OSB Workshop 2014: Building and sharing models of the cortex¶

This meeting was the second main meeting of the Open Source Brain initiative (http://www.opensourcebrain.org).

Dates: 9am Wednesday 14th - 5pm Friday 16th May, 2014

Location: Hotel Calabona, Alghero, Sardinia

Local organisers: Sergio Solinas, Irene Solinas
Organising committee: Padraig Gleeson, Eugenio Piasini, Angus Silver, Boris Marin

Focus of the meeting¶

There are an increasing number of cortical cell and network models being developed and made publicly available, from networks of leaky integrate and fire neurons based on cortical connectivity and firing properties, to multicompartmental, conductance based cell models. Many of these are being reused, reimplemented and extended to address new scientific questions by labs around the world.

In this meeting, we looked at the range cortico-thalamic models out there which are of widespread interest and discussed the best ways to get these into public, open source repositories, in standardised formats such as NeuroML and PyNN. We investigated the steps needed to ensure these models are well tested, annotated and ready for use as research tools by the attendees and the wider community.

There were presentations from experimentalists who are producing the data to constrain these models, as well as simulator and application developers who are creating the infrastructure to build, simulate, analyse and share the models.

Speakers¶

Giuseppe Chindemi, Blue Brain Project, EPFL, Switzerland
Sharon Crook, Arizona State University, USA
Egidio D'Angelo, University of Pavia, ITALY
Markus Diesmann, Research Center Jülich, Germany
Dirk Feldmeyer, Aachen University, Germany
Alon Korngreen, Bar-Ilan University, Israel
Linda Lanyon, International Neuroinformatics Coordinating Facility, Stockholm, Sweden
Dave Lester, SpiNNaker project, University of Manchester, UK
Robert A. McDougal, Yale University School of Medicine, USA
Michele Migliore, National Research Council, Italy & Yale University School of Medicine, USA
Ole Paulsen, University of Cambridge, UK
Horacio G. Rotstein, New Jersey Institute of Technology, Newark (NJ) USA.
Angus Silver, University College London
Werner Van Geit, Blue Brain Project, EPFL, Switzerland
Tim Vogels, University of Oxford, UK
Daniel Wójcik, Nencki Institute, Poland

Agenda¶

There was be a NeuroML Editorial Board meeting held prior to the main OSB meeting on Tues 13th May.

Minutes of this meeting can be found here.

Wednesday 14th May, 9am - 6pm¶

	Morning Session
Welcome & background to the Open Source Brain initiative
Angus Silver	Introduction	Slides
Padraig Gleeson	Overview of OSB & relationship to NeuroML	Slides
Adrian Quintana	Using Open Source Brain	Slides
Relationship to other initiatives
Robert McDougal	ModelView: extracting model structure and presenting it on the web with NEURON	Slides
Linda Lanyon	The International Neuroinformatics Coordinating Facility	Slides

12:30-13:30 Lunch

	Afternoon Session
Detailed modelling of individual cortical neurons
Alon Korngreen	Realistic modelling of cortical pyramidal neurons	Slides
Angus Silver	Glutamate-Bound NMDARs Arising from In Vivo-like Network Activity Extend Spatio-temporal Integration in a L5 Cortical Pyramidal Cell Model
Guy Eyal	Dendrites impact the encoding capabilities of the axon	Slides
Werner Van Geit	Reconstruction of a neocortical microcircuit: Neurons

Thursday 15th May, 9am - 6pm¶

	Morning Session
Enabling technologies
Dave Lester	SpiNNaker Software and Open Standards	Slides
Matteo Cantarelli	Geppetto: A web based multiscale simulator	Slides
Robert Cannon	New features & capabilities under development for NeuroML & LEMS	Slides
Network models of the cortex
Tim Vogels	The dance of excitation and inhibition

12:30-13:30 Lunch

	Afternoon Session
Markus Diesmann	A full-scale spiking model of the local cortical network	Slides
Giuseppe Chindemi	Reconstruction of a neocortical microcircuit: connectivity & synapses
Daniel Wójcik	From generation to publication of simulated data in a large-scale model of thalamo-cortical loop
Chaitanya Chintaluri	Modeling extracellular potentials in a cortical slice preparation	Slides
Dirk Feldmeyer	Excitatory and inhibitory neuron morphologies and their implication for synaptic connectivity

Friday 16th May, 9am - 6pm¶

	Morning Session
OSB Symposium: Oscillation and resonance in CNS network loops	Organiser: Sergio Solinas This symposium aims to cluster the neuroscientists actively working in the field of neuronal network oscillations within the framework of OSB in order to promote the integration of models and tools in this area. For more information see here: Symposium2014
Horacio G. Rotstein	Inhibition-based theta resonance in a hippocampal network: a modeling study	Slides
Ole Paulsen	Oscillations and resonance in hippocampal neurons.
Michele Migliore	Modeling the effects of electric fields from power lines on hippocampal CA1 pyramidal neurons.
Egidio D'Angelo	Theta-frequency resonance at the cerebellum input stage improves spike timing on the millisecond time-scale

12:30-13:30 Lunch

	Afternoon Session
Future plans
Boris Marin	Model testing & validation framework for OSB	Slides
Sharon Crook	NeuroML developments: Editorial Board Report & plans for NeuroML Database
Padraig Gleeson	Requirements gathering for OSB: What is needed for truly collaborative model development in computational neuroscience?

Enquiries¶

If you have any enquiries about this meeting, please don’t hesitate to contact: p.gleeson@ucl.ac.uk.

Support¶

This meeting was generously supported by:

     
 
Symposium sponsors:
       
 

Illustration courtesy of Matteo Farinella