SoftwareApplication
name: Tissue Simulation Toolkit
description: 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.
description: Welcome to Tissue Simulation Toolkit (TST) 2.0, a library for two-dimensional simulations of Glazier and Graner's Cellular Potts model (Glazier and Graner, 1993). TST 2.0 is an efficient C++ library for two-dimensional Cellular Potts Simulations. It is suitable for simulations with live visualization as well as batch simulations on clusters. TST 2.0 provides many recent extensions to the CPM, including - Efficient edgelist algorithm - Infinite number of PDE layers (forward Euler) - A reaction diffusion solver on the CPU and on CUDA - Interaction of CPM cells and PDE (secretion, absorption) - Chemotaxis - Length and connectivity constraints - Act-CPM model (Niculescu et al., PLOS Comput Biol 2015) - Discrete fibrous extracellular matrix (molecular dynamics) The current version of the TST includes example programs for the following published simulations: - Differential adhesion driven cell sorting (Glazier and Graner, 1993) - Cell elongation dependent vasculogenesis (blood vessel growth) (Merks et al., 2006) - Contact-inhibition dependent vasculogenesis and angiogenesis (Merks and Glazier, 2005; Merks and Glazier, 2006; Merks et al, PLoS Comput Biol 2008) - Hybrid cellular Potts and bead-spring modeling of cells in fibrous extracellular matrix (Tsingos and Bakker et al, Biophys J. 2023) and visualization of: - Cells, according to cell type or anything you wish - Chemical fields, using color ramps and contour lines (level sets)
code repository: https://github.com/mathbioleiden/Tissue-Simulation-Toolkit
author: https://orcid.org/0000-0002-8919-9401
author: Person
  given name: Guayo
  family name: Peerdeman
  name: Guayo Peerdeman
author: https://orcid.org/0000-0002-6311-1168
author: 0000-0002-7267-160X
author: 0000-0002-6152-687X
author: 0000-0003-0625-213X
author: https://orcid.org/0000-0001-6974-8090
keywords: Cellular Potts Model
keywords: Embryology
keywords: Chemotaxis
keywords: Extracellular Matrix
programming language: C
programming language: C++
programming language: Cuda
programming language: GLSL
programming language: Makefile
programming language: Python
programming language: QMake
programming language: Shell

https://orcid.org/0000-0002-8919-9401
type: Person
given name: Martijn
family name: de Jong
name: Martijn de Jong

https://orcid.org/0000-0002-6311-1168
type: Person
given name: Lourens
family name: Veen
name: Lourens Veen

0000-0002-7267-160X
type: Person
given name: Erika
family name: Tsingos
name: Erika Tsingos

0000-0002-6152-687X
type: Person
given name: Roeland
family name: Merks
name: Roeland Merks

0000-0003-0625-213X
type: Person
given name: Koen
family name: Keijzer
name: Koen Keijzer

https://orcid.org/0000-0001-6974-8090
type: Person
given name: Bente Hilde
family name: Bakker
name: Bente Hilde Bakker