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IMC
ZIH
TU Dresden
Dept. for Innovative
Methods of Computing
 

Interactive tools

In order to ease the access of students to computer and numerical simulations of biological systems we have developed and manage various interactive simulation platforms.

Morpheus

is a modeling and simulation environment for the study of multi-scale and multicellular systems.

Some of its key features are:

  • multi-scale simulation: simulate multi-scale multicellular systems coupling ODEs, PDEs and cellular Potts models in 2D or 3D.
  • no programming: construct models in graphical interfaces instead of code.
  • model sharing: easily share model descriptions with collaborators.
  • workflow: tools for data export, visualization and parameter scans.
  • automatic scheduling: efficient simulation based on computational graphs.
  • extensible: customize and extend features by developing your own plugins.
  • open-source: source code at gitlab under BSD license.

BIOLGCA-SIM

is a simulation environment for lattice-gas cellular automaton models. It accompanies the book "Cellular Automaton Modeling of Biological Pattern Formation" by A. Deutsch and S. Dormann (Birkhäuser, Boston, 2017, Springer).

BIOLGCA-SIM offers you:

  • a Java Applet with a selection of implemented automaton rules and geometries
  • adjustable parameter values and full control over the simulation
  • visualisation of the simulated dynamics and patterns

PDEsim

is a simulation environment that can be used online to simulate dynamical processes as described by coupled partial differential equations (PDEs). Such equations can model for example heat transport through a material, chemical reactions in a petri dish or biological processes in cells and tissues.

PDEsim offers you:

  • a database with stored model equations, parameter values and results
  • a web interface to browse the model collection, read instructions, tune parameters, run simulations, examine the visualized results online and download the results
  • an efficient simulation engine that inserts your model and parameters directly into the C source code and recompiles for faster simulation performance

We welcome your feedback to Lutz Brusch.

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