Created: 2014-05-19 00:34
Updated: 2018-05-06 13:46
License: other

This repository contains code for "Synthesis of Biological Models from Mutation Experiments" by Ali Sinan Koksal, Yewen Pu, Saurabh Srivastava, Rastislav Bodik, Jasmin Fisher, and Nir Piterman in POPL 2013.

This code is an experimental prototype and is fairly ugly in many places. The code is released for openness, and not for good design or good coding practices.

Scala, ScalaZ3 and Z3 versions used by the tool have been updated to recent versions to make installation and running easier.


The tool runs on Linux (64-bit) and Mac OS X.

You should have Java 7 and sbt 0.13.2 installed to run the tool. To visualize executions, you also need Graphviz.


Sample scripts for invoking the synthesizer are given in the folder scripts.

To run the synthesizer on the "VPC1" Vulval Precursor Cell template described in Section 7 of the paper, run:


Templates and specifications for all models described in the paper are in the folder programs and specifications, respectively.

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