Software

Morpheus

Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale models in biological terms and mathematical expressions rather than programming code. Its graphical user interface supports the entire workflow from model construction and simulation to visualization, archiving and batch processing.

Website imc.zih.tu-dresden.de/wiki/morpheus
Developers Jörn Starruß (TU Dresden)
Walter de Back (TU Dresden)
Period 2011 – present
Funding Virtual Liver Network
German federal ministry for education and research (BMBF)
Reference

Jörn Starruß, Walter de Back, Lutz Brusch, Andreas Deutsch

Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology Journal Article

Bioinformatics, 30 (9), pp. 1331–1332, 2014.

Abstract | Links | BibTeX

GridABM

gridabm_logo

GridABM is a set of open-source templates to simulate agent-based models (ABM) on multicore computers, computing clusters and computational grids. The software combines the agent-based modeling framework RePast with ProActive, a java-based solution for parallel, distributed, multi-core computing.

Website gridabm.sourceforge.net
Developers Gabor Szemes (AITIA)
Walter de Back (Collegium Budapest)
Laszlo Gulyas (AITIA)
George Kampis (Collegium Budapest)
Period 2007 – 2009
Funding QosCosGrid
EU-funded FP6 framework.
References

Laszlo Gulyas, Walter de Back, Gabor Szemes, George Kampis

Templates for Distributed Agent-Based Simulations Inproceedings

5th International Conference on e-Social Science, 2009.

Abstract | BibTeX

Laszlo Gulyas, Gabor Szemes, George Kampis, Walter de Back

A Modeler-Friendly API for ABM Partitioning Inproceedings

Volume 2: 29th Computers and Information in Engineering Conference, Parts A and B, ASME, 2009.

Links | BibTeX