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Sophie Libkind (May 12 2022 at 20:09):Earlier @John Baez suggested using AlgebraicPetri to simulate the Brusselator. Well... I gave it a try and got some reasonable graphs!
Here is an .html file which you can open and take a look at what I did: Brusselator.html
Here is the .ipynb notebook if you want to play around with the example yourself: Brusselator.ipynb
Sam Tenka (May 12 2022 at 20:38):Sophie Libkind said:
Earlier John Baez suggested using AlgebraicPetri to simulate the Brusselator. Well... I gave it a try and got some reasonable graphs!
Here is an .html file which you can open and take a look at what I did: Brusselator.html
Here is the .ipynb notebook if you want to play around with the example yourself: Brusselator.ipynb
Very cool! What if one starts with A, B of very high but not constant concentrations? One expects short term oscillation and long term decay
John Baez (May 12 2022 at 22:25):Hey, this is great, @Sophie Libkind! Maybe you can demonstrate this or walk us through the notebook next time we meet? It'd be good for everyone to start learning how to do things like this.
Sophie Libkind (May 12 2022 at 23:40):Sure! I'd be happy to!
Matteo Capucci (he/him) (May 16 2022 at 10:41):I'm very envious of Petri net people now :) I'd love to have tooling this mature to write down systems I'm interested in. That's just amazing!
John Baez (May 16 2022 at 23:36):@Sophie Libkind - great! Can you meet this Thursday at 1 pm? Or if not that, noon?
Next week I'll be busy at the Grothendieck conference at Chapman on Tuesday, but I'd like to have one final meeting on Thursday next week, talking about projects!
Sophie Libkind (May 17 2022 at 14:41):Unfortunately, I'm "away" this Thursday. I could make it on Friday. Another great option is that @Evan Patterson, @James Fairbanks and @Kris Brown are all familiar with Catlab/AlgebraicPetri and may be up for walking the group through the notebook
John Baez (May 17 2022 at 15:59):Oh. If I'd been more organized I would have figured out a time sooner and done it today. I thought Thursday would give people a chance to attend who haven't been coming yet. I'm pretty busy on Wednesday and Friday.
John Baez (May 17 2022 at 16:02):If you can get someone to show us how the notebooks work at 1 pm this Thursday that would be great.
John Baez (May 17 2022 at 16:03):Otherwise I'll talk to people about other stuff. Either way, please set up a calendar invite for a meeting at 1 pm this week.... there's just not enough other better times to do things. :cry:
Evan Patterson (May 17 2022 at 17:15):I could walk through the notebook. Thursday noon and 1pm PT could both be made to work for me, although noon would be better.
John Baez (May 18 2022 at 00:09):Okay, I could do it at noon and cut short my meeting with @Joe Moeller and @Todd Trimble (which starts at 11). Thanks!
Sam Tenka (May 30 2022 at 15:56):Brusselator.ipynb
copy of brusselsprouts
Sam Tenka (May 30 2022 at 16:01):Note: I had stuff mostly working (beautiful diffeq solution graph rendering except and wacky graph theory graph rendering) with Julia 1.4. Then I upgraded to 1.7 and everything broke. Here's what helped me in the end:
in a terminal run:
jupyter kernelspec list
(it will list some name such as julia-1.4 along with other things such as Python)
jupter kernelspec remove julia-1.4
(but write whatever julia version was in your list)
THEN within the julia repl run:
using IJulia
installkernel("Julia nodeps", "--depwarn=no")
John Baez (May 30 2022 at 16:40):Try it out!
Sophie Libkind (May 31 2022 at 14:31):Ben here :)
Here's the paper on gluing paths together: https://arxiv.org/pdf/2108.04786.pdf