OSB2014 » History » Version 58
Version 57 (Padraig Gleeson, 23 May 2014 11:11) → Version 58/60 (Padraig Gleeson, 03 Jun 2014 14:27)
### 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](http://www.hotelcalabona.com/), [Alghero](http://www.alghero-turismo.it/en/), Sardinia
Local organisers: [Sergio Solinas](/users/23), Irene Solinas
Organising committee: [Padraig Gleeson](/users/4), [Eugenio Piasini](/users/3), [Angus Silver](/users/6), [Boris Marin](/users/67)
### 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](http://people.epfl.ch/giuseppe.chindemi), [Blue Brain Project](http://bluebrain.epfl.ch), EPFL, Switzerland
[Sharon Crook](/users/8), Arizona State University, USA
[Egidio D'Angelo](http://www-5.unipv.it/dangelo/), University of Pavia, ITALY
[Markus Diesmann](http://www.fz-juelich.de/SharedDocs/Personen/INM/INM-6/EN/Diesmann_Markus.html?nn=724694), Research Center Jülich, Germany
[Dirk Feldmeyer](http://www.rwth-aachen.de/go/id/cznk/?lidx=1), Aachen University, Germany
[Alon Korngreen](/users/190), Bar-Ilan University, Israel
[Linda Lanyon](http://incf.org/about/who-we-are/staff), International Neuroinformatics Coordinating Facility, Stockholm, Sweden
[Dave Lester](/users/90), [SpiNNaker project](http://apt.cs.man.ac.uk/projects/SpiNNaker/), University of Manchester, UK
[Robert A. McDougal](http://senselab.med.yale.edu), Yale University School of Medicine, USA
[Michele Migliore](http://www.pa.ibf.cnr.it/personale/migliore/index.html), National Research Council, Italy & Yale University School of Medicine, USA
[Ole Paulsen](http://noggin.pdn.cam.ac.uk/Group/OlePaulsen), University of Cambridge, UK
[Horacio G. Rotstein](http://web.njit.edu/~horacio/), New Jersey Institute of Technology, Newark (NJ) USA.
[Angus Silver](/users/6), University College London
[Werner Van Geit](http://bluebrain.epfl.ch/page-68317-en.html), [Blue Brain Project](http://bluebrain.epfl.ch), EPFL, Switzerland
[Tim Vogels](http://www.cncb.ox.ac.uk/team/group-leaders/tim/), University of Oxford, UK
[Daniel Wójcik](/users/74), Nencki Institute, Poland
### Agenda
There was be a [NeuroML Editorial Board](http://www.neuroml.org/editors.php) meeting held prior to the main OSB meeting on **Tues 13th May**.
Minutes of this meeting can be found [here](http://www.neuroml.org/files/NeuroMLEditorialBoardMay2014.pdf).
#### Wednesday 14th May, 9am - 6pm
| |**Morning Session** | |
|:---|:---|:---|
| *Welcome & background to the Open Source Brain initiative* |
| **Angus Silver** | Introduction | [Slides](http://www.opensourcebrain.org/attachments/download/198/Intro_OSB_RAS_For%20web.pdf) |
| **Padraig Gleeson** | Overview of OSB & relationship to NeuroML | [Slides](/attachments/download/188/OSBIntro-Sardinia2014-public.ppt) |
| **Adrian Quintana** | Using Open Source Brain | [Slides](http://www.opensourcebrain.org/attachments/download/193/OSBSardinia2014_Quintana.pdf) |
| *Relationship to other initiatives* |
| **Robert McDougal** | ModelView: extracting model structure and presenting it on the web with NEURON | [Slides](http://www.opensourcebrain.org/attachments/download/199/modelview-2014-05-14.pdf) |
| **Linda Lanyon** | The International Neuroinformatics Coordinating Facility | [Slides](http://www.opensourcebrain.org/attachments/download/190/OSB-Lanyon.pdf) |
**12:30-13:30 Lunch**
| |**Afternoon Session** | |
|:---|:---|:---|
| *Detailed modelling of individual cortical neurons* |
| **Alon Korngreen** | Realistic modelling of cortical pyramidal neurons| [Slides](http://www.opensourcebrain.org/attachments/download/192/AlonKorngreen_OSB.pdf) |
| **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](http://www.opensourcebrain.org/attachments/download/189/OSB_2014_Guy_Eyal.pptx) |
| **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](https://docs.google.com/presentation/d/1bmM7yJ-J6y6-7ROiXYkLT6lSj8a8xS497qXxVz65uLo/edit?usp=sharing) |
| **Matteo Cantarelli** | Geppetto: A web based multiscale simulator | [Slides](http://www.opensourcebrain.org/attachments/download/195/Geppetto_OSB_2014.pdf) |
| **Robert Cannon** | New features & capabilities under development for NeuroML & LEMS | [Slides](http://www.opensourcebrain.org/attachments/download/196/lems-lems-lite.pdf) |
| 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](http://www.opensourcebrain.org/attachments/download/194/Sardinia14_Diesmann_published.pdf) |
| **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](http://www.opensourcebrain.org/attachments/download/203/OSB2014_Wojcik.pdf) |
| **Chaitanya Chintaluri** | Modeling extracellular potentials in a cortical slice preparation | [Slides](http://www.opensourcebrain.org/attachments/download/197/Modeling_extracellular_potentials_in_cortical_slices.pdf) |
| **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](/users/23)** 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](http://www.opensourcebrain.org/attachments/download/200/RotsteinHG_TalkOSBAlghero_2014-05-16.pdf) |
| **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](http://www.opensourcebrain.org/attachments/download/191/OSBValidationBorisMarin.pdf) |
| **Sharon Crook** | NeuroML developments: [Editorial Board Report](http://www.neuroml.org/files/NeuroMLEditorialBoardMay2014.pdf) & 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](mailto:p.gleeson@ucl.ac.uk).
### Support
This meeting was generously supported by:
 
Symposium sponsors:
  
*Illustration courtesy of [Matteo Farinella](/users/34) *
### 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](http://www.hotelcalabona.com/), [Alghero](http://www.alghero-turismo.it/en/), Sardinia
Local organisers: [Sergio Solinas](/users/23), Irene Solinas
Organising committee: [Padraig Gleeson](/users/4), [Eugenio Piasini](/users/3), [Angus Silver](/users/6), [Boris Marin](/users/67)
### 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](http://people.epfl.ch/giuseppe.chindemi), [Blue Brain Project](http://bluebrain.epfl.ch), EPFL, Switzerland
[Sharon Crook](/users/8), Arizona State University, USA
[Egidio D'Angelo](http://www-5.unipv.it/dangelo/), University of Pavia, ITALY
[Markus Diesmann](http://www.fz-juelich.de/SharedDocs/Personen/INM/INM-6/EN/Diesmann_Markus.html?nn=724694), Research Center Jülich, Germany
[Dirk Feldmeyer](http://www.rwth-aachen.de/go/id/cznk/?lidx=1), Aachen University, Germany
[Alon Korngreen](/users/190), Bar-Ilan University, Israel
[Linda Lanyon](http://incf.org/about/who-we-are/staff), International Neuroinformatics Coordinating Facility, Stockholm, Sweden
[Dave Lester](/users/90), [SpiNNaker project](http://apt.cs.man.ac.uk/projects/SpiNNaker/), University of Manchester, UK
[Robert A. McDougal](http://senselab.med.yale.edu), Yale University School of Medicine, USA
[Michele Migliore](http://www.pa.ibf.cnr.it/personale/migliore/index.html), National Research Council, Italy & Yale University School of Medicine, USA
[Ole Paulsen](http://noggin.pdn.cam.ac.uk/Group/OlePaulsen), University of Cambridge, UK
[Horacio G. Rotstein](http://web.njit.edu/~horacio/), New Jersey Institute of Technology, Newark (NJ) USA.
[Angus Silver](/users/6), University College London
[Werner Van Geit](http://bluebrain.epfl.ch/page-68317-en.html), [Blue Brain Project](http://bluebrain.epfl.ch), EPFL, Switzerland
[Tim Vogels](http://www.cncb.ox.ac.uk/team/group-leaders/tim/), University of Oxford, UK
[Daniel Wójcik](/users/74), Nencki Institute, Poland
### Agenda
There was be a [NeuroML Editorial Board](http://www.neuroml.org/editors.php) meeting held prior to the main OSB meeting on **Tues 13th May**.
Minutes of this meeting can be found [here](http://www.neuroml.org/files/NeuroMLEditorialBoardMay2014.pdf).
#### Wednesday 14th May, 9am - 6pm
| |**Morning Session** | |
|:---|:---|:---|
| *Welcome & background to the Open Source Brain initiative* |
| **Angus Silver** | Introduction | [Slides](http://www.opensourcebrain.org/attachments/download/198/Intro_OSB_RAS_For%20web.pdf) |
| **Padraig Gleeson** | Overview of OSB & relationship to NeuroML | [Slides](/attachments/download/188/OSBIntro-Sardinia2014-public.ppt) |
| **Adrian Quintana** | Using Open Source Brain | [Slides](http://www.opensourcebrain.org/attachments/download/193/OSBSardinia2014_Quintana.pdf) |
| *Relationship to other initiatives* |
| **Robert McDougal** | ModelView: extracting model structure and presenting it on the web with NEURON | [Slides](http://www.opensourcebrain.org/attachments/download/199/modelview-2014-05-14.pdf) |
| **Linda Lanyon** | The International Neuroinformatics Coordinating Facility | [Slides](http://www.opensourcebrain.org/attachments/download/190/OSB-Lanyon.pdf) |
**12:30-13:30 Lunch**
| |**Afternoon Session** | |
|:---|:---|:---|
| *Detailed modelling of individual cortical neurons* |
| **Alon Korngreen** | Realistic modelling of cortical pyramidal neurons| [Slides](http://www.opensourcebrain.org/attachments/download/192/AlonKorngreen_OSB.pdf) |
| **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](http://www.opensourcebrain.org/attachments/download/189/OSB_2014_Guy_Eyal.pptx) |
| **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](https://docs.google.com/presentation/d/1bmM7yJ-J6y6-7ROiXYkLT6lSj8a8xS497qXxVz65uLo/edit?usp=sharing) |
| **Matteo Cantarelli** | Geppetto: A web based multiscale simulator | [Slides](http://www.opensourcebrain.org/attachments/download/195/Geppetto_OSB_2014.pdf) |
| **Robert Cannon** | New features & capabilities under development for NeuroML & LEMS | [Slides](http://www.opensourcebrain.org/attachments/download/196/lems-lems-lite.pdf) |
| 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](http://www.opensourcebrain.org/attachments/download/194/Sardinia14_Diesmann_published.pdf) |
| **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](http://www.opensourcebrain.org/attachments/download/203/OSB2014_Wojcik.pdf) |
| **Chaitanya Chintaluri** | Modeling extracellular potentials in a cortical slice preparation | [Slides](http://www.opensourcebrain.org/attachments/download/197/Modeling_extracellular_potentials_in_cortical_slices.pdf) |
| **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](/users/23)** 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](http://www.opensourcebrain.org/attachments/download/200/RotsteinHG_TalkOSBAlghero_2014-05-16.pdf) |
| **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](http://www.opensourcebrain.org/attachments/download/191/OSBValidationBorisMarin.pdf) |
| **Sharon Crook** | NeuroML developments: [Editorial Board Report](http://www.neuroml.org/files/NeuroMLEditorialBoardMay2014.pdf) & 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](mailto:p.gleeson@ucl.ac.uk).
### Support
This meeting was generously supported by:
 
Symposium sponsors:
  
*Illustration courtesy of [Matteo Farinella](/users/34) *