Search Results for "large eddy simulation"

PhysiCell is a cross-platform C++ framework for large, physics-based multicellular simulations.

Tissue Simulation Toolkit is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.

Moose is the core of a modern software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes. We have moved Github.com. This should be your source for the latest version of the code.

LATEST VERSION NOW LOCATED AT http://git.durrantlab.com/jdurrant/lipidwrapper As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. When building large-scale models of whole subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature are essential. LipidWrapper, written by Jacob Durrant in the lab of Rommie E. Amaro,...

GENESIS (GEneral NEural SImulation System) is a software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes.

UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path...

Compare SBML Test Suite Results =============================== The [SBML Testsuite](http://sbml.org/Facilities/Online_SBML_Test_Suite) allows developers of ODE based simulators to test their implementation against a large number of test cases that test a wide aspect of the [SBML Specifications](http://sbml.org/Documents/Specifications). While implementing my simulator [RoadRunner](http://roadrunner.sf.net) I wanted to be able to compare it using a wider range of parameters: -...

The Boolean Network Toolkit is an efficient and easy-to-use object-oriented C++ library which enables researchers to simulate ad carry out experiments (like attractor sampling and Derrida plot computation) on large boolean networks.

...https://github.com/ecell The development of E-Cell now continues on GitHub. The Subversion repository was abandoned. """ E-Cell System is an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components driven by multiple algorithms with different timescales to coexist in a model.

The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!

CLAM is a model of a large-scale cortical network, which incorporates the interaction between object-based and spatial attention and working memory.

Given a reference sequence, simhtsd will create a large set of short nucleotide reads, simulating the output from today's high-throughput DNA sequencers, such as the Illumina Genome Analyzer II.

SpiNet is a neural simulation tool for large spiking networks with highly heterogeneous synapses. Neurons are modelled as I&F units with dual exponential synaptic conductances. Complex network models can be easily built using the included tool NetBuilder

This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).

3D cellular automata modelling software for large general purpose simulations. Uses custom scripts for rules and can distribute processing over several machines.