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Cell-based computational modeling and simulation software tools

The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events, such as cell…
VPTissue
Desktop

VPTissue Virtual Plant Tissue

Allows to work on plant tissue morphogenesis. VPTissue provides a means for…

Allows to work on plant tissue morphogenesis. VPTissue provides a means for plant researchers to analyze the biophysics of growth and patterning. This tool consists of three main functions: (1) a…

VirtualLeaf
Desktop

VirtualLeaf

A freely available, open-source software framework for modeling plant…

A freely available, open-source software framework for modeling plant development. The aim of VirtualLeaf is to make computational modeling better accessible to experimental plant biologists with…

PROSPECT
Desktop

PROSPECT

Allows to simulate leaf hemispherical reflectance and transmittance in the…

Allows to simulate leaf hemispherical reflectance and transmittance in the 400–800 nm region. PROSPECT can retrieve accurately, multiple photosynthetic pigment concentrations. The main functions of…

rankin-chavane-…
Desktop

rankin-chavane-neural-field

Helps to investigate stimulus driven activity in 2D cortical space with a…

Helps to investigate stimulus driven activity in 2D cortical space with a discrete representation of orientation. rankin-chavane-neural-field provides a dynamical model where the neural field…

SimTracker
Desktop

SimTracker

A package to manage simulations with NEURON network models. SimTracker manages…

A package to manage simulations with NEURON network models. SimTracker manages the complexity of developing, executing and organizing results from large scale, detailed simulations executed on…

QSpike Tools
Desktop

QSpike Tools Queued Spike Tools

Executes unsupervised generic signal pre-processing and analysis of…

Executes unsupervised generic signal pre-processing and analysis of multichannel extracellular signals. QSpike Tools is based on the observation that any CPU-intensive pre-processing needed can be…

Ephus
Desktop

Ephus

Provides general purpose data acquisition. Ephus is an open-source, flexible…

Provides general purpose data acquisition. Ephus is an open-source, flexible software package that includes functionality for a wide variety of applications ranging from traditional in vitro…

PTSD
Algorithm

PTSD Precise Timing Spike Detection

Detects spiking activity. PTSD requires three parameters: (1) the differential…

Detects spiking activity. PTSD requires three parameters: (1) the differential threshold (DT), (2) the peak lifetime period (PLP) and (3) the refractory period (RP). It computes the Relative…

Biophysical-dyn…
Desktop

Biophysical-dynamic-module-for-PIN-polarisation

Consists in a biophysical dynamic module.…

Consists in a biophysical dynamic module. Biophysical-dynamic-module-for-PIN-polarisation is a model prediction build upon the up-to-date experimental results on the influencing factors and cellular…

Neurogenesis_Si…
Desktop

Neurogenesis_Simulator

Aims at explaining the high diversity found across mammalian species.…

Aims at explaining the high diversity found across mammalian species. Neurogenesis_Simulator assists in creation of representation of a minimal set of processes and players involved in the cortical…

MartinezEtAl201…
Algorithm

MartinezEtAl2017

Allows probabilistic division plane prediction for any cell. The probabilistic…

Allows probabilistic division plane prediction for any cell. The probabilistic predictor of division plane orientation in 3D provides a method to predict division based only on cell shape, allowing…

CAMEO
Desktop

CAMEO

Helps the strain design process in metabolic engineering projects. CAMEO is a…

Helps the strain design process in metabolic engineering projects. CAMEO is a library which aims to make in silico cell factory design broadly accessible. The software provides an interface that can…

CellSys
Desktop

CellSys

A modular software tool for efficient off-lattice simulation of growth and…

A modular software tool for efficient off-lattice simulation of growth and organization processes in multi-cellular systems in 2D and 3D. CellSys implements an agent-based model that approximates…

LBIBCell
Desktop

LBIBCell Lattice Boltzmann Immersed Boundary

An extendible and open-source cell-based simulation environment, which is…

An extendible and open-source cell-based simulation environment, which is tailored to study morphogenetic problems. LBIBCell permits the coupled simulation of a physically motivated viscoelastic cell…

MEA-Tools
Desktop

MEA-Tools MicroElectrode Array tools

Allows users to retrieve and analyze data from different hardware systems, to…

Allows users to retrieve and analyze data from different hardware systems, to modify and to share them across different operating systems. MEA-Tools offers a set of tools for visualization and…

CompuCell3D
Desktop

CompuCell3D

Employs biologically relevant models for cell clustering, growth, and…

Employs biologically relevant models for cell clustering, growth, and interaction with chemical fields. COMPUCELL3D is a software framework for three-dimensional (3D) simulation of morphogenesis in…

IBCell
Desktop

IBCell

A biomechanical approach in modelling the growth and division of a single fully…

A biomechanical approach in modelling the growth and division of a single fully deformable cell by using an immersed boundary method with distributed sources. This mathematical technique couples a…

SAIL
Desktop

SAIL Scattering by Arbitrarily Inclined Leaves

Shows the calculation of emissivity, vegetation cover, reflectance, brightness…

Shows the calculation of emissivity, vegetation cover, reflectance, brightness temperature and radiance as a function of leaf area index (LAI). SAIL enables users to partly bridge the current gap…

PROSAIL
Desktop

PROSAIL

Makes to physically interpret spectral and directional reflectance fields as…

Makes to physically interpret spectral and directional reflectance fields as sampled by Earth observation sensors in terms of leaf biochemical contents and canopy architecture. SAIL is coupled with…

WaveSurfer
Desktop

WaveSurfer

Permits to acquire neurophysiology data. WaveSurfer allows set test pulse y…

Permits to acquire neurophysiology data. WaveSurfer allows set test pulse y limits manually. The tool is currently pre-release software.

Symphony
Desktop

Symphony

Permits to acquire data from electrophysiology experiments. Symphony offers a…

Permits to acquire data from electrophysiology experiments. Symphony offers a way to scientists to construct structured and configurable acquisition routines in Matlab. It provides a graphical…

CESE
Desktop

CESE Cell Electrophysiology Simulation Environment

Allows execution of single-cell models and modification and clamping of model…

Allows execution of single-cell models and modification and clamping of model parameters, as well as data visualisation and analysis using a consistent interface. CESE is an integrated environment…

FIND
Web

FIND Finding Information in Neural Data

Interfaces standard electrophysiology data sources and collates various…

Interfaces standard electrophysiology data sources and collates various analysis and simulation tools. FIND allows concise review of methods and algorithms, and opens possibilities for enhancements.…

MeaBench
Desktop

MeaBench

Permits acquisition of multi-electrode data and online analysis. MeaBench can…

Permits acquisition of multi-electrode data and online analysis. MeaBench can communicate in real-time with stimulator hardware. It can be applied in closed-loop stimulation experiments. This tool…

Spike Manager
Desktop

Spike Manager

Analyzes multi-channel signals obtained from multi-site electrophysiological…

Analyzes multi-channel signals obtained from multi-site electrophysiological recordings of neuronal population. Spike Manager is able to produce a detailed statistical analysis of the…

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