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Meredys specifications


Unique identifier OMICS_14695
Name Meredys
Alternative name MEsoscopic REaction DYnamics Simulator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Java 3D
Maintained Yes




No version available



  • person_outline Nicolas Le Novère

Publication for MEsoscopic REaction DYnamics Simulator

Meredys citations


Extending rule based methods to model molecular geometry and 3D model resolution

BMC Syst Biol
PMCID: 4977479
PMID: 27490268
DOI: 10.1186/s12918-016-0294-z

[…] re any additional data files to run, as the molecular geometry is encoded into the rules themselves. In addition, our method only requires the BioNetGen software to run.The stochastic, particle-based Meredys software [] uses Brownian dynamics to simulate reaction-diffusion systems at the mesoscopic level. It requires the specification of details such as molecule positions, molecular geometry, reac […]


Multi state Modeling of Biomolecules

PLoS Comput Biol
PMCID: 4201162
PMID: 25254957
DOI: 10.1371/journal.pcbi.1003844

[…] cal relationships between neighboring subunits or members of a macromolecular complex. One drawback of this method for representing protein complexes, compared to other spatial modeling tools such as Meredys , is that MCell does not allow for the diffusion of complexes and hence of multi-state molecules. This can in some cases be circumvented by adjusting the diffusion constants of ligands that in […]


Simulations of pattern dynamics for reaction diffusion systems via SIMULINK

BMC Syst Biol
PMCID: 4006638
PMID: 24725437
DOI: 10.1186/1752-0509-8-45

[…] ns of nonlinear reaction-diffusion equations. Some of these examples are discussed in detail in Part III of Yang’s book. Alternative to MATLAB, there are other options for pattern simulations such as MEREDYS[], implemented in the Java programming language, interpreting the NEUROML model description language []. Besides, there are other programming environments applicable to modelling pattern forma […]


Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP

BMC Syst Biol
PMCID: 2847995
PMID: 20233407
DOI: 10.1186/1752-0509-4-25

[…] Receptor movement in the synaptic spine was simulated using the Meredys simulation software (Available at: All simulations were run on a Centos 4.2 Linux LSF Cluster. The individual hosts used were a mixture of 32 bi […]


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Meredys institution(s)
Computational Neurobiology Group, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Meredys funding source(s)
Supported by the European Molecular Biology Laboratory.

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