OSB Meeting in Sardinia, 2019#


The OSB workshop 2019 took place in Alghero, Sardinia in September 2019.


9am Monday 9th Sept. - 5pm Wednesday 11th Sept., 2019


Hotel Calabona, Alghero, Sardinia

Organising committee

Padraig Gleeson, Matt Earnshaw, Angus Silver

Overview of the meeting#

Open Source Brain (http://www.opensourcebrain.org) was created as a platform for sharing and collaboratively developing models in computational neuroscience. Models of cells and circuits in standardised formats can be visualised, analysed and simulated through a standard web browser. The aim has been to improve the quality, accessibility and scientific rigour of models used to investigate brain function.

Following a renewal of our funding from the Wellcome Trust, we are expanding the functionality of the platform to also enable sharing of the experimental data behind the models. The OSB workshop 2019 highlighted the latest features of OSB and engaged current and future users of the platform through invited talks, hands on demonstrations, and user presentations.

The two key themes of the meeting were:

1) Accessible sharing of cellular neuroscience data

Through support for the Neurodata Without Borders (NWB) format, OSB will facilitate sharing of multiple types of experimental data used to constrain computational models, including electrophysiological recordings, Ca2+ florescence imaging, 2D, 3D and 4D imaging and behavioural data.

2) Modelling the cortex across scales

Cortical networks are modelled at many scales from abstract representations of interacting populations (neural masses) to networks of biophysically and morphologically detailed cell models. NeuroML is being expanded to cover a greater range of these models, which will allow them to be shared and simulated on OSB, facilitating comparison of models and ideas between researchers. This ongoing work is taking place as part of the SIG on Standardised Representations of Network Structures.


Mon 9th Sept Building and sharing standardised neuronal models#

    Morning session

9:00 Angus Silver Welcome and Introduction to goals of meeting (Slides)

9:10 Padraig Gleeson Open Source Brain and NeuroML - Enabling collaborative model development in computational neuroscience (Slides)

9:50 Yann Zerlaut An overview of the tools for modelling and simulation developed within the Human Brain Project (Slides)

10:30 - 11:00 Coffee break

11:00 Sharon Crook NeuroML-DB: A model sharing platform to promote efficient model selection and reuse (Slides)

11:30 Rajnish Ranjan A kinetic map of the homomeric voltage-gated potassium channel (Kv) family

12:00 Boris Marin Converting models to NeuroML (Slides)

12:30 - 13:30 Lunch

    Afternoon session

13:30 Matteo Cantarelli Geppetto: an open source platform to build neuroscience applications (Slides)

14:00 Ankur Sinha NeuroFedora: Free software for Open Science (Slides)

14:30 Lightning talks Bence András Lázár, Bettina Kata Kádár, Csaba Kazinczi (University of Szeged)

15:00 - 15:30 Coffee break

15:45 - 17:30 Discussion session: How do we make models more accessible and useful to scientists?

  • Are the current features of OSB (for sharing, visualization, analysis, simulation, tutorials and testing) sufficient for you to switch to using it in your model development and dissemination?

  • How can OSB better interact with other initiatives in the field, e.g. HBP/Allen?

  • How can we facilitate model conversion to populate OSB will all the key models available?

  • How can we lower the barrier for building new models and reusing existing components for new scientific questions?

  • What are the current limitations of NeuroML and PyNN?

Tues 10th Sept Standardising and sharing experimental neuroscience data#

    Morning session

9:00 Angus Silver Introduction to session (Slides)

9:05 Diego Restrepo Shedding light on the involvement of the cerebellum in associative learning (Slides)

9:50 Simon Schultz NeuroSEE: a pipeline for processing and analysing data from multiphoton fluorescence brain imaging experiments (Slides)

10:35 - 11:00 Coffee break

11:00 Jeffrey S. Diamond The Blind Men and the Retina: Community Connectomics Prior to Automated Segmentation

11:45 Oliver Rübel NWB:N 2.0: An Ecosystem for Neurophysiology Data Standardization (Slides)

12:30 - 13:30 Lunch

    Afternoon session

13:30 Matteo Cantarelli & Filippo Ledda NWB Explorer: visualize and understand neurophysiology data (Slides)

13:50 Ian Duguid Towards a systems level understanding of volitional motor control: approaches and challenges in data acquisition, management & sharing

14:35 Alex Cayco-Gajic (presented by Angus Silver) Population imaging and dimensionality analysis of cerebellar axons

15:00 - 15:30 Coffee break

15:30 - 17:00 Discussion session: How can we make data sharing accessible and useful?

  • What are the key challenges in standardizing data so that it can be parsed/reused?

  • Are the proposed solutions to data standardization appropriate for handling the size and heterogeneity of neuroscience data (e.g. behavioural analysis, high speed Ca2+ imaging, multi-channel electrophysiology, connectomics, genomics etc.)?

  • What are the key challenges in making data available?

  • What should be shared? Raw data, analysis, data points in figures?

  • Is sharing data worth the (considerable) effort - who will actually use it?

18:00 Bus to conference dinner Pedramare restaurant

Wed 11th Sept Investigating brain function across multiple scales#

    Morning session

9:00 Angus Silver Introduction to session (Slides)

9:02 Jan Fousek The Virtual Brain: building blocks for whole-brain modeling (Slides)

9:45 Sacha van Albada Large-scale spiking neural network modeling of primate cerebral cortex (Slides)

10:30 - 11:00 Coffee break

11:00 Yazan Billeh Large-scale Datasets and Modeling Tools from the Allen Institute for Brain Science (Slides)

11:45 Fleur Zeldenrust Understanding information transfer in the brain: from single cell to network (Slides)

12:15 Sergio Solinas The NeuroAgents ERC project (Slides)

12:30 - 13:30 Lunch

    Afternoon session

13:30 Oren Amsalem Cellular mechanisms of auditory surprise in faithful computer replica of cortical microcircuit

14:00 Padraig Gleeson Creating cortical models across scales in NeuroML (Slides)

14:30 - 15:00 Coffee break

15:30 - 17:30 Discussion session: How can we create better multiscale models of circuits?

  • Are multiscale models of the brain worth the effort?

  • What are the benefits of bringing multiscale models and the experimental data used to build and test them together?

  • What are the key challenges in linking model structure, optimization and testing to experimental data?

  • Do Python notebooks provide the right balance in the trade-off between accessibility and flexibility in model building/data analysis for OSB infrastructure?




Oren Amsalem

Hebrew University, Israel

Yazan Billeh

Allen Institute, USA

Matteo Cantarelli

MetaCell Ltd

Alex Cayco Gajic

University College London, UK & École Normale Supérieure, France

Sharon Crook

Arizona State University, USA

Jeffrey S. Diamond


Ian Duguid

University of Edinburgh, UK

Matt Earnshaw

University College London, UK

Jan Fousek

Aix Marseille Université, France

Padraig Gleeson

University College London, UK

Boris Marin

Universidade Federal do ABC, Brazil

Rajnish Ranjan

Blue Brain Project, EPFL, Switzerland

Diego Restrepo

University of Colorado, USA

Oliver Rübel

Lawrence Berkeley National Lab, USA

Simon Schultz

Imperial College, UK

Angus Silver

University College London, UK

Ankur Sinha

University of Hertfordshire, UK

Sacha van Albada

Jülich Research Centre, Germany

Fleur Zeldenrust

Radboud University, Netherlands

Yann Zerlaut

Centre National de la Recherche Scientifique, France


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


This meeting was generously supported by:


Data in image above courtesy of Antoine Valera, UCL