| 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.avatar | |
| 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.implicants | |
| 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 | |
| org.colomoto.common.task |
Task interface and tools: callables which can run in background.
|
| org.colomoto.common.xml |
Helper to deal with XML files.
|
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