BioLQM Documentation

BioLQM provides a collection of tools for the modification and conversion of Logical Qualitative Models of biological networks, started as part of the CoLoMoTo consortium to facilitate model exchange.

It can be used on the command line, through scripts, or embded in other tools such as GINsim or Epilog using the Java API directly.

Command-Line Interface — Command Line Interface
Install and run bioLQM — Availability, requirements, installation

Core features

I/O formats — Define Import / Export filters
Java API — Using bioLQM from Java code
Model modifiers — Model in, modified model out
Scripting bioLQM — Scripting
Tools — Tools applied to models

Import/Export formats

Formats provide import/export filters for the following file formats.

BoolNet format — Import/Export to the BoolNet format
BoolSim format — Import/Export boolSim models
Booleannet format — Import/Export to the boolean format
CNET format — Import/Export to the cnet format (for BNS)
GNA format — Export to the GNA text format
MaBoSS format — Export logical models for a Markovian Boolean Stochastic Simulator
Multi-valued Net format — Import/Export Multi-valued models as text files
Petri Net Export — Export logical models as Petri net
Pint format — Export to the pint format
SBML-qual — Import/Export regulatory graph to SBML-qual standard format
The GINML format — Export to the XML format used in GINsim
Truth table format — Import/Export logical models as truth tables

Model modifiers

A model modifier takes a model as input (and in some cases some parameters), and constructs a modified version of the model.

Model Perturbations (mutants) — Define perturbations of logical models
Model booleanization — Boolean mapping for multivalued models
Model reduction — Automated reduction of logical models
Model restriction — Restrict a model to a subspace
Model reversal — Models with reversed asynchronous dynamics

Tools

Compute deterministic trace — Compute deterministic trace
Identification of trap-spaces — Finding trap-spaces of a logical model
Random walk — Perform a random walk in the dynamics
Stable state search — Finding fixed (stable) states of a logical model