Multiscale reaction-diffusion simulations with Smoldyn
<p style="text-align:justify;"> <b>Summary:</b> Smoldyn is a software package for stochastic modelling of spatial biochemical networks and intracellular systems. It was originally developed with an accurate off-lattice particle-based model at its core. This has recently...
| Main Authors: | , , |
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| Format: | Journal article |
| Language: | English |
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Oxford University Press
2015
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| _version_ | 1797099481304399872 |
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| author | Robinson, M Andrews, S Erban, R |
| author_facet | Robinson, M Andrews, S Erban, R |
| author_sort | Robinson, M |
| collection | OXFORD |
| description | <p style="text-align:justify;"> <b>Summary:</b> Smoldyn is a software package for stochastic modelling of spatial biochemical networks and intracellular systems. It was originally developed with an accurate off-lattice particle-based model at its core. This has recently been enhanced with the addition of a computationally efficient on-lattice model, which can be run stand-alone or coupled together for multiscale simulations using both models in regions where they are most required, increasing the applicability of Smoldyn to larger molecule numbers and spatial domains. Simulations can switch between models with only small additions to their configuration file, enabling users with existing Smoldyn configuration files to run the new on-lattice model with any reaction, species or surface descriptions they might already have.<br/> <b>Availability and Implementation:</b> Source code and binaries freely available for download at www.smoldyn.org, implemented in C/C++ and supported on Linux, Mac OSX and MS Windows.<br/> <b>Contact:</b>martin.robinson@maths.ox.ac.uk<br/> <b>Supplementary Information:</b> Supplementary data are available at Bioinformatics online and include additional details on model specification and modelling of surfaces, as well as the Smoldyn configuration file used to generate Figure 1. </p> |
| first_indexed | 2024-03-07T05:24:21Z |
| format | Journal article |
| id | oxford-uuid:e00a005b-dbfa-4e1d-b5ca-b9fbb4b466b6 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T05:24:21Z |
| publishDate | 2015 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:e00a005b-dbfa-4e1d-b5ca-b9fbb4b466b62022-03-27T09:43:52ZMultiscale reaction-diffusion simulations with SmoldynJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:e00a005b-dbfa-4e1d-b5ca-b9fbb4b466b6EnglishSymplectic Elements at OxfordOxford University Press2015Robinson, MAndrews, SErban, R <p style="text-align:justify;"> <b>Summary:</b> Smoldyn is a software package for stochastic modelling of spatial biochemical networks and intracellular systems. It was originally developed with an accurate off-lattice particle-based model at its core. This has recently been enhanced with the addition of a computationally efficient on-lattice model, which can be run stand-alone or coupled together for multiscale simulations using both models in regions where they are most required, increasing the applicability of Smoldyn to larger molecule numbers and spatial domains. Simulations can switch between models with only small additions to their configuration file, enabling users with existing Smoldyn configuration files to run the new on-lattice model with any reaction, species or surface descriptions they might already have.<br/> <b>Availability and Implementation:</b> Source code and binaries freely available for download at www.smoldyn.org, implemented in C/C++ and supported on Linux, Mac OSX and MS Windows.<br/> <b>Contact:</b>martin.robinson@maths.ox.ac.uk<br/> <b>Supplementary Information:</b> Supplementary data are available at Bioinformatics online and include additional details on model specification and modelling of surfaces, as well as the Smoldyn configuration file used to generate Figure 1. </p> |
| spellingShingle | Robinson, M Andrews, S Erban, R Multiscale reaction-diffusion simulations with Smoldyn |
| title | Multiscale reaction-diffusion simulations with Smoldyn |
| title_full | Multiscale reaction-diffusion simulations with Smoldyn |
| title_fullStr | Multiscale reaction-diffusion simulations with Smoldyn |
| title_full_unstemmed | Multiscale reaction-diffusion simulations with Smoldyn |
| title_short | Multiscale reaction-diffusion simulations with Smoldyn |
| title_sort | multiscale reaction diffusion simulations with smoldyn |
| work_keys_str_mv | AT robinsonm multiscalereactiondiffusionsimulationswithsmoldyn AT andrewss multiscalereactiondiffusionsimulationswithsmoldyn AT erbanr multiscalereactiondiffusionsimulationswithsmoldyn |