neuroConstruct course

BrainTrain Cerebnet

Introduction to compartmental neuronal modelling with neuroConstruct and recent advances in rapid 2-photon imaging

University College London, May 2nd-4th 2012


This course, being run by the Silver Lab @ UCL, will provide an introduction to 3D biophysically detailed neuronal modelling and recent advances in 2-photon imaging methods for studying rapid neuronal signalling. Creation of multicompartmental, conductance based neuronal models has been greatly facilitated by software packages such as NEURON and GENESIS and a range of detailed cell and network models are available which are faithful to the anatomical and biophysical properties of the corresponding biological entities. neuroConstruct is an application which facilitates the construction and analysis of such models through a 3D graphical interface and automates code generation for a number of widely used simulators.

The course will give an overview of the field of detailed compartmental modelling and how it can complement experimental approaches including 2-photon imaging. It will consist of some introductory lectures on modeling and imaging, provide hands on experience of using neuroConstruct, introduce the existing cortical, cerebellar and hippocampal models which are already available in this format, and outline the process of creating new models from experimental data. The course will also cover the simulator independent model description language NeuroML and the growing number of tools available for handling models in this format.

This course is primarily intended for participants in the BrainTrain and Marie Curie Cerebnet training programs, although there are a limited number of places available for other researchers.



  • Registration for the course is closed! . Contact p.gleeson -at- for any enquiries.
  • The venue for the meeting will be the main campus at UCL, with morning lectures taking place in the Watson lecture theatre (G02) in the Medawar building and afternoon hands on practical sessions taking place in G20 in the Christopher Ingold Building. See here for a map of the locations (or look on Google maps).
  • Booking accomodation in London is the responsibility of attendees (try Hotel Cavendish, Gower House Hotel or search for something within your budget). Cerebnet/BrainTrain members should contact their own course administrators regarding refunding expenses.
  • The course will start at 9am on Wed 2nd May and finish at 5pm on Fri 4th May. The overall format will consist of lectures in the morning, hands on modelling in the afternoon.
  • Participants should bring their own laptops on which they can install software (and have about 2GB of disk space).
  • Lunch (2nd-4th May) and dinner (2nd-3rd May) will be provided.
  • Contact p.gleeson -at- for more details.



  • Padraig Gleeson
  • R. Angus Silver
  • Volker Steuber
  • Arnd Roth
  • Guy Billings
  • Matteo Farinella
  • Eugenio Piasini
  • Emmanuelle Chaigneau
  • Tomás Fernández-Alfonso
  • Paul Kirkby
  • K. M. Naga Srinivas Nadella


     Day 1, Wednesday 2nd May
9:00Welcome, outline of courseAngus SilverWatson lecture theatre, Medawar building
9:15Introduction to cable modellingArnd Roth
10:00Compartmental modelling and the Hodgkin Huxley modelVolker Steuber
11:15Introduction to dendritic computationArnd Roth
12:00Overview of simulatorsPadraig Gleeson
12:30Introduction to neuroConstruct (1)Padraig Gleeson
14:00Introduction to neuroConstruct (2)Padraig GleesonG20 cluster room, Christopher Ingold Building
15:00Hands on modelling with neuroConstruct
19:30Dinner: Navarro's, 67 Charlotte Street
     Day 2, Thursday 3rd May
9:00Introduction to NEURONArnd RothWatson lecture theatre, Medawar building
10:00Modelling synapsesGuy Billings
11:15NeuroML and related tools/databasesPadraig Gleeson
12:00Example of using neuroConstruct in a research project: investigating NMDA spikesMatteo Farinella
12:30The Open Source Brain initiativeEugenio Piasini
13:00LunchHaldane room, Wilkins building
14:00Advanced neuroConstruct: Parallel and PythonPadraig GleesonG20 cluster room, Christopher Ingold Building
15:00Hands on modelling with neuroConstruct
19:30Dinner: The Queens Head and Artichoke, 30-32 Albany Street, Regents Park
     Day 3, Friday 4th May
9:00Introduction to 2-photon microscopyTomás Fernández-AlfonsoWatson lecture theatre, Medawar building
10:00Principles of 2-photon photolysisEmmanuelle Chaigneau
11:15High speed 3D 2-photon imagingAngus Silver
12:15LunchHaldane room, Wilkins building
13:00Silver Lab visit (2 groups in 2 parallel sessions seeing 2-photon experimental set ups)3rd floor, Anatomy Building
    Paul Kirkby/K. M. Naga Srinivas Nadella/Tomás Fernández-Alfonso: High speed 3D 2-photon imaging
    Emmanuelle Chaigneau: 2-photon uncaging
15:00Hands on modelling with neuroConstructPadraig GleesonG20 cluster room, Christopher Ingold Building