DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation
DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by eq...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-03-01
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| Series: | Frontiers in Neuroinformatics |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fninf.2018.00010/full |
| _version_ | 1818235573638266880 |
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| author | Jason S. Sherfey Jason S. Sherfey Austin E. Soplata Salva Ardid Erik A. Roberts David A. Stanley Benjamin R. Pittman-Polletta Nancy J. Kopell |
| author_facet | Jason S. Sherfey Jason S. Sherfey Austin E. Soplata Salva Ardid Erik A. Roberts David A. Stanley Benjamin R. Pittman-Polletta Nancy J. Kopell |
| author_sort | Jason S. Sherfey |
| collection | DOAJ |
| description | DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator) or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations. DynaSim also includes a large set of features that simplify exploring model dynamics over parameter spaces, running simulations in parallel using both multicore processors and high-performance computer clusters, and analyzing and plotting large numbers of simulated data sets in parallel. It also includes a graphical user interface (DynaSim GUI) that supports full functionality without requiring user programming. The software has been implemented in MATLAB to enable advanced neural modeling using MATLAB, given its popularity and a growing interest in modeling neural systems. The design of DynaSim incorporates a novel schema for model specification to facilitate future interoperability with other specifications (e.g., NeuroML, SBML), simulators (e.g., NEURON, Brian, NEST), and web-based applications (e.g., Geppetto) outside MATLAB. DynaSim is freely available at http://dynasimtoolbox.org. This tool promises to reduce barriers for investigating dynamics in large neural models, facilitate collaborative modeling, and complement other tools being developed in the neuroinformatics community. |
| first_indexed | 2024-12-12T11:56:07Z |
| format | Article |
| id | doaj.art-e52a63deacfb4211a80473d13b74d68c |
| institution | Directory Open Access Journal |
| issn | 1662-5196 |
| language | English |
| last_indexed | 2024-12-12T11:56:07Z |
| publishDate | 2018-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroinformatics |
| spelling | doaj.art-e52a63deacfb4211a80473d13b74d68c2022-12-22T00:25:12ZengFrontiers Media S.A.Frontiers in Neuroinformatics1662-51962018-03-011210.3389/fninf.2018.00010325327DynaSim: A MATLAB Toolbox for Neural Modeling and SimulationJason S. Sherfey0Jason S. Sherfey1Austin E. Soplata2Salva Ardid3Erik A. Roberts4David A. Stanley5Benjamin R. Pittman-Polletta6Nancy J. Kopell7Department of Mathematics and Statistics, Boston University, Boston, MA, United StatesCenter for Systems Neuroscience, Psychological and Brain Sciences, Boston University, Boston, MA, United StatesGraduate Program for Neuroscience, Boston University, Boston, MA, United StatesDepartment of Mathematics and Statistics, Boston University, Boston, MA, United StatesDepartment of Biomedical Engineering, Boston University, Boston, MA, United StatesDepartment of Mathematics and Statistics, Boston University, Boston, MA, United StatesDepartment of Mathematics and Statistics, Boston University, Boston, MA, United StatesDepartment of Mathematics and Statistics, Boston University, Boston, MA, United StatesDynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator) or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations. DynaSim also includes a large set of features that simplify exploring model dynamics over parameter spaces, running simulations in parallel using both multicore processors and high-performance computer clusters, and analyzing and plotting large numbers of simulated data sets in parallel. It also includes a graphical user interface (DynaSim GUI) that supports full functionality without requiring user programming. The software has been implemented in MATLAB to enable advanced neural modeling using MATLAB, given its popularity and a growing interest in modeling neural systems. The design of DynaSim incorporates a novel schema for model specification to facilitate future interoperability with other specifications (e.g., NeuroML, SBML), simulators (e.g., NEURON, Brian, NEST), and web-based applications (e.g., Geppetto) outside MATLAB. DynaSim is freely available at http://dynasimtoolbox.org. This tool promises to reduce barriers for investigating dynamics in large neural models, facilitate collaborative modeling, and complement other tools being developed in the neuroinformatics community.http://journal.frontiersin.org/article/10.3389/fninf.2018.00010/fulldynamical systemsneural modelsGNU octaveneuroscience gatewaygraphical user interfacecode generation |
| spellingShingle | Jason S. Sherfey Jason S. Sherfey Austin E. Soplata Salva Ardid Erik A. Roberts David A. Stanley Benjamin R. Pittman-Polletta Nancy J. Kopell DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation Frontiers in Neuroinformatics dynamical systems neural models GNU octave neuroscience gateway graphical user interface code generation |
| title | DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation |
| title_full | DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation |
| title_fullStr | DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation |
| title_full_unstemmed | DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation |
| title_short | DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation |
| title_sort | dynasim a matlab toolbox for neural modeling and simulation |
| topic | dynamical systems neural models GNU octave neuroscience gateway graphical user interface code generation |
| url | http://journal.frontiersin.org/article/10.3389/fninf.2018.00010/full |
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