TissueOpt

Optimizing the Tissue Simulation Toolkit

The purpose of the Tissue Simulation Toolkit (TST) is to simulate the single cell and collective behavior of animal cells and extracellular materials and signals during embryonic development, blood vessel formation, in cancer and in cell cultures. The software implements the widely used cellular Potts model. Here we focus on modelling the mechanical and chemical interactions between cells and the extracellular matrix (ECM), the jelly and fibrous materials that surround cells.

This project focused on optimising the computational performance of the TST.

Participating organisations

Leiden University
Netherlands eScience Center
Life Sciences
Life Sciences

Team

RM
Roeland Merks
ET
Erika Tsingos
Niels  Drost
Niels Drost
Programme Manager
Netherlands eScience Center

Related projects

e-MUSC

Enhancing multiscale computing with sensitivity analysis and uncertainty quantification

Updated 19 months ago
Finished

Related software

MUSCLE3

MU

MUSCLE3 is a coupling library for building multiscale simulations out of single-scale models.

Updated 9 months ago
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Tissue Simulation Toolkit

TI

Tissue Simulation Toolkit (TST) 2.0 is an efficient C++ library for two-dimensional simulations of Glazier and Graner's Cellular Potts model (Glazier and Graner, 1993). It is suitable for simulations with live visualization as well as batch simulations on clusters.

Updated 3 months ago
7