List of embedded tools

The CoLoMoTo Docker image provides access to the following softwares:

Software tool	Homepage	Description	Jupyter interface
ActoNet	algorecell/pyActoNet	Abduction-based control of fixed points of Boolean networks	Python module actonet
AEON.py	sybila/biodivine-aeon-py	Symbolic analysis (attractors, reachability) of (partially specified) Boolean networks	Python module biodivine_aeon
bioLQM	https://colomoto.github.io/biolqm/	Logical Qualitative Modelling toolkit	Python module biolqm
BNS	https://people.kth.se/~dubrova/BNS/user_manual.html	Identification of synchronous attractors	Python module bns
BoNesis	https://bnediction.github.io/bonesis	Synthesis of Boolean Networks from architecture and dynamical properties	Python module bonesis
BooleanNet	ialbert/booleannet	Simulation of Boolean regulatory networks	Python module boolean2
boolSim	https://www.vital-it.ch/research/software/boolSim	Attractors and reachable sets in synchronous and asynchronous Boolean networks	Python module boolsim
BooN	https://franck-delaplace.github.io/BooN/	Boolean Network Analysis: dynamics, stable states, control	Python module boon
CABEAN	https://satoss.uni.lu/software/CABEAN/	A Software Tool for the Control of Asynchronous Boolean Networks	Python module cabean
Caspo	https://bioasp.github.io/caspo/	Reasoning on the response of logical signaling networks with Answer Set Programming	Python module caspo_control
CaSQ	soli/casq	Convert static interaction maps into executable models	Python module casq
CellCollective	https://cellcollective.org	Model repository and knowledge base	Python module cellcollective
ERODE	colomoto/ERODE-CoLoMoTo	Backward Boolean Equivalence of Boolean networks	Python module erode
GINsim	http://ginsim.org	Boolean and multi-valued network modelling	Python module ginsim
MaBoSS	https://maboss.curie.fr	Markovian Boolean Stochastic Simulator	Python module maboss
minibn	colomoto/colomoto-jupyter	Simple Boolean network manipulation API	Python module colomoto.minibn
mpbn	pauleve/mpbn	Analysis and simulation of Most Permissive Boolean Networks	Python module mpbn
NORDic	clreda/NORDic	Network Oriented Repurposing of Drugs	Python module NORDic
NuSMV	http://nusmv.fbk.eu	Symbolic model-checker	Python module nusmv
Pint	https://loicpauleve.name/pint	Static analyzer for dynamics of Automata Networks	Python module pypint
PyBoolNet	hklarner/PyBoolNet	Generation, modification and analysis of Boolean networks	Python module PyBoolNet
PyDrugLogics	https://druglogics.github.io/pydruglogics/	Construct, optimize Boolean Models and perform in-silico perturbations of the models	Python module pydruglogics
pyStableMotifs	jcrozum/pystablemotifs	Target-control of Boolean networks	Python module pystablemotifs
R-BoolNet	https://cran.r-project.org/package=BoolNet	Analysis and reconstruction of Boolean networks dynamics	RPY2 python interface
scBoolSeq	bnediction/scBoolSeq	scRNA-Seq data binarisation and synthetic generation from Boolean dynamics	Python module scboolseq