Padraig Gleeson
Speaker of Workshop 4
Will talk about: The Open Source Brain Initiative, enabling collaborative model development in computational neuroscience
Padraig is a postdoc in the lab of Angus Silver at University College London (http://www.ucl.ac.uk/silverlab). He initially joined the lab as software developer following a number of years working in research and development in the telecommunications industry. His initial work towards developing more anatomically detailed models of the cerebellar cortex led to the development of the application neuroConstruct (http://www.neuroconstruct.org) which has been widely used for creating other detailed 3D network models. This application's ability to generate code for multiple neuronal simulators got him involved in the development of the NeuroML language for model specification in computational neuroscience (http://www.neuroml.org/), which has had a major update over the past two years for version 2.0 of the language. He has recently been leading the development of the Open Source Brain repository (http://www.opensourcebrain.org) for collaborative model development, which will be the subject of his presentation.
Computational modelling is important for understanding how brain function and dysfunction emerge from lower level neurophysiological mechanisms. However, computational neuroscience has been hampered by poor accessibility, transparency, validation and reuse of models. The Open Source Brain (OSB) initiative (http://www.opensourcebrain.org) has been created to address these issues. This aims to create a repository of neuronal and network models from multiple brain regions and species that will be in accessible, standardised formats and work across multiple simulators. OSB will create a collaborative space to facilitate model creation and sharing, where both computational and experimental researchers can contribute to their development.
OSB combines advanced open source technologies for tracking, annotating and combining models developed across research teams, with software for building, validating, visualising, simulating and analysing models. While models can be developed and shared in any format we actively encourage and support their conversion to open, standardised modelling languages like NeuroML (http://www.NeuroML.org) and PyNN (http://neuralensemble.org/PyNN). OSB will also benefit from close interaction with other important neuroinformatics resources like NeuroMorpho, ModelDB, NIF and NeuroElectro.
Padraig will introduce the aims of the OSB initiative, describe the current functionality of the website and the range of models already available, and present future plans for the project. By increasing the scientific rigour of model construction, improving their robustness and transparency and lowering technological barriers, OSB will increase the power of computational approaches and make them accessible to a wider range of neuroscientists.
