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  Staff Overview

  Professors

  • Rüdiger Reischuk
  • Till Tantau
  • Maciej Liskiewicz

  Secretary

  • Elisa Merkel-Weißer

  Contact

  • Rooms • Phone • Mail

  Research assistants

  • Max Bannach
  • Katharina Dannenberg
  Zacharias Heinrich
  • Florian Thaeter
  • Benito van der Zander
  • Marcel Wienöbst

  Technical staff

  • Jens Heinrichs
• Winter semester 2020

Institute for Theoretical Computer Science

LImmSim

LImmSim

LImmSim is an agent based model of the vertebrate adaptive immune response. It is based on the Celada-Seiden model (see P. E. Seiden and F. Celada, A Model for Simulating Cognate Recognition and Response in the Immune System, Journal of Theoretical Biology 158:329-357, 1992) and existing implementation by Filippo Castiglione (C-ImmSim, see M. Bernaschi and F. Castiglione, Design and implementation of an Immune System Simulator, Computers in Biology and Medicine, 31(5):303-331, 2001). Some interesting features of LImmSim are:

• Hybrid simulation: Both stochastic and deterministic versions of all simulation algorithms are available. The switch between stochastic and deterministic algorithms is controlled by thresholds.
• Object-oriented implementation: The implementation is easily extensible by new types of cells, molecules and interactions.
• Multithreading: LImmSim is happy about that quad-core machine or Sun Fire server ...
• Free software: LImmSim is available under the GNU GPL.

How to Download and Use LImmSim

1. Download the gzipped tar-ball and extract it. (A new directory named limmsim will be created).
2. Type "make" to compile LImmSim. You need g++ installed. An alternative makefile "Makefile.solaris" is provided which works (for us) on Solaris. If the makefile does not work for you, please drop me a line so I can improve it.
3. Get started by executing "limmsim-gui.tcl" and playing with the parameters. To run the GUI, you need the tcl/tkl shell "wish". On Ubuntu Linux, for example, you can install the package "tcl8.4"
4. Read the file named "README" which contains a bit more information.
5. Send me your feedback and questions. Make improvements to LImmSim and release them under the GPL :)

Alternatives to LImmSim

The following alternative implementations of the Celada-Seiden model are known to me:

• ImmSim and friends by Steven Kleinstein are provided as binaries for windows.
• CImmSim by Filippo Castiglione is the most recent and complete implementation of the CS model. The source code is available on request.

Files

limmsim.tgz - gzipped tar-ball containing the LImmSim source.

Ah, by the way ... "LImmSim" stands for "Lübecker Immunsystem-Simulator".