Provides an interactive web application for high-throughput biological data modeling and visualization. HTPmod includes modules for plant growth modeling based on time-series data (growMod), prediction of important traits based on high-dimensional data (predMod) and visualization of high-throughput data (htpdVis). This platform suits for modeling and visualizing large-scale, high-dimensional data sets under a broad context.
Offers a nonlinear finite element solver for biomechanical applications. FEBiO provides modeling scenarios, constitutive models and boundary conditions. The application supplies algorithms to model tied or sliding contact under large deformations between elastic, biphasic, or multiphasic materials. Users can run five different types of analysis: (i) nonlinear elasticity and viscoelasticity; (ii) rigid body mechanics; (iii) multiphasic mechanics; (iv) interstitial growth mechanics and (v) heat conduction.
Allows structural identifiability analysis of models describing biological systems under multiple experimental conditions. GenSSI is a software toolbox that performs structural identifiability analysis of linear and nonlinear ordinary differential equation (ODE) models. The software provides a Systems Biology Markup Language (SBML) import, automatic methods for multi-experiment structural identifiability analysis, and methods for the transformation of models. It permits users to obtain subsets/combinations of structurally identifiable parameters, which can be used to reformulate the model.
Allows building, analysis, simulation and reproducibility of models in systems and synthetic biology. Tellurium is an integrated development environment (IDE) that comes with several pre-installed Python libraries, plugins, and tools tailored for biological simulation. The software also includes plugins and modules ranging from visualization tools to algorithms for bifurcation analysis and multidimensional parameter scanning. It supports the COMBINE archive, a file format containing all the information needed to reproduce a simulation experiment.
Provides implementation of set-based algorithms for modeling and analysis of various types of networks and motifs. ADMIT is a MatLab-based toolbox that uses a set-based uncertainty description and convex relaxation and optimization framework for model invalidation and parameter estimation. This approach allows to define statements on entire regions in the parameter space.
Assists in automating the checking of biological systems models. SMC is a standalone software able to guide users towards the computational method that suited the most for its needs according the submitted model and pattern. The application is based on a machine learning algorithm that advises the use of a stochastic model checker by promoting the required time for the verification process.
Affords a suite for model analysis and data integration. SBSI is composed of three major software: (i) SBSINumerics, containing a library with parallelized implementations of global optimization algorithms; (ii) SBSIDispatcher, providing access to back-end HPC machines; and (iii) SBSIVisual, a client application to configure parameter optimization jobs, to link with external databases and to view the results of optimizations. There are no dependencies between modules.
Simplifies parameter inference for complex biological systems. PyDREAM is an open-source implementation of the DREAM(ZS) and MT-DREAM(ZS) sampling algorithms for efficient inference of complex, high-dimensional, and posterior parameter distributions. It uses a common multi-chain architecture and creates candidate points in each chain on the fly via differential evolution. This tool focuses on three points: (1) specification of the prior parameter distribution, (2) selection of an appropriate likelihood function, and (3) Markov chain Monte Carlo (MCMC) simulation.
Provides a web interface for annotating gene-regulatory and biochemical network models. PAYAO authorizes to share models which can be customized by inserting tags, comments and discussion by a whole community. Users can add information such as keywords, links, pubmedID and free text as tags to specified components.
Offers a method for scheduling genetic crosses to produce a desired set of mutant strains. CrossPlan is an approach based on an integer-linear-program (ILP). The software is able to calculate a sequence of genetic cross experiments organized into batches such that the crosses can be performed in each batch in parallel. It was tested on a mathematical model of the budding yeast cell cycle.
Allows users to handle vision science computation. ISETBIO is an open-source software that performs calculations, through the optics, from the scene radiance and into the front end of biological visual systems. It authorizes to estimate a wide range of factors such as the optics and retinal image, bipolar responses or the capture of light by the photopigment.
Offers a platform dedicated to models’ community management. MAGPIE is accessible through three different ways: (i) a demo platform hosted on a web application; (ii) a source code allowing a local installation; and (iii) a R API. The application provides a repository of models and analysis tools that can be freely customized by multiple users. It also includes additional features for easing the visualization of results and a sharing results system based on twitter's hashtags model.
Allows users to study the roles of stochastic Ca2+ release channel (RyR) gating and Ca2+ wave dynamics on the statistical distribution of delayed afterdepolarizations (DADs) under pathophysiological conditions. This method permits to make estimation of changes in model parameters influence the probability of rare events that are “surrogates” for ectopic beats. It is based on the non-spatial Greenstein-Winslow canine ventricular myocyte model.
Provides an implementation of a physiologically grounded model of afferented muscle. Afferented-Muscle-Model a closed-loop simulation that is an extension of a previous model of spinal-like regulator. It is composed of: (i) a musculo-tendon unit; (ii) muscle spindle and (iii) a Golgi tendon organ (GTO), controlled by a tracking controller. It can be used for determining the sources of frequency-specific force variability and their interactions.
Provides a real-time model for classical conditioning and timing. RWDDM is a model combines elements from two theories, (i) the Rescorla-Wagner conditioning model and; (ii) the Timing DriftDiffusion Model (TDDM) interval timing theory, which is based on the drift-diffusion model, widely used in decision making theory, and it provides an adaptive time representation that has commonalities with pacemaker-based models.
Models the hippocampal activity and processes inputs from external cues and the path integrator. CANN is a model of the hippocampal circuitry, capable of storing multiple cognitive maps. This software enables prediction of the frequency of the cognitive map instability, its duration, and the detailed nature of the place-cell population activity.
Assists users in simplifing forward modelling of the effect of different intervention options. fluEvidenceSynthesis is a package that allows users to infer parameters using a Bayesian approach, perform forward modelling of the likely results of the proposed intervention and finally perform cost effectiveness analysis of the results. It is based on a method to inform vaccination strategies for influenza, with extensions to make it easily adaptable to other diseases and data sources.
Handles electrodiffusive processes on spatiotemporal scales. KNPsim is an open source framework dedicated to ion concentration solving. The application can be used to reproduce electrodiffusive dynamics of ion-concentrations and the electrical potential in the extracellular space (ECS). It aims to assist users in investigating occurrences involving ion concentration shifts at the tissue level and pathological conditions linked to variations in the ECS.
Computes extracellular potentials around morphologically rebuilt neurons. LFPy is a Python package that leans on NEURON software to compute transmembrane currents of each neuron and, then, uses those currents to calculate the extracellular potential. The application can be employed to compute local field potentials (LFPs) as well as to simulate high-frequency signals including extracellular spikes.
Supplies a method for Taenia solium control and transmission. cystiSim is a software allowing design of future program according to T. solium and its elimination as a public health problem. It contains environmental contamination, host immunity and parasite mutation.