%0 Journal Article %1 gleeson_neuroml:_2010 %A Gleeson, Padraig %A Crook, Sharon %A Cannon, Robert C. %A Hines, Michael L. %A Billings, Guy O. %A Farinella, Matteo %A Morse, Thomas M. %A Davison, Andrew P. %A Ray, Subhasis %A Bhalla, Upinder S. %A Barnes, Simon R. %A Dimitrova, Yoana D. %A Silver, R. Angus %D 2010 %J PLoS Comput Biol %K modeling xml %N 6 %P e1000815 %R 10.1371/journal.pcbi.1000815 %T NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail %U http://dx.doi.org/10.1371/journal.pcbi.1000815 %V 6 %X Computer modeling is becoming an increasingly valuable tool in the study of the complex interactions underlying the behavior of the brain. Software applications have been developed which make it easier to create models of neural networks as well as detailed models which replicate the electrical activity of individual neurons. The code formats used by each of these applications are generally incompatible however, making it difficult to exchange models and ideas between researchers. Here we present the structure of a neuronal model description language, NeuroML. This provides a way to express these complex models in a common format based on the underlying physiology, allowing them to be mapped to multiple applications. We have tested this language by converting published neuronal models to NeuroML format and comparing their behavior on a number of commonly used simulators. Creating a common, accessible model description format will expose more of the model details to the wider neuroscience community, thus increasing their quality and reliability, as for other Open Source software. NeuroML will also allow a greater “ecosystem” of tools to be developed for building, simulating and analyzing these complex neuronal systems.

@article{gleeson_neuroml:_2010, abstract = {Computer modeling is becoming an increasingly valuable tool in the study of the complex interactions underlying the behavior of the brain. Software applications have been developed which make it easier to create models of neural networks as well as detailed models which replicate the electrical activity of individual neurons. The code formats used by each of these applications are generally incompatible however, making it difficult to exchange models and ideas between researchers. Here we present the structure of a neuronal model description language, {NeuroML.} This provides a way to express these complex models in a common format based on the underlying physiology, allowing them to be mapped to multiple applications. We have tested this language by converting published neuronal models to {NeuroML} format and comparing their behavior on a number of commonly used simulators. Creating a common, accessible model description format will expose more of the model details to the wider neuroscience community, thus increasing their quality and reliability, as for other Open Source software. {NeuroML} will also allow a greater {\textquotedblleft}ecosystem{\textquotedblright} of tools to be developed for building, simulating and analyzing these complex neuronal systems.}, added-at = {2014-01-19T08:37:04.000+0100}, author = {Gleeson, Padraig and Crook, Sharon and Cannon, Robert C. and Hines, Michael L. and Billings, Guy O. and Farinella, Matteo and Morse, Thomas M. and Davison, Andrew P. and Ray, Subhasis and Bhalla, Upinder S. and Barnes, Simon R. and Dimitrova, Yoana D. and Silver, R. Angus}, bdsk-url-1 = {http://dx.doi.org/10.1371/journal.pcbi.1000815}, biburl = {https://www.bibsonomy.org/bibtex/23426f63d26616579a41d056c7f08a1f6/neurokernel}, doi = {10.1371/journal.pcbi.1000815}, interhash = {dce7ae7b27752770d8ff3c78fb826fe8}, intrahash = {3426f63d26616579a41d056c7f08a1f6}, journal = {{PLoS} Comput Biol}, keywords = {modeling xml}, month = jun, number = 6, pages = {e1000815}, shorttitle = {{NeuroML}}, timestamp = {2014-01-19T08:37:04.000+0100}, title = {{NeuroML:} A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail}, url = {http://dx.doi.org/10.1371/journal.pcbi.1000815}, urldate = {2011-05-18}, volume = 6, year = 2010 }