14 NSFBIO: Seamless Integration of Neuroscience Models and Tools with HPC - Easy Path to Supercomputing for Neuroscience

Lead Research Organisation: University College London
Department Name: Neuroscience Physiology and Pharmacology

Abstract

This is a collaboration between University College London, University of California San Diego and Yale University to develop a science gateway for the computational neuroscience community. The gateway, called NSG-R, is designed to help improve our understanding of how the brain works by making it easier for neuroscientists to use complex models of brain cells and circuits in their research. Powerful software has been developed for building and using neuronal models, and on-line resources such as Open Source Brain (OSB), ModelDB,
Neuroscience Information Framework (NIF) have been created to help neuroscientists find existing models, collaborate in developing new ones, and share the results of their work with others.

However, many detailed neuronal models are becoming too complex for the computer hardware that is available to most neuroscientists, resulting in a critical need to use high performance computing resources (HPC). NSG-R builds on the NSG project ("Neuroscience Gateway"), which was developed to eliminate or reduce many of the technical and administrative difficulties that previously limited neuroscientists' access to HPC. That said, NSG users must still log in, upload models, launch simulations, and download results; a process that involves many time-consuming, error-prone steps. NSG-R eliminates these steps by enabling on-demand, automated communication between the NSG server and client applications such as the OSB server.

This seamless access to HPC is implemented in NSG-R by a software infrastructure that uses REpresentational State Transfer ("REST", the R in NSG-R), exposing the capabilities of NSG via publicly available application programmer interfaces. This will allow users of neuroscience resources such as OSB, ModelDB and NIF to readily access HPC from their respective websites via NSG-R. It therefore results in greater research productivity and enables wider use of large scale computational modelling by scientists and students.

Technical Summary

This is a collaboration between University College London, University of California San Diego and Yale University to develop a science gateway for the computational neuroscience community. The gateway, called NSG-R, is designed to help improve our understanding of how the brain works by making it easier for neuroscientists to use complex models of brain cells and circuits in their research. Powerful software has been developed for building and using neuronal models, and on-line resources such as Open Source Brain (OSB), ModelDB,
Neuroscience Information Framework (NIF) have been created to help neuroscientists find existing models, collaborate in developing new ones, and share the results of their work with others.

However, many detailed neuronal models are becoming too complex for the computer hardware that is available to most neuroscientists, resulting in a critical need to use high performance computing resources (HPC). NSG-R builds on the NSG project ("Neuroscience Gateway"), which was developed to eliminate or reduce many of the technical and administrative difficulties that previously limited neuroscientists' access to HPC. That said, NSG users must still log in, upload models, launch simulations, and download results; a process that involves many time-consuming, error-prone steps. NSG-R eliminates these steps by enabling on-demand, automated communication between the NSG server and client applications such as the OSB server.

This seamless access to HPC is implemented in NSG-R by a software infrastructure that uses REpresentational State Transfer ("REST", the R in NSG-R), exposing the capabilities of NSG via publicly available application programmer interfaces. This will allow users of neuroscience resources such as OSB, ModelDB and NIF to readily access HPC from their respective websites via NSG-R. It therefore results in greater research productivity and enables wider use of large scale computational modelling by scientists and students.

Planned Impact

This proposal will facilitate access to High Performance Computing (HPC) resources for non-computational neuroscientists, making complex models of brain function accessible to and usable by a greater range of researchers for investigations of the functioning of the nervous system in health and disease.

Publications

10 25 50
 
Description Access to supercomputing facilities will become more and more essential for neuroscientists as the data and models they use to investigate brain function become more complex. While there are organisations like the US National Science Foundation making such resources available, they often require specialist programming knowledge to use them effectively. In this grant we have investigated ways to make it easier for the online resource www.OpenSourceBrain.org to provide access for researchers to such high performance computers, just through their browsers, without installing software or learning a new programming language. The software we have developed to help make this link is open source and provided freely, so anyone can use it in a different scientific field. As a side result of this project, we have also developed an online tutorial on neuroinformatics resources, which can teach neuroscientists about a range of computational tools, applications and databases which can help them with their research. This has also been made freely available.
Exploitation Route All of the software is freely available, and can be used to help create and test a RESTful API to a science portal like Neuroscience Gateway (e.g. one which interacts with the NSF's Extreme Science and Engineering Discovery Environment (XSEDE) platform).
Sectors Digital/Communication/Information Technologies (including Software),Education,Pharmaceuticals and Medical Biotechnology,Other

URL https://github.com/OpenSourceBrain/NSGPortalShowcase
 
Description Organization of the 2018 International Neuroinformatics Congress, Montreal, Canada
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
 
Description Sharing standardised experimental data and models of neural systems through the Open Source Brain repository
Amount £1,037,773 (GBP)
Funding ID 212941/Z/18/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2018 
End 11/2023
 
Title Code for interacting with Neuroscience Gateway (NSG) portal web interface 
Description We have developed a set of scripts to facilitate submission of computational models in neuroscience to the Neuroscience Gateway (NSG) REST API (web interface). These have been released as open source here: http://www.opensourcebrain.org/projects/nsgportalshowcase 
Type Of Material Technology assay or reagent 
Year Produced 2016 
Provided To Others? Yes  
Impact These scripts greatly facilitate our goal of making open source computational models easy to run on the high performance computing facilities as provided by NSG. Anyone can download these scripts and use them in their own research. 
URL http://www.opensourcebrain.org/projects/nsgportalshowcase
 
Title Open Source Brain Repository 
Description Open Source Brain is a repository of standardized models for computational neuroscience. This award enabled large scale simulations to be run on this resource. 
Type Of Material Computer model/algorithm 
Year Produced 2013 
Provided To Others? Yes  
Impact 800 research groups worldwide have registered on Open Source Brain 
URL http://www.opensourcebrain.org
 
Description Facilitating access to large scale neuronal simulations 
Organisation Stony Brook University
Country United States 
Sector Academic/University 
PI Contribution We are partnering with a number of infrastructure developers in computational neuroscience to make it easier for neuroscientists to build and run large scale neuronal models
Collaborator Contribution UCSD have created the Neuroscience Gateway (NSG) portal to allow computational neuroscientists to access high performance computing resources (https://www.nsgportal.org). SUNY have created NetPyNE (http://www.neurosimlab.org/netpyne/), a Python based platform which will make it easier to run neuronal models across multiple processors.
Impact Models in Open Source Brain can currently be run on the Neuroscience Gateway portal from within a web browser.
Start Year 2015
 
Description Facilitating access to large scale neuronal simulations 
Organisation University of California, San Diego (UCSD)
Country United States 
Sector Academic/University 
PI Contribution We are partnering with a number of infrastructure developers in computational neuroscience to make it easier for neuroscientists to build and run large scale neuronal models
Collaborator Contribution UCSD have created the Neuroscience Gateway (NSG) portal to allow computational neuroscientists to access high performance computing resources (https://www.nsgportal.org). SUNY have created NetPyNE (http://www.neurosimlab.org/netpyne/), a Python based platform which will make it easier to run neuronal models across multiple processors.
Impact Models in Open Source Brain can currently be run on the Neuroscience Gateway portal from within a web browser.
Start Year 2015
 
Title Online Neuroinformatics Tutorial 
Description Part of this project involved interacting with a number of online resources for computational neuroscience. One outcome of this was collecting this knowledge into a set of online slides which can be used for a tutorial on neuroinformatics resources (including Open source Brain and Neuroscience Gateway). This has been made freely available to the community for anyone to use (under Creative Commons Attribution 4.0 International License). 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact This was first presented as a tutorial at CNS 2017 in Antwerp, and will be given again (by Padraig Gleeson) at CNS 2018 in Seattle. 
URL https://github.com/NeuralEnsemble/NeuroinformaticsTutorial
 
Description Invited keynote talk at INCF Congress 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited talk on at the International Neuroinformatics congress in Kuala Lumpar
Year(s) Of Engagement Activity 2017
 
Description Joint poster at Society for Neuroscience & workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact As part of the initial work on this joint NSF/BBSRC collaboration we presented a poster (Seamless integration of neuroscience models and tools with high performance computing) at the annual Society for Neuroscience on plans for the joint resource to allow greater access to high performance computational resources for neuroscientists. One of the UK participants to this grant, Padraig Gleeson, also presented at a workshop organised by the US collaborators on "Using the Neuroscience Gateway Portal for Parallel Simulation" prior to the SfN meeting.
Year(s) Of Engagement Activity 2015
URL http://www.nsgportal.org/workshop.html
 
Description Organization of and dissemination at International meeting entitle 'Collaborative Development of Data-Driven Models of Neural Systems' at Janelia Research Campus, VA, USA. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Collaborative Development of Data-Driven Models of Neural Systems

This conference brought together a range of experimentalists, theoreticians and neuroinformatics developers with the aim of facilitating a global, open infrastructure for collaborative model development in neuroscience.
Year(s) Of Engagement Activity 2016
URL https://www.janelia.org/you-janelia/conferences/collaborative-development-data-driven-models-neural-...
 
Description Poster presentaton at INCF congress 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the INCF congress in Montreal, Canada.
Year(s) Of Engagement Activity 2018
 
Description Workshop presentation at CNS 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Presentation of one of the main outcomes of this joint project to the computational neuroscience community at CNS 2017 in Antwerp . Padraig Gleeson presented on "Using models from the Open Source Brain repository on the NSG portal infrastructure" at a workshop organised by the Neuroscience Gateway developers (with whom we have this joint BBSRC-NSF grant).
Year(s) Of Engagement Activity 2017
URL http://www.nsgportal.org/NSGWorkshop-OCNS-2017.html