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Tracking_bigraph

An addon to the OCaml library "Bigraph". It allows tracking of nodes between state transitions.

Credits

This is just an addon to the bigraph library, available here: https://bitbucket.org/uog-bigraph/bigraph-tools. It uses some code for rewriting bigraphs from the original library. Hence, the original author is included in the LICENSE file.

Installation

As of 2022 the easiest way to install this library on Debian-like operating system is to do the following on a system with OCaml 4.13 and opam installed:

  • Clone source code of bigraph-tools v0.0.2
git clone --dept 1 --branch v0.0.2 https://bitbucket.org/uog-bigraph/bigraph-tools uog-bigraph-tools-0.0.2
  • Install dune,dune-configurator,jsonm.1.0.1,cmdliner.1.0.4,menhir.20200123,ounit2, csv, parmap and zarith via opam:
opam install dune dune-configurator jsonm.1.0.1 cmdliner.1.0.4 menhir.20200123 ounit2 csv parmap zarith
  • Install minisat and zlib1g-dev via package manager:
apt-get install minisat zlib1g-dev
  • Install bigraph-tools from previously downloaded source:
cd uog-bigraph-tools-0.0.2
dune build
dune install
cd ..
  • Download sources of conf-nauty, onauty and trs packages:
git clone https://github.com/zajer/conf-nauty
git clone https://github.com/zajer/onauty
git clone https://github.com/zajer/trs
  • Install libnauty2-dev via package manager:
apt-get install libnauty2-dev
  • Pin conf-nauty package to the downloaded source:
cd conf-nauty
opam install .
cd ..
  • Install onauty:
cd onauty
dune build
dune install
cd ..
  • Finally install trs library from source:
cd trs
dune build
dune install

Usage

See the file(s) in the example folder.

For more in depth description of the idea behind this tool and possible use case scenarios please refer to this paper: https://www.mdpi.com/1424-8220/21/2/622