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Qualitative modeling software tools | Mathematical modeling

Most biological processes are controlled by regulatory networks, which involve various kinds of molecular interactions, including protein-mediated transcriptional regulations, polypeptide receptor–ligand associations, protein modifications by specific enzymes, etc. Decades of genetic and molecular analyses, more recently complemented by high-throughput functional genomic experiments, have progressively uncovered many of the numerous interactions controlling several crucial biological processes (including cell cycle and various developmental pathways). The complexity of the networks delineated often defies intuitive reasoning, consequently calling for the development of proper computational tools. Different mathematical approaches have been proposed to model such genetic networks and to simulate their dynamical behaviour, ranging from quantitative formalisms to crude Boolean models.

Source text:
(Gonzalez et al, 2006) GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems.

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CellNetAnalyzer
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 networks on the basis of topological, stoichiometric, qualitative (logical) and semi-quantitative modeling approaches requiring no or only few parameters. Metabolic networks can be studied based on stoichiometric and constraint-based modeling approaches whereas signaling and regulatory networks can be explored by qualitative and semi-quantitative modeling approaches.
GINsim / Gene Interaction Network simulation
Supports the definition, the simulation and the analysis of regulatory graphs, based on the logical formalism. GINsim is a software that displays a window enabling the creation of a new model, the import of a model in a supported format, or the opening of a previously defined model. This tool leans on two main types of graphs: Logical Regulatory Graphs, which model regulatory networks, and State Transition Graphs, which represent their dynamical behavior.
GNA / Genetic Network Analyzer
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 regulatory network, build a model of this network, determine the steady states of the system, generate a state transition graph starting from an initial state and analyse the latter graph using model-checking tools. The software has been used to analyse a number of bacterial regulatory networks.
PHONEMeS / PHOsphorylation NEtworks for Mass Spectrometry
Assists in modeling signaling networks based on untargeted phosphoproteomics mass spectrometry (MS) data and kinase/phosphatase-substrate interactions. PHONEMeS is able to resume known relationships between distinct perturbed kinases and their substrates. It allows users to access the results data as a network of regulatory relationships. The software also offers the feature to rebuild paths from kinases inhibited on drug treatment to sites perturbed by these inhibitions.
Cell Collective
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 software allows scientists to deposit and track dynamical information about biological processes and integrate and interrogate this knowledge in the context of the biological process as a whole. It has a potential as an educational tool for undergraduate and graduate biology students with diverse mathematical/computer science skills.
Odefy
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 provides access to different models sources, the conversion process and various analysis and export methods. A discrete model converted to an ODE by Odefy displays similar dynamical properties as a mechanistically derived ODE model of the same system.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 provides access to different models sources, the conversion process and various analysis and export methods. A discrete model converted to an ODE by Odefy displays similar dynamical properties as a mechanistically derived ODE model of the same system.
SimBoolNet
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 user-specified level of stimulation to signal receptors, SimBoolNet simulates the response of downstream molecules and visualizes with animation and records the dynamic changes of the network. It can be used to generate hypotheses and facilitate experimental studies about causal relations and crosstalk among cellular signaling pathways.
SPIDDOR / Systems Pharmacology for effIcient Drug Development On R
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 models can be used to analyze the dynamics of signaling networks associated to diseases to predict the pathogenesis mechanisms and identify potential therapeutic targets. SPIDDOR also includes an attractor search algorithm that searches the attractors for networks with less than 20 nodes, as the number of initial conditions to test grow exponentially with the number of nodes.
Cheburator
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 absorbance or luminescence-based assays. It is designed to analyze the results of assays performed on 96-well plates. To ensure good data quality and to minimize the impact of pipetting errors, each particular compound concentration is assessed based on the absorbance values from 3 separate wells.
SQUAD / Stardardized Qualitative Dynamical Modelling Suite
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 provide only the connectivity of a regulatory network; no rate values, interaction strengths, or kinetic data is needed as input. Second, the stable steady states of activation of the continuous model are automatically found, without the need of running the system from several initial states. And third, the resulting equations have diverse tunable parameters so as to provide the possibility to fit the continuous model to existing experimental data.
optimusqual
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). Using a genetic algorithm, a model network is built as a sub-network of the PKN and trained against experimental data to reproduce the experimentally observed behaviour in terms of attractors and the transitions that occur between them under specific perturbations. The resulting model network is therefore contextualized to the experimental conditions and constitutes a dynamical Boolean model closer to the observed biological process used to train the model than the original PKN. These contextualized models have improved utility for hypothesis generation and experimental design.
CellNOpt / CellNetOptimizer
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. CellNOptR features different logic formalisms, from Boolean models to differential equations, in a common framework. These different logic model representations accommodate state and time values with increasing levels of detail. Models built with CellNOptR are useful tools to understand how signals are processed by cells and how this is altered in disease. They can be used to predict the effect of perturbations (individual or in combinations), and potentially to engineer therapies that have differential effects/side effects depending on the cell type or context.
MaBoSS
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 the following pipeline: (i) construct a logical model, by writing directly the .bnd and .cfg files or by exporting them from ginsim; (ii) run the model, analyze the results within a spreadsheet, and visualize the results; (iii) test parameter sensitivity; (iv) confront the model to known experimental observations (mutations, drug effects), and (v) set up a protocol for comparing experiments to model results for new biological insights.
BioDiVinE
Allows parallel analysis of biological models. BioDiVinE implements rectangular abstraction of continuous models of biochemical reaction systems. The NewBioDiVinE version combines model checking tool BioDiVinE 1.0 with parameter estimation tool based on DiVinE. This program includes several features: (1) an user interface for specification of models in terms of chemical equations; (2) a formal representation of the model by means of multi-affine ordinary differential equations (ODEs); or (3) graphical simulation of the discretized state space.
ADAM / Analysis of Dynamic Algebraic Models
Obsolete
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 algorithms. It unifies different modeling types by providing analysis methods for all of them and thus can be used by a larger community. Its main application is the analysis of the dynamic features of a model, which includes the identification of stable attractors.
MuVal / Multi-valued logic
Obsolete
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 applied assumptions of concerted or independent inhibitory mechanisms, which lead to false inferences in “classical” Boolean (or multi-valued) treatment if the reactions analyzed are being influenced by several regulators simultaneously. By the sequential use of MuVal and CNA signalling, the models of the networks can be simulated in terms of multi-valued logic with graded-inhibitory (or activation) responses.
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