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The CoLoMoTo Docker and Notebook

Usage

Usage guide
Adding your tool
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Resources

Use cases
Materials

Software tools

List of embedded tools
ActoNet
- Fixed point reprogramming with ActoNet
AEON.py
bioLQM
- Layouts for displaying regulatory graphs
- BioLQM tutorial
BNS
- BNS tutorial for fixed points and synchronous attractors
BoNesis
- Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis
- Synthesis of Boolean networks from influence graph and dynamical constraints
BooleanNet
- Introduction to BooleanNet
boolSim
- Computing attractors with boolSim
- Computing reachable states with boolSim
BooN
- BooN basic features
CABEAN
- Myeolid reprogramming with CABEAN
Caspo
- Control of Bladder model using Caspo-control
CasQ
CellCollective
- CellCollective Knowledge Base
ERODE
- Reduction of synchronous Boolean networks with ERODE
GINsim
- Regulatory graph visualization with GINsim
MaBoSS
minibn
mpbn
NORDic
- Introduction to NORDic
NuSMV
- NuSMV with GINsim
Pint
- Pint - Quick Tutorial
PyBoolNet
- PyBoolNet tutorial
PyDrugLogics
- Tutorial for PyDrugLogics
pyStableMotifs
- Tutorial for basic usage of pystablemotifs
- pystablemotifs - Control tutorial
R-BoolNet
- R-BoolNet: Random BN generation, loading with biolqm and minibn
scBoolSeq
- scRNA-Seq binarization with scBoolSeq
- scRNA-Seq generation from Boolean dynamics

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GINsim

GINsim#

Webpage: http://ginsim.org

Boolean and multi-valued network modelling

Notebooks

Regulatory graph visualization with GINsim

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Reduction of synchronous Boolean networks with ERODE

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Regulatory graph visualization with GINsim

By Consortium for Logical Models and Tools (CoLoMoTo) - colomoto.org

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