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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


Maintainer


  • person_outline Johan Elf

Publications for MesoRD

MesoRD citations

 (21)
library_books

Computationally Efficient Modelling of Stochastic Spatio Temporal Dynamics in Biomolecular Networks

2018
Sci Rep
PMCID: 5823887
PMID: 29472589
DOI: 10.1038/s41598-018-21826-8

[…] 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 […]

library_books

Transcriptional bursting in Drosophila development: Stochastic dynamics of eve stripe 2 expression

2017
PLoS One
PMCID: 5402966
PMID: 28437444
DOI: 10.1371/journal.pone.0176228

[…] 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 […]

library_books

Parallel STEPS: Large Scale Stochastic Spatial Reaction Diffusion Simulation with High Performance Computers

2017
Front Neuroinform
PMCID: 5301017
PMID: 28239346
DOI: 10.3389/fninf.2017.00013

[…] -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 […]

library_books

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist

2016
PLoS Comput Biol
PMCID: 5145134
PMID: 27930676
DOI: 10.1371/journal.pcbi.1005220

[…] 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 […]

library_books

A glance at the applications of Singular Spectrum Analysis in gene expression data

2015
PMCID: 4822218
PMID: 27077034
DOI: 10.1016/j.bdq.2015.04.001

[…] 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 […]

library_books

Mid Embryo Patterning and Precision in Drosophila Segmentation: Krüppel Dual Regulation of hunchback

2015
PLoS One
PMCID: 4368514
PMID: 25793381
DOI: 10.1371/journal.pone.0118450

[…] 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

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MesoRD institution(s)
Department of Cell & Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
MesoRD funding source(s)
This work was supported by the European Research Council (ERC no. 203083), the Swedish Foundation for Strategic Research, the Swedish Research Council (VR), Göran Gustafsson Stiftelse and the Knut and Alice Wallenberg Foundation.

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