[Verdex]

It feels like the following PDF better expresses what they're trying to accomplish.

http://mgs.spatial-computing.org/PUBLICATIONS/lami-RR72--com...

As far as I can tell, they're trying to model things like chemical reactions (and other stuff) where given a bunch of "stuff" in some solution it will combine with other "stuff" if it's in the same topological neighborhood (which I think is basically the idea that ALL of the "stuff" doesn't have to be next to each other b/c if you let a solution just sit there eventually reactions are going to react).

It's kind of neat, but their website seems to indicate that it is not being actively supported. Or at the very least they don't seem to have any reason to make publicly available documentation after since around 2010.

EDIT: So for example, you could use their "trans" transform primitive to implement conway's game of life by defining the birth rule as a pattern of an empty cell with three alive cells and a transform that results in the empty cell being alive and the alive cells being the same. The death rules in similar fashion. Neighbor here would be defined as being physically next to something (but the point is that because this is about topologies, then neighbor doesn't have to mean physical proximity ... although I'm not sure where that's defined ... in the collection maybe?).

And then you just run the transform on a collection with some initial state.

EDIT EDIT: Yeah, the notion of neighbor is defined on the collection. This allows you to use the same transform on different collection types and get the appropriate result.

ALSO checkout figure 5 in the PDF I linked because it's an incredibly concise description of exactly what they're doing.

EDIT EDIT EDIT:

This also feels vaguely similar to what the Egison language is doing with their pattern matching. Documentation for Egison feels better at least to me.

https://www.egison.org/

However, I don't think that egison allows you to define arbitrary notions of neighbors in a collection like MGS does. But I haven't exactly tried to use it very much.

[iamwil]

Figure 5 kinda reminds me of...Datalog? Where you have rules and a data set. Given the rules, you iteratively compute on the data set until there are no more rules that match the given data--the fixed point.

Is that right?

[Verdex]

I think that's accurate except it looks like you need to manually continue the applications of your transform.

It looks like they've got a pure functional thing going on.

[amelius]

I'm puzzled by what's happening on page 9 of that PDF.

Ok, I quickly browsed through it, but a chemical reaction where two identical molecules react into those same molecules plus another molecule? How can this be possible?

[Verdex]

I'm not up to speed on all of the things that computational biology is up to. But IIRC there are some metabolic pathways that cascade into producing a lot of whatever it is the organism is trying to produce. Which sounds kind of like what you're describing.

[Cacti]

Is this for modeling a single reaction or chain of reactions? ie you don’t need neighborhoods if you are modeling 7 trillion of one thing combined with 14 trillion of another?

[Verdex]

It looks like chains of reactions etc. As you say for something simple you don't need something complex.

It's a DSL for computational biology where very little documentation has apparently made it to a public forum. I can decode the programming language part of it but I'm not up to scratch on computational biology so I'm not sure exactly what they want it for.