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¶

Tuesday 14th May, 9am - 6pm¶

Wednesday 15th May, 9am - 5pm¶

Posters presented¶

Maximum poster size: 1.5m x 1.5m

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?

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.

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¶

12:30-13:30 Lunch

Thursday 15th May, 9am - 6pm¶

12:30-13:30 Lunch

Friday 16th May, 9am - 6pm¶

12:30-13:30 Lunch

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.

OSB Workshop 2015¶

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

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.

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¶

12:30-13:30 Lunch

17:30 Bus to workshop dinner at Pedramare

Wednesday 13th May, 9am - 6pm¶

12:30-13:30 Lunch

Thursday 14th May, 9am - 5pm¶

12:30-13:30 Lunch

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¶

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 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.

Developing, standardising and sharing large scale cortical network models¶

A workshop at CNS 2018, Tues 17th July, Allen Institute, Seattle

A number of groups around the world are developing complex, experimentally constrained models of cortical function. Creating the software infrastructure to develop, simulate and share these types of models takes a significant amount of time for any of the groups involved and there can be a lot of overlap, duplication in work and repeated effort.

This workshop was organised to highlight some of the initiatives currently underway to build detailed cortical models as well as those projects building the infrastructure to make it easier to develop, disseminate and compare the models. Attendees of this workshop were provided with an overview of the state of the art in large scale cortical model development and the efforts underway to make these more accessible and reusable for other researchers.

This workshop was the first activity of the INCF Special Interest Group on Standardised Representations of
Network Structures.

Organiser: Padraig Gleeson (University College London)

Program¶

9:00 Sacha van Albada, Jülich Research Centre, Germany

Large scale model development from the NEST perspective (abstract)

9:30 Anton Arkhipov, Allen Institute, Seattle, USA and Eilif Muller, Blue Brain Project, Switzerland

Data-Driven Modeling of Brain Circuits and the SONATA Data Format (abstract)

10:30 Coffee break

11:00 Salvador Dura-Bernal, SUNY Downstate Medical Center, Brooklyn, NY, USA

Development of large scale data-driven network models in NetPyNE, a high-level interface to NEURON

11:30 Padraig Gleeson, University College London, UK

Large scale cortical models in NeuroML format on Open Source Brain

12:00 Open Discussion: How best to move forward and what needs of the community are not being met? How can the SIG help in this respect?

Workshop Report¶

A short report following the workshop, along with links to the presentations, can be found here.

Enquiries¶

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

A workshop at Neuroinformatics 2018, Wed 8th August, McGill University, Montréal. This workshop will give an introduction to the background and aims of the Open Source Brain initative, show some of the cortial, cerebellar, hippocampal and other models which have been made available on the repository, and highlight the recent functionality for viewing, analysing and simulating models through the OSB website. There will also be introducations to NeuroML and PyNN, the main standardised formats supported by OSB, and we will demonstrate the options for converting your own models to these formats to make full use of the features of OSB.

The workshop will take place on the morning of the day prior to the main Neuroinformatics meeting.

Organisers: Padraig Gleeson & Angus Silver (University College London)

Registration: The workshop is free, but registration is required. Please register here.

Location: Room 613 in the Education Building, 3700 McTavish Street, Montréal (map)

Program¶

Morning

Afternoon

As part of the Hackathon sessions (taking place in Thompson House in the ballroom), the speakers will be available for hands on assistance using OSB & converting models to standardised formats.

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

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

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.

Agenda¶

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?

Speakers¶

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:

^{Data in image above courtesy of Antoine Valera, UCL}