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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

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Documentation


Maintainer


  • person_outline Johan Elf <>

Publications for MesoRD

MesoRD in publications

 (13)
PMCID: 5823887
PMID: 29472589
DOI: 10.1038/s41598-018-21826-8

[…] 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 […]

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

[…] 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 […]

PMCID: 4082941
PMID: 25045716
DOI: 10.1155/2014/980501

[…] [], and gridcel []), while voxel-based methods calculate changes in the number of molecules occurring in small well-stirred compartments in which the space modelled is partitioned (e.g., steps [], mesord [], and neurord [])., particle-based modelling is very computationally intensive, because it means to solve the equation of motion for each molecule of the system, which is appropriate […]

PMCID: 3854456
PMID: 24339757
DOI: 10.1371/journal.pcbi.1003347

[…] values and , respectively, whereas the densities of membrane-bound proteins were initially set to zero., to simulate the stochastic reaction diffusion kinetics (1)–(7) in three dimensions, we used mesord , a tool to solve the stochastic master equation using a reaction diffusion master equation. it is based on the next subvolume method ., we thank r.d. mullins for introducing us to a22 […]

PMCID: 3834793
PMID: 24021382
DOI: 10.1093/bioinformatics/btt523

[…] and movement of species., to support diffusion and transport, sk adds ‘next-subvolume’ diffusion () to the kappa framework. this positions sk among other meso-scale modelling techniques, e.g. mesord () and smartcell (). several existing approaches handle spatially constrained models (), but none builds on a rule-based approach, with the notable exception of cbng which extends the bng […]


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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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