URDME

URDME is a tool to simulate general stochastic reaction-transport and modeling. The URDME algorithm uses Unstructured triangular and tetrahedral meshes to resolve general geometries and the Reaction-Diffusion Master Equation formalism.

Topic

Molecular biology;Systems biology;Molecular dynamics

Detail

  • Operation: Molecular dynamics

  • Software interface: Command-line user interface

  • Language: MATLAB

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.4

  • Credit: The Swedish Graduate School in Mathematics and Computing, the Swedish Research Council and the Linnaeus centre of excellence, the Royal Swedish Academy of Sciences, SSF, U.S. NSF, U.S DOE, Institute for Collaborative Biotechnologies grant from the U.S. Army Research Office, the National Institute of Biomedial Imaging And Bioengineering of the National Institute of Health.

  • Input: -

  • Output: -

  • Contact: Andreas Hellander: andreash@cs.ucsb.edu, Brian Drawert: bdrawert@cs.ucsb.edu, Stefan Engblom: stefane@it.uu.se, bdrawert@cs.ucsb.edu

  • Collection: -

  • Maturity: Emerging

Publications

  • Sensitivity estimation and inverse problems in spatial stochastic models of chemical kinetics
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.1007/978-3-319-10705-9_51
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  • Stochastic simulation of pattern formation in growing tissue: a multilevel approach
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.1007/s11538-018-0454-y
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  • Computing the Moments of High Dimensional Solutions of the Master Equation
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.1016/j.amc.2005.12.032
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  • Multiscale modelling via split-step methods in neural firing
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.1080/13873954.2018.1488740
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  • Scalable population-level modelling of biological cells incorporating mechanics and kinetics in continuous time
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.1098/rsos.180379
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  • Mesoscopic Modeling of Random Walk and Reactions in Crowded Media
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.1103/PhysRevE.98.033304
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  • Simulation of stochastic reaction--diffusion processes on unstructured meshes
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.1137/080721388
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  • URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries.
  • Drawert B, Engblom S, Hellander A. URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries. BMC Syst Biol. 2012 Jun 22;6:76.
  • https://doi.org/10.1186/1752-0509-6-76
  • PMID: 22727185
  • PMC: PMC3439286

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