Uses of Package
org.colomoto.biolqm

Packages that use org.colomoto.biolqm

Package	Description
org.colomoto.biolqm	Core for the bioLQM toolkit: Main data structures for Logical Models Service loader and manager Launcher and Command-Line Interface Script mode
org.colomoto.biolqm.helper.clingo
org.colomoto.biolqm.io	Input/Output for Logical Model.
org.colomoto.biolqm.io.antlr
org.colomoto.biolqm.io.bnet	The format used by boolnet and pyboolnet
org.colomoto.biolqm.io.booleannet	The format used by booleannet and related tools in Reka Albert's group
org.colomoto.biolqm.io.boolsim	The format used by boolsim/GenYsis.
org.colomoto.biolqm.io.cnet	The format used by boolnet and pyboolnet
org.colomoto.biolqm.io.functions	logical functions.
org.colomoto.biolqm.io.ginml	GINML support.
org.colomoto.biolqm.io.gna	GNA (non-xml) support.
org.colomoto.biolqm.io.maboss	The format used by MaBoSS - https://maboss.curie.fr/
org.colomoto.biolqm.io.petrinet	Petri net support.
org.colomoto.biolqm.io.pint	The format used by Pint - http://loicpauleve.name/pint
org.colomoto.biolqm.io.sbml	SBML qual support.
org.colomoto.biolqm.io.truthtable	TruthTable file reader.
org.colomoto.biolqm.modifier
org.colomoto.biolqm.modifier.booleanize	Construct Boolean versions of Multi-valued models
org.colomoto.biolqm.modifier.perturbation	Perturbation of logical models: local modifications of its logical functions.
org.colomoto.biolqm.modifier.reduction	model modification: remove components from the core.
org.colomoto.biolqm.modifier.reverse	model modification: creates a new model capable of generating the reverse dynamics.
org.colomoto.biolqm.modifier.subspace
org.colomoto.biolqm.tool	Tool definition, used to run actions from the command-line interface.
org.colomoto.biolqm.tool.attractor	Identification of the stable states of a logical model.
org.colomoto.biolqm.tool.inferinteraction	Infer interactions and their signs from a logical model.
org.colomoto.biolqm.tool.simulation	Some tools to run simulations on logical models.
org.colomoto.biolqm.tool.simulation.updater	Implementation of updating schemes: update the state of a model (i.e.
org.colomoto.biolqm.tool.stablestate	Identification of the stable states of a logical model.
org.colomoto.biolqm.tool.trapspaces

Classes in org.colomoto.biolqm used by org.colomoto.biolqm

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
LogicalModelImpl Implementation of the LogicalModel interface.
NodeInfo Contains the basic informations of a regulatory node (gene) : - nodeID : a unique identifier for the gene - max : the maximal regulatory level
StatefulLogicalModel Extension of a logical model with the possibility to store initial states and oracles

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.helper.clingo

Class and Description
HelperTool Locate and call external tools.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.antlr

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
NodeInfo Contains the basic informations of a regulatory node (gene) : - nodeID : a unique identifier for the gene - max : the maximal regulatory level

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.bnet

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.booleannet

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.boolsim

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.cnet

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.functions

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.ginml

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.gna

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.maboss

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.petrinet

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
NodeInfo Contains the basic informations of a regulatory node (gene) : - nodeID : a unique identifier for the gene - max : the maximal regulatory level

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.pint

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.sbml

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
NodeInfo Contains the basic informations of a regulatory node (gene) : - nodeID : a unique identifier for the gene - max : the maximal regulatory level

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.io.truthtable

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.modifier

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
Service Simple service description interface.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.modifier.booleanize

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
NodeInfo Contains the basic informations of a regulatory node (gene) : - nodeID : a unique identifier for the gene - max : the maximal regulatory level
Service Simple service description interface.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.modifier.perturbation

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
NodeInfo Contains the basic informations of a regulatory node (gene) : - nodeID : a unique identifier for the gene - max : the maximal regulatory level
Service Simple service description interface.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.modifier.reduction

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
Service Simple service description interface.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.modifier.reverse

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
Service Simple service description interface.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.modifier.subspace

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
Service Simple service description interface.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.tool

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
Service Simple service description interface.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.tool.attractor

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
Service Simple service description interface.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.tool.inferinteraction

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.tool.simulation

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.tool.simulation.updater

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.tool.stablestate

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
NodeInfo Contains the basic informations of a regulatory node (gene) : - nodeID : a unique identifier for the gene - max : the maximal regulatory level
Service Simple service description interface.

Classes in org.colomoto.biolqm used by org.colomoto.biolqm.tool.trapspaces

Class and Description
LogicalModel A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.
NodeInfo Contains the basic informations of a regulatory node (gene) : - nodeID : a unique identifier for the gene - max : the maximal regulatory level
Service Simple service description interface.