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sbl's Introduction

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.

Dependencies

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.

Running

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:

./scripts/synthesize-vpc1

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

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sbl's Issues

Running this repository with `sbt` throws error

Hi @koksal,

From the root directory of the project, I ran sbt "run --solve" which went through successfully.
But I want to run sbt "run --summarize" to get the output of TraceSummarization.scala. Unfortunately
it throws the following error :

shadab@hp:~/Downloads/sbl$ sbt "run --summarize"
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
[info] Set current project to sbl (in build file:/home/shadab/Downloads/sbl/)
[info] Running elegans.Main --summarize
Loading scalaz3
[ERROR] Sanity check for symbolic run: FAILED
[ERROR] sanity check fails
java.lang.RuntimeException: Nonzero exit code returned from runner: 1
	at scala.sys.package$.error(package.scala:27)
[trace] Stack trace suppressed: run last compile:run for the full output.
[error] (compile:run) Nonzero exit code returned from runner: 1
[error] Total time: 5 s, completed May 3, 2018 3:09:23 PM
shadab@hp:~/Downloads/sbl$

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