Reaction Systems (RSs) are a successful computational framework inspired by biological systems. A RS pairs a set of entities with a set of reactions over them. Entities can be used to enable or inhibit each reaction, and are produced by reactions.[1]
This project is based on [1], and is a more usable and efficient reimplementation of the Prolog's version.
The program's goal is, given a set of reactions, a context (or multiple parallel) and a possibly empty environment, to generate a DOT file graph representing all the flow of computation of the results.
The user has thus to provide the mandatory sets of reactions and context(s) in order to start the computation.
Companion slides are included for a faster look at the program's functioning.
The project contains five main classes, four of which are examples based on those provided by https://pages.di.unipi.it/bruni/LTSRS/.
Examples show a typical flow of executing the program programmatically, which is the original way of using the program.
The BioResolve main class is, instead, meant to ease the execution of the program by providing a basic (yet functional)
interface where to insert the three sets.
The graphical interface also provides an option to hide or show the intermediate results of the execution, mainly to be able to see what is the flow of the various components of the program.
The final result is a DOT graph file with a default name of result.dot.
This instructions require Maven to be installed
To compile:
mvn compile
To execute:
java -cp target/classes bioresolve.BioResolve
A typical graphical transformation command for the DOT file:
dot -Tsvg result.dot > result.svg
[1] Linda Brodo, Roberto Bruni, Moreno Falaschi. A logical and graphical framework for reaction systems, Theoretical Computer Science 875 (2021) 1–27, https://doi.org/10.1016/j.tcs.2021.03.024.