MerrinASP -

Generic Answer Set Programming (ASP) solver for pseudo-Boolean optimization under logic and quantified linear arithmetic constraints (up to one level of quantifier). It extends the ASP solver clingo with quantified linear constraints and constraints partitioning.

Merrin -

Tools for the inference of Boolean regulatory rules controlling the cell metabolism from time series kinetics, fluxomics, and/or transcriptomics observations. It relies on the regulatory Flux Balance Analysis to ensure compatibility between inferred regulatory rules and the observations.

Benchmarks of Optimization Modulo Quantified Linear Arithmetics - [Zenodo]

First benchmark of Optimization Modulo Quantified Linear Arithmetics problems. Instances are inspired by an inverse problem in bioinformatics: the inference of regulatory rules controlling the metabolism. Each instance is associated with an equivalent quantifier-free problem.
This benchmark has been used to validate merrinasp.

Regulated Metabolic Models of E. coli -

Set of 3 regulated metabolic networks of E. coli at small, medium, and large scales. Each model has been reconstructed according to their description in the literature. They are implemented in SBML (metabolic network) and SBML-qual / bnet (regulatory network) format.
These models have been used to validate merrin.