title: LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2.
abstract: Computational models are increasingly important for studying complex neurophysiological systems. As scientific tools, it is essential that such models can be reproduced and critically evaluated by a range of scientists. However, published models are currently implemented using a diverse set of modeling approaches, simulation tools, and computer languages making them inaccessible and difficult to reproduce. Models also typically contain concepts that are tightly linked to domain-specific simulators, or depend on knowledge that is described exclusively in text-based documentation. To address these issues we have developed a compact, hierarchical, XML-based language called LEMS (Low Entropy Model Specification), that can define the structure and dynamics of a wide range of biological models in a fully machine readable format. We describe how LEMS underpins the latest version of NeuroML and show that this framework can define models of ion channels, synapses, neurons and networks. Unit handling, often a source of error when reusing models, is built into the core of the language by specifying physical quantities in models in terms of the base dimensions. We show how LEMS, together with the open source Java and Python based libraries we have developed, facilitates the generation of scripts for multiple neuronal simulators and provides a route for simulator free code generation. We establish that LEMS can be used to define models from systems biology and map them to neuroscience-domain specific simulators, enabling models to be shared between these traditionally separate disciplines. LEMS and NeuroML 2 provide a new, comprehensive framework for defining computational models of neuronal and other biological systems in a machine readable format, making them more reproducible and increasing the transparency and accessibility of their underlying structure and properties.
authors.affiliation: Textensor Limited Edinburgh, UK.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Cannon
authors.affiliation: Department of Neuroscience, Physiology and Physiology, University College London London, UK.
authors.forename: Padraig
authors.initials: P
authors.lastname: Gleeson
authors.affiliation: School of Mathematical and Statistical Sciences and School of Life Sciences, Arizona State University Tempe, AZ, USA.
authors.forename: Sharon
authors.initials: S
authors.lastname: Crook
authors.affiliation: Textensor Limited Edinburgh, UK.
authors.forename: Gautham
authors.initials: G
authors.lastname: Ganapathy
authors.affiliation: Department of Neuroscience, Physiology and Physiology, University College London London, UK ; CAPES Foundation, Ministry of Education of Brazil Brasilia, Brazil.
authors.forename: Boris
authors.initials: B
authors.lastname: Marin
authors.affiliation: Department of Neuroscience, Physiology and Physiology, University College London London, UK.
authors.forename: Eugenio
authors.initials: E
authors.lastname: Piasini
authors.affiliation: Department of Neuroscience, Physiology and Physiology, University College London London, UK.
authors.forename: R Angus
authors.initials: RA
authors.lastname: Silver
keywords: model description language; model sharing; simulation; spiking neural networks; standardization