LImmSim — a Free implementation of the Celada-Seiden model
- gzipped tar-ball containing the LImmSim source.
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
- Download the gzipped tar-ball and extract it. (A new directory named limmsim will be created).
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.
- 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"
- Read the file named "README" which contains a bit more information.
- Send me your feedback and questions. Make improvements to LImmSim and release them under the GPL :)
Reading About and Citing LImmSim
The algorithms underlying LImmSim are described in the following paper:
Johannes Textor, Björn Hansen:
Hybrid Simulation Algorithms for an Agent Based Model of the Immune Response.
Cybernetics and Systems, 40(5):390-417, 2009.
Go to website | Show PDF
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.
Ah, by the way ... "LImmSim" stands for "Lübecker Immunsystem-Simulator".