This title appears in the Scientific Report :
2020
Systematic textual and graphical description of connectivity
Systematic textual and graphical description of connectivity
Sustainable research on neuronal network models requires published models to be understandable, reproducible, and extendable. Left-out details about mathematical concepts and assumptions, algorithmic implementations, or parameterizations adversely affect progress. Such flaws are unfortunately freque...
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Sustainable research on neuronal network models requires published models to be understandable, reproducible, and extendable. Left-out details about mathematical concepts and assumptions, algorithmic implementations, or parameterizations adversely affect progress. Such flaws are unfortunately frequent and one reason is a lack of readily applicable standards and tools for model description [1]. Here, we review models made available by the Computational Neuroscience community in databases like ModelDB [2] and Open Source Brain [3], and investigate the corresponding connectivity structures and their descriptions in both manuscript and code. Based on this review, we derive a set of connectivity concepts in combination with guidelines for a comprehensive, complete, and concise description of network connectivity. In particular, we propose a unified graphical notation for network diagrams to foster an intuitive understanding of network properties (compare [4]). This work also aims to guide the implementation of connection routines in simulation software like NEST [5] and neuromorphic hardware systems.References1. Nordlie E et al. (2009) Towards Reproducible Descriptions of Neuronal Network Models. PLoS Comput Biol. 5(8):e1000456, 10.1371/journal.pcbi.10004562. McDougal R A et al. (2017) Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. J Comput Neurosci. 42:1-10, 10.1007/s10827-016-0623-73. Gleeson P et al. (2019) Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating and Developing Standardized Models of Neurons and Circuits. Neuron. 103(3):395-411.e5, 10.1016/j.neuron.2019.05.0194. Le Novère N et al. (2009) The Systems Biology Graphical Notation. Nat Biotechnol. 27(8):735-41, 10.1038/nbt.15585. Gewaltig M-O and Diesmann M (2007). NEST (NEural Simulation Tool). Scholarpedia. 2(4):1430, 10.4249/scholarpedia.1430 |