MesoRD statistics
Tool stats & trends
Looking to identify usage trends or leading experts?

MesoRD specifications
Information
Unique identifier | OMICS_11482 |
---|---|
Name | MesoRD |
Software type | Package/Module |
Interface | Command line interface |
Restrictions to use | None |
Operating system | Unix/Linux |
Programming languages | C++ |
License | GNU General Public License version 3.0 |
Computer skills | Advanced |
Version | 1.1 |
Maintained | Yes |
Versioning
No version available
Documentation
- Documentation: http://mesord.sourceforge.net/documentation.php
Maintainer
- person_outline Johan Elf
Publications for MesoRD
Stochastic reaction-diffusion simulation with MesoRD.
MesoRD citations
(21)Computationally Efficient Modelling of Stochastic Spatio Temporal Dynamics in Biomolecular Networks
[…] on the surface of the cell, which is assumed to be a sphere of the radius 100 μm. Since Gillespie’s algorithm cannot take into account spatial effects, we solve the reaction-diffusion equations using MesoRD (Mesoscopic Reaction-Diffusion Simulator), a numerical solver for stochastic reaction diffusion equations using the next subvolume method.In reality, it is highly probable that there would be s […]
Transcriptional bursting in Drosophila development: Stochastic dynamics of eve stripe 2 expression
[…] All reactions–binding/unbinding of TFs, transcriptional initiation and termination–are solved using the MesoRD package (http://mesord.sourceforge.net/, []). Deterministic solution of the model (as a system of ODEs, ordinary differential equations; 4th order Runge-Kutta) is used to constrain the rate con […]
Parallel STEPS: Large Scale Stochastic Spatial Reaction Diffusion Simulation with High Performance Computers
[…] -diffusion simulators. These simulators can be separated into two major categories, voxel-based and particle-based. Voxel-based simulators, such as STEPS (Hepburn et al., ), URDME (Drawert et al., ), MesoRD (Hattne et al., ), and NeuroRD (Oliveira et al., ), divide the geometry into small voxels where different spatial variants of the Gillespie Stochastic Simulation Algorithm (Gillespie SSA) (Gill […]
Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist
[…] eaddy [] feature microscale, particle-tracking algorithms for spatial stochastic simulation. STEPS [] and MesoRD [] support mesoscopic spatial stochastic simulations; STEPS on unstructured meshes and MesoRD on structured meshes. In contrast to the above software packages, StochSS features capabilities at the deterministic well-mixed level, the stochastic well-mixed level, and the mesoscopic spatia […]
A glance at the applications of Singular Spectrum Analysis in gene expression data
[…] ion of the hb gene by the Bcd protein gradient in the anterior part was studied by modelling the noise observed in hb regulation using a chemical master equation approach. For solving this model, the MesoRD software package has been used which mainly follows a stochastic approach and the results indicate that Hb output noise is mostly dependent on the transcription and translation dynamics of its […]
Mid Embryo Patterning and Precision in Drosophila Segmentation: Krüppel Dual Regulation of hunchback
[…] Stochastic and deterministic solutions of the model were computed with the MesoRD software package ([]; http://mesord.sourceforge.net). 1D computations were solved in a one-dimensional series of 60 subvolumes (each a cube 5μm on a side), corresponding to energids (nucleus pl […]
Citations
Looking to check out a full list of citations?

MesoRD reviews
Be the first to review MesoRD