CARMEN e-Science Portal

Lead Research Organisation: Newcastle University
Department Name: Institute of Neuroscience

Abstract

The study of the brain and of nervous systems is one of the priority areas for biological research in the UK and internationally. Neuroscience research commonly employs techniques that generate large data files (called time-series data) that record the activity of one or many nerve cells as well as other accompanying data, such as physiological measures, behaviour, or a stimulus that is used to activate the system. This mass of data requires detailed analysis in order to extract the important information and to look for patterns which can provide insight into the way the brain functions. CARMEN (an acronym for Code Analysis, Repository and Modelling for e-Neuroscience) harnesses the power of the web in order to enable researchers to accomplish this analysis and at the same time provide a way to share data, either within private user groups or openly within the science community. Starting in October 2006 a collaborative effort between computer scientists and neuroscientists at 11 UK universities has developed the first version of this resource. Using remote access through a web portal users can upload their data files to the CARMEN platform. At the same time the system allows information about the experiment and the data files (metadata) to be gathered so that others can understand the experiment. Users can also upload software tools that can be used to analyse the data or use tools provided by others in the community. We are also developing ways that the upload can happen whilst the experiment is being performed in order that collaborators can perform recording and analysis at the same time (real time distributed collaboration). Importantly, CARMEN has been developed so that this sharing of the resource is not restricted by the format of the files used to capture the data or the way in which the analysis methods have been written (interoperability). There is also a security structure that allows users to initially work on the files privately but, once the data have been published the data files can be made public so that others can use them. In this way CARMEN can both curate experimental data and provide a resource for secondary analysis or combination of data from different laboratories. This ability to reuse data adds significantly to their value, particularly for experiments that are complex to perform or which employ rare tissue. The current project will maintain and develop the CARMEN portal for a further four years. Importantly the project will support the transition from the initial development stage to a wider community engagement. This will involve Help Desk support for new users, troubleshooting of system problems, and further development of the web portal in response to user feedback. In addition, we will undertake development of new functions to allow specific data types to be uploaded, shared and analysed. In this respect we will focus effort on two main areas: (i) electroencephalogram (EEG) recordings and the brain responses to stimuli (event-related potentials), and (ii) neural activity data that can be extracted from video images. In the latter case this will enable CARMEN to be used for recordings that employ the latest generation of optical recording techniques. Finally, we will develop ways to link into other bioinformatics projects in order that details of brain structure, gene expresion, etc. might be stored and analysed at the same time. This last effort will be assisted by our involvement with the International Neuroinformatics Coordinating Facility (INCF) which was recently established to support links between databases and informatics resources in neuroscience. CARMEN is a unique facility that has addressed the specific issues of storing and analysing neurophysiological data on the web in order to facilitate collaboration and data sharing. With future development of the computing power of the web (cloud computing) it is likely that this will increasingly become the accepted method of research.

Technical Summary

The study of the brain is a priority area for biological research. Neurophysiological techniques (intra/extracellular recording, multielectrode arrays, EEG etc) are widely used to understand how individual neurons and networks contribute to brain activity. The mass of data generated requires detailed analysis to extract important information about regulatory mechanisms and patterns which contribute to overall activity. CARMEN is an e-science web portal specifically developed to enable researchers to share time-series data and analysis services within a virtual working environment. Since 2006 a collaboration across 11 UK universities has developed the first version of this resource. Using web access, data files can be uploaded to the platform and metadata added via a structured schema. Community-derived services are then used for analysis, with a common internal file format facilitating interoperability of different data and service formats. A security layer allows users to initially work in private groups, but once published data can be made public. Thus, CARMEN both curates experimental data and provides a public resource for secondary analysis. This reuse of data adds significantly to their value, particularly for complex or rare experimental contexts. The current project will maintain and develop the CARMEN resource for a further 4 years, particularly supporting transition to wider engagement. The main objectives include: significant promotional activity; technical workshops and 'help desk' support for new users; further versioning of the portal; technical development to support EEG recording and time-series data extracted from optical methods; and, through close links with the INCF, interfacing CARMEN with other bioinformatics resources to create a federated repository. Thus, CARMEN will leverage advances in cloud computing to deliver a unique resource to facilitate collaboration and data sharing, with significant impact on understanding of neural systems.

Planned Impact

Who will benefit from this research? Whilst the principal beneficiaries will be the academic neuroscience community for whom CARMEN provides a platform for data analysis and sharing, benefit will extend to the commercial research sector, especially pharmaceutical, which conducts appropriate neurophysiological investigations. The development of a platform for novel analyses of EEG has a high potential to benefit those in the medical field who employ this method in diagnostic screening, especially for neurological conditions. Ultimately with the growth of the data repository the Research Funding Agencies will benefit from the enhanced value of research that can be shared and undergo secondary analysis or combined for meta-analysis. Research and development activity in disciplines that involve analysis of time-series data (e.g. various fields of engineering) can benefit from both novel algorithms and development of an e-science platform for sharing. In respect of this interdisciplinarity it should be noted that visualisation and event search capabilities which are implemented in CARMEN originated from Austin's group at York as part of the EPSRC-funded DAME (Distributed Aircraft Engine Maintenance) project. Finally, the platform development will have the potential to impact on advances in e-science and distributed computing. How will they benefit from this research? The principal application area for CARMEN is neuroscience and, as such, has the potential for significant impact on health. Projects employing the resource will increase our understanding of the brain, both in health and disease, leading to benefits in terms of preventative and curative medicine including pharmaceutical development, all of which have an economic as well as social impact on the UK as a whole. For example, one current user group is using CARMEN to analyse and share data of recordings from cortical tissue obtained from epileptic patients and using this to understand the cause and treatment of seizure activity. In this respect the impact is immediate, although the expectation is that the wider scope of work focused on EEG will only start to occur in 2013 after implementation of the specific technical developments and population of CARMEN with data. The potential for use in diagnostics based on EEG will have a similar timescale. What will be done to ensure that they have the opportunity to benefit from this research? A key element of the project is a major programme of engagement activities design to serve the existing user base and to attract new users, data and service contributors, and potential collaborators for future development. To engage the primary user community we will target major neuroscience congresses for demonstrations and distribution of promotional material, as well as the opportunity for training and troubleshooting. Congresses will be those of the British Neuroscience Association, Federation of European Neuroscience Societies, US Society for Neuroscience, and INCF (or its UK Node). We have a track record of demonstrating at these and other meetings and have commissioned a professional stand and publicity materials. Transdisciplinary application of the CARMEN infrastructure will be explored through existing links within the e-science community and by opportunities to demonstrate at appropriate e-science meetings (e.g. UK All-Hands). Annual meetings of the development consortium and regular training workshops and user group meetings will maximize knowledge transfer. For less direct engagement the project web site is widely linked and actively promoted by INCF. As well as providing a gateway to the CARMEN portal, publications, technical reports, and project information are available here. A regular electronic newsletter will be used to inform potential beneficiaries of developments and outcomes. Papers arising from the use of CARMEN will help publicise its utility and major outcomes will be publicised through media engagement.
 
Description The aim of this project was to further develop the infrastructure of the eplatform CARMEN that allows neurophysiologists to share data and analysis tools over the internet.
Many people had complained in the past that using the platform was not intuitive, and rather difficult
During this award, we made the platform much more user friendly, with better search tools and also developed powerful data visualisation tools for online use.
We also improved the website, made it more user friendly.
We developed an important tool to work with the now most widely accepted file format, HDF5.
Exploitation Route We have learned many important lessons from CARMEN, and feel that they could be very useful for developing a new platform with similar general aims
Sectors Digital/Communication/Information Technologies (including Software),Healthcare,Pharmaceuticals and Medical Biotechnology
 
Description The CARMEN platform benefits also the commercial research sector, especially pharmaceutical, which conducts neurophysiological investigation of their products. CARMEN has also started benefiting clinicians and researchers working with EEG data to perform diagnostic screening, especially for neurological conditions. CARMEN has been presented at major neuroscience conferences (SfN, FENS, BNA, INCF), with appropriate demonstrations and and distribution of propotional material and training for troubleshooting.
First Year Of Impact 2011
Sector Digital/Communication/Information Technologies (including Software),Education,Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal
 
Description APS recordings collaborations 
Organisation Italian Institute of Technology (Istituto Italiano di Tecnologia IIT)
Country Italy, Italian Republic 
Sector Public 
PI Contribution we developed the use of the high density array system to record from the retina
Collaborator Contribution They contributed the technology, the high density system as well as some analytical softwares At INRIA they help us with the analysis of the very complex data generated with the system
Impact multidisciplinary: neuroscience, electronic and software engineering outcomes: one paper several conference proceedings new funding acquisition of the hardware at great discount 2 more papers in review process
Start Year 2012
 
Description APS recordings collaborations 
Organisation The National Institute for Research in Computer Science and Control (INRIA)
Country France, French Republic 
Sector Public 
PI Contribution we developed the use of the high density array system to record from the retina
Collaborator Contribution They contributed the technology, the high density system as well as some analytical softwares At INRIA they help us with the analysis of the very complex data generated with the system
Impact multidisciplinary: neuroscience, electronic and software engineering outcomes: one paper several conference proceedings new funding acquisition of the hardware at great discount 2 more papers in review process
Start Year 2012