Meetings

OSB Kick off meeting, Sardinia, 13-15 May 2013

Dates: 9am Monday 13th - 5pm Wednesday 15th May, 2013

Location: Hotel Calabona, Alghero, Sardinia

Local organisers: Sergio Solinas, Irene Solinas
Organising committee: Matteo Cantarelli, Sharon Crook, Padraig Gleeson, Eugenio Piasini, Angus Silver

Focus of meeting

The focus of this meeting was on cerebellar cell & network models.

See the slides below from a number of the presenters, or see a blog post from the OpenWorm project on the meeting.

One specific outcome of the meeting was the setting up of a project to try to create a community developed model (or models) of the cerebellar granule cell.

Agenda

Monday 13th May, 9am - 6pm
Morning Session
9:00        Angus Silver Introduction to the aims of the initiative
9:15 Matteo Cantarelli        Overview of current OSB features & models, current website (Slides)
10:00 Latest on NeuroML & LEMS developments
Padraig Gleeson NeuroML 2 developments (Slides)
Robert Cannon LEMS background & latest developments
Sharon Crook Archival and Search of NeuroML Models and Model Components
11:00 Coffee break
11:15 Tools and resources for large scale modelling
Mike Vella libNeuroML: A Python API for NeuroML (Slides)
Richard Gerkin NeuroUnit: Unit tests for neuroscience models (Slides)
Hugo Cornelis Interoperability in the GENESIS 3.0 Software Federation: the NEURON Simulator as an Example
12:30 Lunch
Afternoon Session
13:30 Tools and resources for large scale modelling
Thomas Close Challenges of simulator-independent network modeling (Slides)
Steve Marsh HiveMind: Generating efficient simulators from NeuroML (Slides)
Paul Fox From tens to millions of neurons: how computer architecture can help (Slides)
14:30 NeuroML: what’s missing/required?
Open session. Chair: Sharon Crook
15:00 Poster session & coffee
16:00 Open discussion on collaborative modelling
Chair:Robert Cannon
Tuesday 14th May, 9am - 6pm
Morning Session
  Cerebellar modelling presentations
9:00 Egidio D’Angelo Cerebellar models: from cellular to network properties
9:45 Stéphane Dieudonné Understanding cerebellar granular layer transcoding
10:30 Tadashi Yamazaki Realtime simulation of a cerebellar spiking network model using a GPU (Slides)
10:45 Coffee break & poster session
11:30 Cerebellar modelling presentations (continued)
Paul Dean Adaptive Filter Models (Slides)
Christian Roessert Compatibility of a detailed model of cerebellar granular layer processing with adaptive filter computations
Jesus Garrido Distributed synaptic plasticity controls spike-timing at the cerebellar granular layer: predictions from a computational model (Slides)
12:30 Lunch
Afternoon Session
13:30 Angus Silver Information flow through the cerebellar granule cell layer
14:15 Eugenio Piasini Tutorials on Git & GitHub (Slides, OSB project used for demo)
14:30 Hands on collaborative modelling session
15:00 Coffee break
15:30 Hands on collaborative modelling session (continued)
Evening
19:30 Conference Dinner: Movida Restaurant
Wednesday 15th May, 9am - 5pm
Morning Session
  Cerebellar modelling presentations
9:00 Chris De Zeeuw Creating Cerebellar Coordination by Distributed Synergistic Plasticity
9:45 Volker Steuber Multi-scale models of synaptic plasticity in the cerebellum (Slides)
10:30 Sergio Solinas Realistic modeling of the cerebellar cortex (Slides)
10:45 Coffee break
11:00 Arnd Roth Untangling cerebellar circuits with scanning electron microscopy and focused ion beam milling
11:45 Continued hands on collaboration session
12:30 Lunch
Afternoon Session
13:30 Continued hands on collaboration session
13:30 Parallel Session: Private CEREBNET planning meeting
15:00 Coffee break
15:30 Presentations of results & feedback
16:30 Future plans for OSB

Posters presented

Maximum poster size: 1.5m x 1.5m

Presenter Title
Sathyaa Subramaniyam The mechanisms of late-onset synaptic responses in a realistic model of Unipolar Brush Cells    
Giovanni Idili OpenWorm - progress report
Stefano Masoli A realistic Purkinje cell model
Jesus Garrido Event-and-time driven simulator accelerated with CPU-GPU co-processing (PDF)
Helena Głąbska Meaningful decompositions of multielectrode LFP recordings (PDF)

Enquiries

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


(Illustration courtesy of Matteo Farinella)

OSB Hackathon 2013

(Looking for details on the Open Source Brain kick off meeting in Sardinia?)

Dates: 9am Wednesday 6th - 5pm Thursday 7th November, 2013

Location: University College London, UK.

Local organisers: Matteo Cantarelli, Padraig Gleeson, Eugenio Piasini, Angus Silver, Boris Marin

Focus of meeting

The focus of this meeting was on open source multicompartmental, conductance based cortical cell & network models.

There are an increasing number of multicompartmental, conductance based (thalamo)cortical cell models being made available and reused/modified by interested parties to address different scientific questions. An example is the Traub et al 2005 thalamocortical network model for which Fortran, NEURON, MOOSE and NeuroML versions have been developed in various labs. This meeting was to look at the range of models out there from the neocortex and thalamus which are interesting for multiple parties and work towards getting these onto public, open source repositories, in standardised formats (NeuroML & potentially PyNN) and get them well tested, annotated and ready for use as research tools by the attendees and the wider community.

Aims

There were 3 specific aims of the meeting:

1) Consolidate the versions of the Traub network model which aim to reproduce the results of the 2005 paper; document what stage these versions are at and what the issues are with each implementation.

2) Create plans for a new network model at this level of detail, with updated cells and connectivity, initially based on a refined Traub model; this model should be open source from the start and as simulator independent as possible; gather requirements on the experimental data needed for this updated model and the electrical properties they should display; create a framework for optimising these models against the data.

3) Look at the range of other multicompartmental, conductance based cortical models which could benefit from this process too (and potentially could be candidates for modification for use in the model of 2)

Attendees

Laszlo Bicskei, Andrew Brown (Southampton), Matteo Cantarelli, Chaitanya Chintaluri, Thomas Greg Corcoran, Helena Głąbska, Padraig Gleeson, Lea Goetz, Boris Marin, Philipe Mendonca, Simon O’Connor, Paola Perin, Eugenio Piasini, Subhasis Ray, Martina Rizza, Arnd Roth, Angus Silver, Richard Tomsett, Mike Vella

Agenda

Wednesday 6th November

Overall theme: Thalamocortical modelling, specifically Thalamocortical network - Traub et al. 2005

Topics for discussion

  • Traub’s model logistic issues and known fixes [FORTRAN (parallel) versus NEURON (parallel) versus NeuroML versus MOOSE]
  • Reproducibility of results from Traub’s paper
  • Shortcomings/flaws/updates of Traub’s model - Cell level and Network level
  • What can Traub’s model tell us?
  • Is it worth fixing?
  • Research interests for modelling a detailed compartmental TC columnar loop [Compartmental modelling versus spiking neurons].
  • A consensus on a good TC loop model - benchmark sorts. [other existing alternate models]
  • Can we match (any) experiments? If so which kind?
Morning Session
9:00 Angus Silver Welcome
9:05 Padraig Gleeson Introduction & goals of Hackathon; introduction to Traub model (Slides)
09:30 Matteo Cantarelli Introduction to the latest features on Open Source Brain (Slides)
10:00 Chaitanya Chintaluri & Helena Głąbska Experiences with Traub model in Parallel NEURON (WIKI, Slides)
10:30 Subhasis Ray Experiences with Traub model in MOOSE (WIKI, Slides)
11:00 Coffee break
11:15 Padraig Gleeson Experiences converting Traub model to NeuroML (WIKI, Slides)
11:45 Richard Tomsett Large scale modelling of the cortex using reduced cell models (Slides)
12:15 Arnd Roth Optimization and testing of a reduced model of pyramidal neurons (Paper, Slides)
12:45 General discussion on Cortical modelling (WIKI) and issues with Traub model (WIKI)
13:00 Lunch
Afternoon Session
14:00 Hacking session I: installing, testing & documenting one another’s models; running network models on high performance computing infrastructure
15:30 Coffee break
15:45 Continued: General discussion on Cortical modelling (WIKI) and issues with Traub model (WIKI
16:15 A consensus on a good TC loop model (WIKI)
17:30 Close of day
19:30 Dinner
Thursday 7th November

Overall theme: Layer 5 pyramidal cell models

Topics for discussion

  • Inconsistencies in existing L5 Pyramidal cell models - a comparison.
  • A consensus on a good model on L5Py cell.
  • Nomenclature consensus for single cells - essential for interchangeability and testing.
  • Milestones for the next meeting and commitments for parties towards development.
  • Essential tools and requirements. [Data sharing, interoperability, testing etc]
  • Debate on “columnar structure” of cortex - if this is the right way to think about cortex?
  • Auditory cortex versus somatosensory barrel cortex
  • Automated testing tools - fortnightly tests depending on participation.
Morning Session
9:00 Chaitanya Chintaluri & Helena Głąbska Incorporating Layer 5b Pyramidal cell - Hay et al. 2011 biophysical properties into Traub model (Slides)
9:30 Mike Vella L5 Pyramidal cell modelling & Neurotune (Slides)
10:00 Simon O’Connor Piriform cortex pyramidal cell model of Vanier (OSB project, Slides)
10:30 Angus Silver Background network activity extends spatial and temporal integration in a L5 cortical pyramidal cell model
11:00 Coffee break
11:30 General discussion on L5 cell modelling (WIKI)
13:00 Lunch
Afternoon Session
14:00 Hacking session II: installing, testing pyramidal cell models; testing packages for model optimisation
15:00 Pipeline for testing realistic models (WIKI)
15:30 Coffee break
15:45 Next steps How do we proceed (WIKI?) Planning for OSB 2014
17:30 Close of meeting

Next steps

Some ideas/suggestions for improving OSB interface

Add a search box beside tree view (issue). Related to this

Make themes more obvious (issue)

Link to GitHub issues/stars/forks (issue)

List of contributors to the wiki more prominent (issue)

Thalamocortical modelling

A list of the priorities/agreed action points from the meeting are here.

Practicalities

The meeting was held on the main UCL campus: http://www.ucl.ac.uk/maps. Room for both days was: Foster Court 243.

Suggestions for accommodation in the vicinity:
http://www.gowerhousehotel.co.uk
http://www.jenkinshotel.demon.co.uk

Enquiries

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

OSB Workshop 2014: Building and sharing models of the cortex

This meeting was the second main meeting of the Open Source Brain initiative.

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 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 Slides
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  

Open collaboration in computational neuroscience

A workshop at Neuroinformatics 2014

Wednesday 27th August 2014, Leiden, Netherlands

Neuroscience has traditionally been a discipline where isolated labs have produced their own experimental data and created their own models to interpret their findings. However, it is becoming clear that no one lab can create cell and network models rich enough to address all the relevant biological questions, or to generate and analyse all the data required to inform, constrain, and test these models. The success of the open source software development movement suggests that both model building and data collection/curation would be greatly enhanced by public, collaborative efforts to solve these problems. This workshop highlighted several examples of such efforts taking place in neuroinformatics, and presented open tools and resources that can be instrumental in facilitating further efforts.

See here for more information on speakers etc.

Program
Angus Silver Introduction to the workshop Slides
Stephen Larson Open Worm: A community developed in silico model of C. Elegans Slides
Padraig Gleeson The Open Source Brain Initiative, enabling collaborative model development in computational neuroscience Slides
Shreejoy Tripathy NeuroElectro: A window to the world's neurophysiology data Slides
Rick Gerkin Data-driven validation of neuroscience models Slides
Aurel A. Lazar Neurokernel: Emulating the drosophila brain on multiple GPUs

OSB Workshop 2015

This meeting was the third main meeting of the Open Source Brain initiative.

Dates 9am Tuesday 12th - 5pm Thursday 14th May, 2015
Location Hotel Calabona, Alghero, Sardinia
Local organisers Sergio Solinas, Paolo Enrico
Organising committee Padraig Gleeson, Angus Silver, Boris Marin, Sharon Crook

Overview of the meeting

As with past OSB meetings this workshop provided an introduction to the OSB initiative and associated technologies and there were a number of presentations from modellers, experimentalists and tool developers interested in creating open, community developed models of neuronal systems.

One day of the meeting was dedicated to creating and sharing experimentally constrained models of the hippocampus.

Speakers
Giorgio Ascoli Krasnow Institute, George Mason University, USA
Tiago Branco MRC Laboratory of Molecular Biology, Cambridge, UK
Claudia Clopath Imperial College London, UK
Michael Hines Yale University, USA
Peter Jonas Institute of Science and Technology, Austria
Julija Krupic O'Keefe Group, University College London, UK
Artur Luczak University of Lethbridge, Canada
Troy Margrie MRC National Institute for Medical Research, London, UK
Michele Migliore National Research Council, Italy & Yale University School of Medicine, USA
Yiota Poirazi Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Greece
Martin Pyka University of Bochum, Germany
Stefan Remy German Center for Neurodegenerative Diseases, Bonn, Germany
Nelson Spruston Howard Hughes Medical Institute, Janelia Farm Research Campus, Virginia

Agenda

There was a NeuroML Editorial Board meeting held prior to the main OSB meeting on Monday 11th May.

Minutes of this meeting can be found here.

Tuesday 12th May, 9am - 5pm

Morning Session
Angus Silver Introduction to the workshop Slides
Padraig Gleeson Overview of OSB & NeuroML Slides
Adrian Quintana Latest features of Open Source Brain
Matteo Cantarelli Latest developments with Geppetto & OpenWorm
Coffee break
Sergio Solinas Creating a 3D model of the cerebellar cortex using NeuroML & OSB Slides
Simon O’Connor A Community Mitral Cell Model Slides

12:30-13:30 Lunch

Afternoon Session
Tiago Branco Synaptic integration in circuits controlling innate behaviours
Troy Margrie The functional diversity, connectivity and intrinsic properties of visual cortical networks
Coffee break & Poster Session
Gabriela Michel Cortical self-construction using Cx3D
Eilif Muller Approaches for reducing fragmentation in the computational modelling community
Discussion session How do OSB and related technologies fit into wider initatives in neuroscience?

17:30 Bus to workshop dinner at Pedramare

Wednesday 13th May, 9am - 6pm

Morning Session
Giorgio Ascoli Hippocampome.org - Neuron classification for real-scale hippocampal modeling
Peter Jonas Biological networks and models of pattern completion
Coffee break
Michele Migliore Computational properties of CA1 pyramidal neurons
Yiota Poirazi Binding memories via dendritic and neuronal co-allocation

12:30-13:30 Lunch

Afternoon Session
Stefan Remy Locomotion, theta oscillations and the speed-correlated firing of hippocampal neurons are controlled by a medial septal glutamatergic circuit
Nelson Spruston Neuronal Diversity and Complexity in the Hippocampus
Coffee break
Martin Pyka Parametric Anatomical Modeling: Creating an anatomically constrained model of the hippocampus Slides
Julija Krupic Framing the grid: effect of boundaries on grid cells and navigation
Armando Romani Data-driven Hippocampus CA1 Modeling in the Human Brain Project

Thursday 14th May, 9am - 5pm

Morning Session
Michael Hines A Parallel Computational Database Idiom Slides
Alex Seeholzer, William Podlaski Visualizing the similarity and pedigree of neuronal ion channel models for NEURON
Claudia Clopath Modelling synaptic plasticity
Coffee break
Artur Luczak Packets of neuronal activity
Oren Amsalem Incorporating Gap Junctions in the Human Brain Project in silico Microcircuitry

12:30-13:30 Lunch

Afternoon Session
Open discussion/planning session Next steps for making detailed neuronal models more accessible for the wider neuroscience community

Enquiries

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

Support

This meeting was being generously supported by:


 

Illustration courtesy of Matteo Farinella  

Open collaboration in computational neuroscience: A workshop at CNS 2015

9am - 5pm, Thursday July 23 2015, University of Economics, Prague, Czech Republic

Building and analysing biophysically and anatomically detailed neuronal networks is a complex and time consuming task, which ideally involves researchers with a range of backgrounds and technical skills. However, most labs cannot expect to have all of these researchers present at any given time. This can lead to stalled projects, lost data/software and needless repetition of experimental and computational work.

A number of initiatives have been started which address these issues. Some are creating public resources with freely available data to constrain such models. Others are using best practices from open source software development to encourage building and sharing of models in a collaborative environment. This workshop served as an informative introduction to these projects as well as a discussion forum for getting feedback and gathering requirements from the community for the developers of these initiatives.

Organisers: Padraig Gleeson (University College London) & Aurel A. Lazar (Columbia University)

Program

Time Presenter Title/subject
9:00 Introduction/welcome
9:01 Jan Antolik (CNRS) Collaboration in neuronal modelling: model sharing, workflows and provenance
9:30 Nicholas Cain (Allen Brain Institute) Resources for Open Collaboration at the Allen Brain Institute (Slides)
10:00 Coffee break
10:30 Padraig Gleeson (University College London) NeuroML & the Open Source Brain Initiative (Slides)
11:00 Adrian Quintana (University College London) Geppetto: online visualisation & simulation for neuronal models (Slides)
11:30 Lightning Talks Michael Sonntag The NIX Project: Comprehensive Storage of Neuroscience Data and Metadata (Slides)
Victor Jirsa The Virtual Brain
Chaitanya Chintaluri NSDF: neuroscience simulation data format (Slides)
12:00 Lunch
13:30 Matteo Cantarelli (MetaCell Ltd) OpenWorm (Slides)
14:00 Aurel A. Lazar (Columbia University) Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain
14:30 Bill Lytton (SUNY Downstate Medical Center) ModelDB (Slides)
15:00 Coffee break
15:30 Eilif Muller (EPFL) Human Brain Project resources for the integrative modelling community (Slides)
16:00 Shreejoy Tripathy (University of British Columbia) Open electrophysiology data and Neuroelectro.org (Slides)
16:30 Open Discussion
17:00 Wrap up

For any enquiries about this workshop, please contact Padraig Gleeson (p.gleeson -at- ucl.ac.uk)

Collaborative Development of Data-Driven Models of Neural Systems

September 18 - 21, 2016, Janelia Farm Research Campus, Virginia, USA

Detailed computational models are critical for elucidating neuronal and network function.
They enable different levels of description to be linked, a wide range of neurophysiological
experiments to be interpreted and quantitative predictions to be made. These factors are
important for understanding large-scale complex systems, like neural circuits; however, more
extensive use and scaling up of these data driven models pose challenges in ensuring that models
are scientifically rigorous, as well as accessible and usable by both theoretical and experimental
researchers alike. This conference will bring together a range of experimentalists, theoreticians
and neuroinformatics developers with the aim of facilitating a global, open infrastructure for
collaborative model development in neuroscience.

More information on the conference, and details on how to register can be found here.