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Qualitative modeling software tools

GNA
Desktop

GNA Genetic Network Analyzer

Allows users to model and simulate genetic regulatory networks. GNA is…

Allows users to model and simulate genetic regulatory networks. GNA is specifically developed for the analysis of gene regulatory networks by means of piecewise-linear (PL) models. Users can define a…

Odefy
Desktop

Odefy

Converts Boolean models into systems of ordinary differential equations (ODE).…

Converts Boolean models into systems of ordinary differential equations (ODE). Odefy is a user-friendly implementation of the HillCube technique suitable for large-scale networks. The software…

Cell Collective
Web

Cell Collective

Allows modeling of complex biological networks. Cell Collective is an online…

Allows modeling of complex biological networks. Cell Collective is an online community modeling system based on understanding of the logic of the interactions of the individual components. The…

CoLoMoTo
Dataset

CoLoMoTo Consortium for Logical Models and Tools

Provides information about software tools and biological models. CoLoMoTo is an…

Provides information about software tools and biological models. CoLoMoTo is an international open community that brings together modellers, curators and developers of methods and tools. The…

Holmes
Desktop

Holmes

Supports systems biologists in the process of creation and analysis models of…

Supports systems biologists in the process of creation and analysis models of biological systems. More particularly, Holmes allows to create, simulate and analyze models based on various types of…

SPIDDOR
Desktop

SPIDDOR Systems Pharmacology for effIcient Drug Development On R

Performs Boolean modeling of Systems Biology/Pharmacology networks. SPIDDOR is…

Performs Boolean modeling of Systems Biology/Pharmacology networks. SPIDDOR is based on a model for immune response to autoantigens and gives a feel of what can be done with its use. The resulting…

optimusqual
Desktop

optimusqual

A Boolean regulatory network reconstruction using literature based knowledge.…

A Boolean regulatory network reconstruction using literature based knowledge. optimusqual has been implemented with a method which contextualized models from generic Prior knowledge networks (PKNs).…

MaBoSS
Desktop

MaBoSS

Provides a simulation software for continuous time Boolean modeling. MaBoSS has…

Provides a simulation software for continuous time Boolean modeling. MaBoSS has been developed to answer specific needs of modelers. It can be combined with its associated environment and used into…

Pint
Desktop

Pint

Extracts bifurcation transitions from discrete models of large interaction…

Extracts bifurcation transitions from discrete models of large interaction networks. Pint is a scalable method for automata networks (ANs) identification that relies on declarative programming with…

PyBoolNet
Desktop

PyBoolNet

A Python package for the generation, modification and analysis of Boolean…

A Python package for the generation, modification and analysis of Boolean networks. The motivation for developing PyBoolNet was to offer a simple, well-documented interface to manipulating Boolean…

ViSiBooL
Desktop

ViSiBooL Visualization and Simulation of Boolean networks

A tool for GUI-based modeling of Boolean Networks. ViSiBooL supports an…

A tool for GUI-based modeling of Boolean Networks. ViSiBooL supports an extended version of synchronous Boolean Networks with temporal predicates. ViSiBooL allows user-friendly modeling, organization…

Snoopy
Desktop

Snoopy

Allows to design and animate hierarchical graphs, among others Petri nets.…

Allows to design and animate hierarchical graphs, among others Petri nets. Snoopy is a hybrid simulator that supports state-of-the-art hybrid simulation approaches. It is deployed as a component of…

ChemChains
Desktop

ChemChains

Allows network simulation and analysis. ChemChains is a simulation and analysis…

Allows network simulation and analysis. ChemChains is a simulation and analysis suite allowing to visualize the dynamics of biological processes using non-mathematical, parameter-free logical models.…

Braincirc
Desktop

Braincirc

Assists in simulation of brain circulation. Braincirc allows investigation of…

Assists in simulation of brain circulation. Braincirc allows investigation of autoregulation and it includes equations representing blood flow, ion channel activity in the vascular smooth muscle and…

BoolNet
Desktop

BoolNet

Integrates methods for synchronous, asynchronous and probabilistic (Boolean…

Integrates methods for synchronous, asynchronous and probabilistic (Boolean networks) BNs. This includes reconstructing networks from time series, generating random networks, robustness analysis via…

ADAM
Web

ADAM Analysis of Dynamic Algebraic Models

Analyses different types of discrete models. ADAM is a web-based tool to study…

Analyses different types of discrete models. ADAM is a web-based tool to study the dynamics of a wide range of discrete models. The software provides analysis methods based on mathematical…

CellNetAnalyzer
Desktop

CellNetAnalyzer

Allows to perform structural and qualitative analysis of both mass-flow- and…

Allows to perform structural and qualitative analysis of both mass-flow- and signal-flow-based cellular networks. CellNetAnalyzer is a toolbox for analyzing structure and function of biological…

GINsim
Desktop

GINsim Gene Interaction Network simulation

A Java software suite devoted to the qualitative modelling, analysis and…

A Java software suite devoted to the qualitative modelling, analysis and simulation of genetic regulatory networks. GINsim encompasses an intuitive graph editor, enabling the definition and the…

CellNOpt
Desktop

CellNOpt CellNetOptimizer

An open-source R software package for building predictive logic models of…

An open-source R software package for building predictive logic models of signaling networks by training networks derived from prior knowledge to signaling (typically phosphoproteomic) data.…

SimBoolNet
Desktop

SimBoolNet

A Cytoscape plugin to simulate the dynamics of signaling transduction using…

A Cytoscape plugin to simulate the dynamics of signaling transduction using Boolean networks. SimBoolNet simulates the dynamics of signaling transduction using Boolean networks. Given a…

Cheburator
Desktop

Cheburator

Conducts data evaluations and computes the inhibitory concentration 50% (IC50).…

Conducts data evaluations and computes the inhibitory concentration 50% (IC50). Cheburator is able to perform data from sulforhodamine B (SRB) or tetrazolium dye (MTT) assays and can be used with any…

SQUAD
Desktop

SQUAD Stardardized Qualitative Dynamical Modelling Suite

A software for the dynamic modelling of regulatory networks using the…

A software for the dynamic modelling of regulatory networks using the Standardized Qualitative Approach. SQUAD has three novel aspects with respect to other approaches. First, the user needs to…

EpiLog
Desktop

EpiLog Epithelium Logical modelling

Allows users to define, simulate and visualise qualitative models for…

Allows users to define, simulate and visualise qualitative models for epithelial pattern formation.

LogicModelClass…
Desktop

LogicModelClassifier

Allows the explicit enumeration and storage of models that are incompletely…

Allows the explicit enumeration and storage of models that are incompletely specified, in a SQL database. LogicModelClassifier provides various scripts for the creation of a model pool (CSP…

BooleanNet
Desktop

BooleanNet

The goal of this software package is to provide intuitive and accessible tools…

The goal of this software package is to provide intuitive and accessible tools for simulating biological regulatory networks in a Boolean formalism. Using this simulator biologist and…

MuVal
Web

MuVal Multi-valued logic

Converts CellNetAnalyzer (CNA) compliant logic models of signalling networks to…

Converts CellNetAnalyzer (CNA) compliant logic models of signalling networks to facilitate handling of combinatorial regulation. MuVal is a free web service that provides an alternative to the…

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