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The NeuroML C. elegans Connectome

Tim Busbice1*, Padraig Gleeson2, Sergey Khayrulin3, Matteo Cantarelli4, Alexander Dibert3, Giovanni Idili4, Andrey Palyanov3 and Stephen Larson4
  • 1 Interintelligence Research, United States
  • 2 University College London, United Kingdom
  • 3 A.P. Ershov Institute of Informatics Systems, Russian Federation
  • 4 OpenWorm.org, Italy

We have merged and extended the C. elegans connectome (Varshney et al., 2006) and a three-dimensional cellular anatomy model (Grove & Sternberg, 2011) in the context of the OpenWorm project, an open source project to build a data integration and simulation framework for the C. elegans. To do so, we have leveraged the NeuroML standard (Gleeson et al., 2010), a language for describing neuronal morphologies, ion channels, synapse models and position and network structure in a simulator independent format. It facilitates the exchange of these key model components between computational neuroscience applications. We have converted the neurons described as 3D objects into NeuroML multi-compartmental neuron models and populated the connection statements between these neurons with the Varshney et al. (2006) connection graph. We have used NeuroConstruct (Gleeson et al., 2007) as the rallying point for these data integration efforts and we have demonstrated a successful export from NeuroConstruct into a simulation engine. We have also made available a WebGL based browser that enables the neurons to be seen in the 3D context of the rest of the C. elegans anatomy ( http://browser.openworm.org ). While not yet sufficient to explain the activity of its neurons, we believe this is a necessary prerequisite for deep investigations into the non-linear dynamics and neuronal computation of the C. elegans neuronal network. Supported by the Neurolinx Research Institute ( http://neurolinx.org )

References

Gleeson, P., Steuber, V., & Silver, R. A. (2007). neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron, 54(2), 219-35. http://dx.doi.org/10.1016/j.neuron.2007.03.025
Gleeson, P., Crook, S., Cannon, R. C., Hines, M. L., Billings, G. O., Farinella, M., Morse, T. M., et al. (2010). NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail. (K. J. Friston, Ed.) PLoS Computational Biology, 6(6), e1000815. http://dx.doi.org/10.1371/journal.pcbi.1000815
Grove, C.A., Sternberg, P.W.. (2011) The Virtual Worm: A Three-Dimensional Model of the Anatomy of Caenorhabditis elegans at Cellular Resolution. 18th International C. elegans meeting. Retrieved from http://www.celegans.org/2011/pdf/abstracts_web.pdf
Varshney, L. R., Chen, B. L., Paniagua, E., Hall, D. H., & Chklovskii, D. B. (2009). Structural properties of the caenorhabditis elegans neuronal network. Arxiv preprint arXiv:0907.2373, 12596, 1-41.

Keywords: computational neuroscience, neuroinformatics, C.elegans, neuroml, connectome

Conference: 5th INCF Congress of Neuroinformatics, Munich, Germany, 10 Sep - 12 Sep, 2012.

Presentation Type: Poster

Topic: Neuroinformatics

Citation: Busbice T, Gleeson P, Khayrulin S, Cantarelli M, Dibert A, Idili G, Palyanov A and Larson S (2013). The NeuroML C. elegans Connectome. Front. Neuroinform. Conference Abstract: 5th INCF Congress of Neuroinformatics. doi: 10.3389/conf.fninf.2013.08.00017

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Received: 21 Mar 2013; Published Online: 27 Nov 2013.

* Correspondence: Dr. Tim Busbice, Interintelligence Research, unset, United States, tim@openworm.org