readme

Author: Ioana

README.md

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+
+PosetLogic is a model checker on Kappa causal flows (stories). It is designed to be used as an accompaying analysis tool for a KaSim simulation. Users can write influence statements about a Kappa model and PosetLogic will query the pool of stories to check if there exists a 'mechanistic' explanation of the influence statement.
+
+## Installation
+
+To compile PosetLogic you need
+
+- the OCaml native compiler version 4.02.3 or above as well as _ocamlbuild_, _findlib_ and _Yojson_ library.
+- the KappaLib that you can get from https://github.com/Kappa-Dev/KaSim
+
+If you use opam KappaLib, OCaml compilers, ocamlbuild and findlib are provided by it.
+
+## Usage
+
+You first need a pool of Kappa stories in a json format. You can produce them by running a KaSim simulation (please visit Kappa's documentation on http://dev.executableknowledge.org/docs/KaSim-manual-master/KaSim_manual.htm). Or you can use the stories provided in the example set.
+
+Then you need to write a formula file. Each line in the file is either a formula or a variable assignation.
+
+## Run the example
+
+In the folder [examples] you'll find the set of stories produced by the model test3.ka with the simulation options of inputs.ka. The stories are both in a json format (necessary for PosetLogic) and in a dot format, for visualisation. The files test1 and test2 are files with formulas.
+
+You can test whether the model in test3.ka satisfies the formulas in the files test1 and test2 by typing
+
+'./main.native examples/test3/c0.json examples/test3/c1.json examples/test3/c2.json examples/test3/c3.json examples/test3/c4.json examples/test3/c5.json -env examples/test3/env.json -f examples/test3/test2'
+
+Alternatively you can use the script 'script_test3'.

script_test3

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-./main.native posets_test/test3/c0.json posets_test/test3/c1.json posets_test/test3/c2.json posets_test/test3/c3.json posets_test/test3/c4.json posets_test/test3/c5.json -env posets_test/test3/env.json -f posets_test/test3/test2
+./main.native examples/test3/c0.json examples/test3/c1.json examples/test3/c2.json examples/test3/c3.json examples/test3/c4.json examples/test3/c5.json -env examples/test3/env.json -f examples/test3/test2