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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 this tool are: (1) the ability to simulate accurately, in vivo leaf directional hemispherical reflectance (DHR) and directional hemispherical transmittance (DHT) spectra, (2) it can be used to retrieve leaf Chlorophyll s (Chls) and Cars with similar accuracies, and (3) it provides an additional capability for retrieving individual Chla and Chlb concentrations.
Chaste / Cancer Heart And Soft Tissue Environment
An open-source library for computational biology that has well-developed cardiac electrophysiology tissue simulation support. Chaste is a general purpose simulation package aimed at multi-scale, computationally demanding problems arising in biology and physiology. Current functionality includes tissue and cell level electrophysiology, discrete tissue modelling, and soft tissue modelling. This generic extensible library has focused primarily on two distinct application areas: continuum modelling of cardiac electrophysiology and individual-based modelling of cell populations, with specific application to tissue homeostasis and carcinogenesis.
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 different organisms that uses design patterns for speed, efficient memory management, extensibility, and flexibility to allow an almost unlimited variety of simulations. It computes the time evolution of differentiating cells in 3D using a stochastic cellular potts model (CPM) and a Cell-Type-Map implemented as a discrete cellular automaton.
Allows users to model, simulate and analyze complex, heterogeneous and multi-scale systems like a cell. E-Cell is a generic software package for cell simulation, based on structured Substance–Reactor Model (SRM), an object-oriented modeling theory. The software accepts multi-algorithms, multi-timescales and multi-spatial-representations as its central feature. It includes ordinary differential equations, Gillespie algorithm (the direct method), and spatial Gillespie algorithm.
SAIL / Scattering by Arbitrarily Inclined Leaves
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 between the analytical canopy–soil models operating separately in the optical and the thermal-infrared (TIR) spectral domains. It might lead to better exploitation of the possible synergies offered by simultaneous co-registered optical and TIR remote sensing observations.
Offers a set of models to estimate the basic capabilities of simulators at the single neuron level. Rallpacks is composed of three models: (i) Rallpack 1, a linear cable model that test basic ability of a simulator to model a uniform unbranched cable; (ii) Rallpack 2, a branched cable model, that evaluate the simulator performance on a highly branched model with non-uniform branch sizes.; (iii) and Rallpack 3, a linear axon model that estimate the ability of the tested simulator to solve the Hodgkin-Huxley equations.
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 cells as isotropic, elastic and adhesive objects. Cell migration is modeled by an equation of motion for each cell. It includes many modules specifically tailored to support the simulation and analysis of virtual tissues including real-time 3D visualization and VRML 2.0 support. All cell and environment parameters can be independently varied which facilitates species specific simulations and allows for detailed analyses of growth dynamics and links between cellular and multi-cellular phenotypes.
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 continuous description of a viscous incompressible cytoplasm with the dynamics of separate elastic cells, containing their own point nuclei, elastic plasma membranes with membrane receptors, and individually regulated cell processes. IBCell enables one to focus on the biomechanical properties of individual cells and on communication between cells and their microenvironment, simultaneously allowing for the formation of clusters or sheets of cells that act together as one complex tissue.
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 be used without knowing any metabolic modeling or how different algorithms are implemented. It enables cell factory engineers to enumerate and prioritize designs without having to be experts in metabolic modeling themselves and provides method developers with a library that simplifies the implementation of new cell factory design methods.
Aims to overcome the challenges of modelling spatio-temporal Ca2+ dynamics. This tool uses the experimentally reconstructed 3-D structures for the transverse-tubule (TT) and sarcoplasmic reticulum (SR) at the whole-cell scale. It can capture spatio-temporal calcium dynamics with a realistic network SR structure and membrane fluxes distributed according to the sarcolemma/TTs. The tool permits users to understand structure-function relationships in physiological and pathophysiological cardiac electro-mechanics.
VPTissue / Virtual Plant Tissue
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 simulator, including capability for conversion between output file formats and for post-processing the simulation output; (2) a tissue editor and a graphical editor capable of editing the geometry of the mesh representing the plant organ; (3) a parameter explorer, simplifies the study of the parameter dependence of the simulation results by distributing calculations over multiple systems.
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 electrophysiology to highly customized circuit mapping and in vivo behavioral protocols. It offers a collection of both application-specific tools, such as those for electrophysiology, scanning and mapping, video imaging, as well as common (shared) tools for data binding, configuration switching, and experimental timing.
PTSD / Precise Timing Spike Detection
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 Maximum/Minimum (RMM) of the raw data signal. This tool shows good performances when applied to recordings coming from real cortical cultures or when tested against synthetic signals generated by a neuronal network model which mimics the behavior of a dense network cultured over a Micro Electrode Array (MEA).
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 multiple supercomputers and addresses the problem of making detailed neural models accessible to experimentalists. The tool can also track hundreds of parameters in these complex models and can organize, analyze, and store results from hundreds or thousands of simulations executed with multiple model configurations.
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 dissection of the relative contributions of shape as opposed to mechanical or developmental regulation. The model was used to demonstrate that pre-prophase bands (PPBs), microtubule and microfilament structures that accurately predict the future division plane in typical land plant cells, closely match the predicted division planes unless a four-way junction is present.
NDD / Noise-driven differentiation model
Determines how organization can emerge from chaos. NDD is in keeping with the recent emphasis on the importance and the prevalence of noise in biological functions, specifically cell fate. It accounts for the peculiarities of biological phenomenon by weaving noise into an explanation of cellular behaviours at the time of differentiation. This tool permits realistic depiction of a process that results in phenotypic differentiation in a population.
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 neurogenesis of the mammalian brain. It allows user to select and calibrate the neurogenesis model, observing how the temporal population dynamics vary when changing parameter values. With it, users can select and compare strategies of neocortical neurogenesis across different species.
SOCR / Statistics Online Computational Resource
Aims to design, validate and disseminate knowledge. SOCR is a technique that enables investigation of biological mechanisms related to morphological changes in cell nucleus through quantitative analysis of changes in its size and shape. It provides portable online aids for probability and statistics education, technology based instruction, statistical computing, and predictive big data analytics. Its tools and resources include a repository of interactive applets, computational web application and graphing tools, instructional and course materials.
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