated separately and end up inconsistent.
- I was away for one week and someone added a `utils` file to the code base. `utils` files are an antipattern because it's a meaningless name, an unclear grouping. (A utils folder is ok if the files have good names). And it tends to be where evil code lives. often without tests. Cos "its just utils".
- I wish github had a thing that would let me right click an item in a check-list and open a subissue with it's text as the title. And edit the original post's checklist to be a link to that subissue. That would make breaking stuff down for project management purposes much better.
- I thought Dask was supposed to be this really reliable thing, especially when using it with Coiled so I can't screw up my infrastructure. But I have been fighting it all day, of it seemingly getting to a point where it stops talking back to client...
- NetworkX allowing anything to be the nodes in graphs is solidly nicer than Graphs.jl Look how nice it is to go from a CobraPy model (a reaction network) to a (bipartite) Graph:
