Green Brain - Computational Modelling of the Honeybee Brain
Lead Research Organisation:
University of Sussex
Department Name: Sch of Engineering and Informatics
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Publications
Nowotny T
(2013)
Machine learning for automatic prediction of the quality of electrophysiological recordings.
in PloS one
Nowotny T
(2013)
Data-driven honeybee antennal lobe model suggests how stimulus-onset asynchrony can aid odour segregation.
in Brain research
Serrano E
(2013)
Gain control network conditions in early sensory coding.
in PLoS computational biology
Cope A
(2013)
Biomimetic and Biohybrid Systems
Nowotny T
(2014)
Drosophila olfactory receptors as classifiers for volatiles from disparate real world applications.
in Bioinspiration & biomimetics
Nowotny T
(2014)
Two Challenges of Correct Validation in Pattern Recognition
in Frontiers in Robotics and AI
Nowotny T
(2014)
SpineML and Brian 2.0 interfaces for using GPU enhanced Neuronal Networks (GeNN)
in BMC Neuroscience
Diamond A
(2014)
Classifying chemical sensor data using GPU-accelerated bio-mimetic neuronal networks based on the insect olfactory system
in BMC Neuroscience
Yavuz E
(2014)
Simulating spiking neural networks on massively parallel graphical processing units using a code generation approach with GeNN
in BMC Neuroscience
| Description | We have developed the code generation based GeNN framework for accelerated neuronal network simulations on GPUs. In brief, the GeNN framework allows scientists and engineers to describe a neuronal network model in a comparatively simple C++ API and GeNN transforms this description into optimised GPU accelerated code. This is an important step forward as the intricacies of effective GPU acceleration have been a roadblock to all but the most expert GPU users. The GeNN framework has enabled our partners in Sheffield to build an autonomous robot that is performing obstacle avoidance based on a bio-mimetic neuronal network controller simulated on an embedded GPU accelerator. |
| Exploitation Route | The GeNN framework is freely available under the open source GPL v2 license. It can be used for research in computational neuroscience and artificial intelligence. It can also be used as a basis for developing further software for GPU acceleration. Since the research has been completed we have won additional funding from the EPSRC in the Brains on Board program grant (EP/P006094/1). The GeNN software is one of the main pillars underpinning a large program of research with strong emerging impacts in this new initiative. |
| Sectors | Digital/Communication/Information Technologies (including Software),Education,Other |
| URL | https://github.com/genn-team/genn |
| Description | We have worked with a large IT company to generate research software products based on the GeNN framework. The main product is a machine learning front-end for GeNN called ML GeNN (https://github.com/genn-team/ml_genn) which supports machine learning researchers to use GeNN by providing a Python based syntax that they will be familiar with from Keras/TensorFlow. |
| First Year Of Impact | 2020 |
| Sector | Digital/Communication/Information Technologies (including Software) |
| Impact Types | Economic |
| Description | EPSRC Programme Grant |
| Amount | £4,816,675 (GBP) |
| Funding ID | EP/P006094/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2016 |
| End | 11/2021 |
| Description | EfuturesXD staff award |
| Amount | £46,346 (GBP) |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2014 |
| End | 09/2014 |
| Description | HFSP Program Grant |
| Amount | $337,500 (USD) |
| Funding ID | RGP0053/2015 |
| Organisation | Human Frontier Science Program (HFSP) |
| Sector | Charity/Non Profit |
| Country | France |
| Start | 07/2015 |
| End | 06/2018 |
| Description | Marie Sklodowska Curie Fellow Dr. Michael Schmuker |
| Amount | € 231,283 (EUR) |
| Organisation | European Commission |
| Department | Seventh Framework Programme (FP7) |
| Sector | Public |
| Country | European Union (EU) |
| Start | 09/2014 |
| End | 08/2016 |
| Description | Task 11.3.6 of the Human Brain Project FET Flagship |
| Amount | € 113,276 (EUR) |
| Organisation | European Commission |
| Department | Seventh Framework Programme (FP7) |
| Sector | Public |
| Country | European Union (EU) |
| Start | 04/2014 |
| End | 03/2016 |
| Description | The Leverhulme Trust Senior Research Fellowship |
| Amount | £44,522 (GBP) |
| Organisation | Royal Academy of Engineering |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2014 |
| End | 08/2015 |
| Description | Collaboration with University of Sheffield |
| Organisation | University of Sheffield |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We work together on the Green Brain project. Our team at Sussex contributes the GPU computing expertise and in particular the GeNN framework. We also provide models of olfaction. |
| Collaborator Contribution | The Sheffield partners provide robotics and visual system modelling. |
| Impact | The outputs are recorded as outputs of our joint EPSCR grant. |
| Start Year | 2013 |
| Title | GPU enhanced Neuronal Networks (GeNN) |
| Description | Software package to simulate neuronal networks on GPU accelerators using a domain specific language/ code-generation approach. (latest release 1.2, 2014) |
| Type Of Technology | Software |
| Year Produced | 2013 |
| Open Source License? | Yes |
| Impact | The tool is still in alpha. Notable impacts are expected somewhat later. |
| URL | https://github.com/genn-team/genn |
| Title | SpineCreator |
| Description | The SpineCreator graphical tool is a cross platform (OSX with retina support, Linux and (potentially) Windows) graphical drag and drop tool for SpineML model editing and simulation. It features OpenGL visualisation of networks, simulator integration and graphical analysis tools. See http://bimpa.group.shef.ac.uk/SpineML/index.php/Gui for details. |
| Type Of Technology | Software |
| Year Produced | 2014 |
| Open Source License? | Yes |
| Impact | The software is being used in the European seventh framework project NoTremor (http://notremor.eu/notremor/) |
| URL | https://github.com/SpineML/SpineCreator |
| Title | SpineML_2_GeNN |
| Description | SpineML_2_GeNN converts neural models described in the SpineML description format into the GeNN GPU simulation framework |
| Type Of Technology | Software |
| Year Produced | 2014 |
| Open Source License? | Yes |
| Impact | This software allows computational neuroscience models to be easily simulated on the embarrassingly parallel hardware of modern NVidia graphics cards, vastly decreasing the cost required to improve simulation performance. |
| URL | https://github.com/genn-team/genn |
| Title | brian2genn |
| Description | This software provides an interface from the popular "Brian" simulator (version 2) to our GPU enhanced neuronal networks (GeNN) framework that allows users to define computational neuroscience models in Brian 2 and with a single command run them on a GPU accelerator. Depending on the type of model and accelerator, considerable speedups are possible without any additional effort by the users. The software is in pre-alpha stage and will be released in beta together with the first full release of Brian 2. |
| Type Of Technology | Software |
| Year Produced | 2015 |
| Open Source License? | Yes |
| Impact | We are waiting on measurable impacts which we expect upon the first public release. |
| URL | https://github.com/brian-team/brian2genn |
| Description | Big Bang Observatory Science Centre 2014 - outreach activity about bee vision |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | Yes |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Large interest of school children to see and try our virtual reality simulation of bee vision. We had some very positive feedback from individual visitors afterwards. We do not have access to data. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Big Bang Solent 2014 - outreach activity about bee vision |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | Yes |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | We had long queues of school children who wanted to try our virtual reality simulation of bee vision. This was one of the most popular activities in the entire event. We do not have access to this data. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Big Bang SouthEast 2014 - outreach activity about bee vision |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | Yes |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Lots of interest in the activity; we brought 2 separate setups to accommodate large numbers of visitors and yet still incurred waiting lines. We do not have access to this data. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Cafe Scientifique Brighton |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Presentation of research including the Green Brain Project and Human Frontiers Odor Objects project to the general public, including detailed Q&A. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Closed Loop Electrophysiology - AIMS workshop on closed loop interaction, Madrid 2014 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other academic audiences (collaborators, peers etc.) |
| Results and Impact | Lively discussion after the talk which was very well received. no measurable data available. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Green Brain: Modeling the honeybee brain |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other academic audiences (collaborators, peers etc.) |
| Results and Impact | There were several questions after the talk and lively informal discussions. no measureable data available. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Invited scientific talk at Keele Univeristy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | I presented recent research at Keele University to an audience of researchers and students. Much of the work reported was based on the Green Brain Project. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Invited talk at the Neural Codign workshop in Koeln, Germany |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Scientific talk covering work from the Green Brain project and the HFSP funded "Odor Objects" project. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Invited talk at the Neuromorphic Computing workshop (NICE) in Berkeley, California |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Invited talk in which I presented our benchmarking work of neural network algorithms, comparing neuromorphic platforms against our GPU accelerator framework (developed within the Green Brain project) |
| Year(s) Of Engagement Activity | 2016 |
| Description | Media coverage including New Scientist and Sunday Times |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | - Coverage included (among others) "Summon the bee bots: Can flying robots save our crops?", November 18th November 2013, New Scientist (on the cover). "Flight of the robo-bee to save fruit crops", 7th October 2012, The Sunday Times. |
| Year(s) Of Engagement Activity | 2012,2013 |
| Description | Oral presentation in Bernstein Conference, Green Brain workshop in Goettingen (2-5 September 2014) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other academic audiences (collaborators, peers etc.) |
| Results and Impact | The talk helped better understanding of our goal and achievements by colleagues and it was followed by a discussion. After the talk I could discuss with experts in my field about my and their methods and results. |
| Year(s) Of Engagement Activity | 2014 |
| URL | http://www.nncn.de/en/bernstein-conference/2014/workshops/green-brain-how-models-of-invertebrate-bra... |
| Description | Outreach event for school aged children |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | We organized two days of activities on "behavioral robotics" involving school aged children to work with simple controllers for autonomous robots in order to solve set challenges, e.g. following a light trace. The activities took place in teh framework of teh Brighton Science Festival "BrightSparks" event. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Panelist at the National Women in Engineering Day - Celebration Event |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | 20 female students and 10 faculty members attended talks by female scientists and a panel discussion about women in neuroscience. The audience reported that they learned a lot from the experience of the participants and that the event encouraged them to pursue their career as a woman in STEM. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.sussex.ac.uk/informatics/about/newsandevents?id=35932 |
| Description | Parameter Estimation using GPU super-computing - Neural Coding Workshop Versailles 2014 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other academic audiences (collaborators, peers etc.) |
| Results and Impact | Several questions from the audience. No measurable data. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Presentation at the "X Science Fair" |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Prof Thomas Nowotny presented the work in the Green Brain project at the X Science Fair at the X headquarters in Mountainview, California. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Presentation at the joint SP4/SP9 Human Brain Project workshop on at the European Institute for Theoretical Neuroscience in Paris |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Gave a presentation on models that tolerate diversity and engaged on a debate on the theory and practice of neuromorphic computing. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Presentation at the mini air show event in Brighton, UK |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | I gave a presentation related to the Green Brain project to an audience of drone enthusiasts at the min air show event, related to International Drone Day. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.miniatureairshow.com/ |
| Description | Presentation at the workshop on Code Generation at the Institute for Theoretical Neuroscience in Paris |
| 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 | In this workshop I reported on our work of building a GPU meta-compiler for efficient simulation of Neural Networks on GPU accelerators. The remainder of the event was a lively exchange among practitioners of research involving advanced software development/ code generation. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Presentation of Green Brain and Brains on Board projects |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | I presented our research portfolio at the "Digi Drop-in" of the Brighton Digital Catapult centre. Both, work from the Green Brain and the planned work for the Brains on Board project were presented. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Press release on our results of Drosophila Receptor responses to a large set of chemicals |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | The press release sparked large media attention including print and online news, radio interviews and a short report on the local TV station. overall there were about - 58 items in print and online media - Interviews/news items on BBC world service (Reach: 409000), BBC Radio Sussex (Reach 73000), BBC Radio Shropshire (Reach 29666), BBC Radio Wales (Reach 137000), and more. - News item on BBC Southeast (TV) I do not know how to measure impacts on thousands of listeners/viewers. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Public talk in the FabLab London, within the "Hacking the Senses" series |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Invited talk presenting our research on insect olfaction (related to the Green Brain poject). Also demonstrated our Bee Eye virtual reality simulator. |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://www.eventbrite.com/e/hack-the-senses-s01e04-animal-perception-tickets-22776381771# |
| Description | Scientific talk at the "Brains and Roses" workshop in London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Gave a presentation partially based on the work in the Green Brain project. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Scientific talk at the Jubilee of Prof Ulrich Behn, University of Leipzig, Germany |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Scientific talk drawing on results from the Green Brain Project among others. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Scientific talk at the University of Edinburgh |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Gave and invited talk in the Informatics Forum of the University of Edinburgh drawing partially on the work in the Green Brain project. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Speaker in the Lewes U3A Science Series |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Presentation of a research lecture involving work from the Green Brain project, Odor Objects project and the planned work in Brains on Board. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Visit and exhibition at the X Science fair in Mountain View California |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | I was invited and accepted to present our research (in particular Green Brain and Odor Objects projects) at the X science fair, organized at X headquarters in Mountain View, California. |
| Year(s) Of Engagement Activity | 2016 |