A cell-based simulation software for multi-cellular systems

Abstract

CellSys is a modular software tool for efficient off-lattice simulation of growth and organization processes in multi-cellular systems in 2D and 3D. It 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. The software 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.Availability: CellSys is freely available for non-commercial use at http://msysbio.com/software/cellsys. The current version of CellSys permits the simulation of growing monolayer cultures and avascular tumor spheroids in liquid environment. Further functionality will be made available ongoing with published papers.Contact: hoehme@izbi.uni-leipzig.de; dirk.drasdo@inria.frSupplementary information: Supplementary data are available at Bioinformatics online.

A semi-stochastic cell-based formalism to model the dynamics of migration of cells in colonies

“…The positions of the mother cell and daughter cell are such that they are shifted at a random orientation to the displacement vector with an additional displacement of magnitude R. We realize that this is a major simplification since the actual orientation is a stochastic variable as well. However, Hoehme and Drasdo (2010) model the separation of a cell into two daughter cells by a stochastic process using a Langevin equation. This will be dealt with in a more rigorous way in future studies.…”

Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results

“…18), and liver (e.g., liver lobules, Fig. 15), with cell numbers starting from few and ranging up to 10 6 [83,150]. Refined image analysis techniques and available software increasingly permit a quantitative analysis of tissues in 3D at micro-meter resolution [38,151].…”

“…Refined image analysis techniques and available software increasingly permit a quantitative analysis of tissues in 3D at micro-meter resolution [38,151]. The data infered can subsequently be transfered into modeling software such as CellSys [150], to simulate the tissue organization process of interest as demonstrated for the example of the regenerating liver (Fig. 15, [33,152]).…”

Particle methods to solve modelling problems in wound healing and tumor growth

“…A mapping of the solution onto the cellular centres is needed to compute the concentration. In [22], similar modelling techniques are considered regarding the solution of concentration equations on a rectangular discretisation mesh and forces of the cells on the substrate or extracellular matrix. In the last-mentioned article the simulation toolbox is described.…”

“…This approach could be combined with modelling the growth of a tumor which possibly halts due to depletion of oxygen and continues to grow as soon as oxygen levels increase due to the arrival of small blood vessels where angiogenesis is triggered by chemokines that are released by death of tumor cells in the necrotic core. Here the modelling could largely benefit from the principles outlined especially in [13,22,23].…”