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CANTATA is an approach to find missing interactions in Boolean networks using prior network knowledge and experimental results.
Using genetic programming the prior network is adapted to match the desired behavior as specified in the experimental results.

Content overview:
src - source code for CANTATA software.
Makefile - Makefile to install CANTATA locally using g++ compiler.
fissionyeast* - files to run a CANTATA demo using the fission yeast cell cycle model by Davidich et al., 2008.
runDemo - script to run the CANTATA demo with exemplary settings. This script runs for about 10s on a MacBook Pro 2017, with 3.1 GHz.
cantata-manual.pdf - A manual with detailed description how to use CANTATA.
Fissionyeast_results - A folder which contains the scripts to reproduce the results which are shown in the manuscript. This folder comprises the original network, the perturbed copies, the reconstructed results and the R-scripts to analyse the results.

Install the CANTATA software using "make". The command will compile the source code and create a binary executable "cantata" in ./bin/
The CANTATA software run on all main operating systems with GNU C++ compiler g++. Other compilers might also work but are not tested. We tested the software on Ubuntu 18.04, MacOS 15.4 and Windows 10 using the g++ compiler.
Installation is completed in ~1 minute on standard computers.

Run the software: 
Run CANTATA using "./bin/cantata". The software will print the set of required and optional parameters to run the software. 
Additionally, files to run a demo are included. 
The demo runs a modified version of the fission yeast cell cycle model (Davidich, 2008), "fissionyeast_trunc_1.txt". Boolean networks are specified in the BoolNet text format. 
As experimental results, we specified the most significant attractors of the unmodified yeast network in "fissionyeast-rules.txt". 
The demo can be started using "sh ./". This script runs for about 10s on a MacBook Pro 2017, with 3.1 GHz. The demo creates the output-file "fissionyeast_results.txt".
For detailed description of the software see the manual.


Code and Demo sources for CANTATA - inference of missing interactions in Boolean Networks







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