The Open Source Brain repository

(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.


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)


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


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.


The meeting was held on the main UCL campus: Room for both days was: Foster Court 243.

Suggestions for accommodation in the vicinity:


If you have any enquiries about this meeting, please don’t hesitate to contact: