CARMEN e-Science Portal

Lead Research Organisation: University of York
Department Name: Computer Science


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 metaanalysis. Research and development activity in disciplines that involve analysis of timeseries 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.


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Austin J (2011) CARMEN: Code analysis, Repository and Modeling for e-Neuroscience in Procedia Computer Science

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Jessop M (2010) CARMEN: a practical approach to metadata management. in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

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Townend P (2013) e-Science-towards the cloud: infrastructures, applications and research. in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

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Weeks M (2013) The CARMEN software as a service infrastructure. in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

Description The project was aimed at developing a platform for individuals to share data from experiments and to share programs. It was based upon cloud technology allowing users to login to our website and view theirs or others items on the site. We found primarily that it is very difficult to build these type of systems. Although the platform was built and was highly sophisticated and are still being used by some individuals, the development of such systems requires a much larger team than we had. Also it is vital that further funding on a continuous basis is provided to allow the platform to exist into the future - particularly where data and software is held in an archival format.
Exploitation Route Carmen platform continues to be used. From a York perspective the work resulted in a number of important spin-offs. In particular a spin out company took the idea of Carmen and developed a platform for diagnostics and prognostics. The company is called Cybula Ltd. in addition the company has developed a computer platform for high-performance analysis of data. This system will use the Carmen platform as a front-end to allow users to use the hardware. During the project we were funded by HEFCE to generalise the platform for wider use, this was done resulting in the you share platform, which was the same as Carmen only for all users.
The platform is being used in a number of projects within Cybula Ltd. in particular one with Unilever looking at the use of chemicals, and the project with Sheffield University and Thames Water looking at monitoring water quality, and the project with the University of York funded by crack it looking at diagnosis.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Chemicals,Communities and Social Services/Policy,Construction,Creative Economy,Digital/Communication/Information Technologies (including Software),Education,Electronics,Energy,Environment,Financial Services, and Management Consultancy,Healthcare,Leisure Activities, including Sports, Recreation and Tourism,Government, Democracy and Justice,Manufacturing, including Industrial Biotechology,Culture, Heritage, Museums and Collections,Pharmace

Description The Carmen platform developed under this project has been used by a York spin out company, Cybula Ltd., set up some years before by Prof Austin. The platform is being used in the project involving Unilever looking at the use of chemicals which are byproducts from their manufacturing. Does be used in a project with Sheffield University funded by the EU looking at leaks in pipes within the water industry, including Thames Water and many other partners. Has been used in a project called crack it with the Department of Electronics at York for diagnosis of illness. In addition it has been used as the front-end for a new powerful parallel computer, the cool computer, developed by the company. The software is being used as the portal to the machine. Since 2016 Cybula has developed a new software platform drawing on the research for diagnostics and prognostics in Engineering.
First Year Of Impact 2015
Sector Chemicals,Digital/Communication/Information Technologies (including Software),Electronics,Energy,Environment,Healthcare
Impact Types Societal,Economic

Title The Carmen and you share platforms 
Description The Carmen platform was developed within two funded projects. The work aimed to develop a system for neuroscience that would allow both collection of data and software as a result of research onto a cloud platform/grid platform. In addition it allows the software to be run on the platform, unique the time it was developed, against data stored on the platform. It provides facilities to link out to papers and other citations which can directly link to assets on the system. It provides provenance all items on system. It tracks the use of the system latter analysis. Users are able to provide different sharing capabilities of the assets to know one, groups, named groups and publicly. The Carmen platform was aimed at electrophysiology, and timeseries data. It contained many analytical functions that could be strung together in workflows built out of the systems analytical functions and ones provided by others. System was generalised to all research areas in a project called you share funded hefce. One of the challenges of this system has been to keep it running after the end of projects. Currently it is being supported by the University spin out company linked to a Janet reach project which provides a gigabit link to the universities from the company's datacentre. Computers supported by BBSRC allow users to run software on the system. The moment it has limited functionality which will be enhanced as the company develops its offering in this area. The company use the software for the number of commercial projects as discussed elsewhere. 
Type Of Material Data handling & control 
Provided To Others? Yes  
Impact We think that the use of the project output within commercial applications with Unilever and other EU -related projects is an illustration of impact. The work was highly cited in many publications. Although its use now is limited it has influenced the development of software within a number of companies and organisations. At the end of the common project its future was uncertain and thus it lost users. With its future development now placed within the groups spin out company we may be to build the user base again. It is clear that the software needs updating some components no longer match modern versions and won't run under new browsers. 
Description CYBULA LTD 
Organisation Cybula
Country United Kingdom 
Sector Private 
PI Contribution The collaboration with this company is very close as it is a spin out of research group. Technology of the research group is marketed and developed by the company. Currently they sell software and hardware from the University. We provide time for staff to help this transfer. Technology is related to diagnostics and prognostics (SDE), archival data storage and software in the cloud (Carmen), hardware for data logging (N a T) and a number of other technologies.
Collaborator Contribution The company provides a sales for the technology resulting in royalty income. Average this is about £10,000 a year. And is likely to grow in the future. They also provide a basis for commercialisation experience to staff. This helps them to direct their research more fully towards real-world problems. We also use some test instruments from the company for example 1 GHz oscilloscopes costing over £11,000. More likely the company is putting in a link to the University which will allow access via a 1 Gb ethernet network to a new computer that the company is building. The cool computer will help to develop the diagnostics and prognostics research as well as of the work within the department and university.
Impact The output from this collaboration is in the form of commercialisation of the University's research this provides a funding income for the group in addition it provides commercial experience and direction. The main areas of collaboration is in software, theory, hardware relating to computer architectures and neural networks as well as computer vision.
Title The Carmen platform 
Description The Carmen platform is a system that allows users to share software and data and run the software on the cloud. It is described in detail elsewhere. 
IP Reference  
Protection Copyrighted (e.g. software)
Year Protection Granted 2016
Licensed Yes
Impact The system is now used anime commercial projects with major international companies and research organizations. This is mainly through Cybula Ltd. Yorks spin off. The service has been transferred to the company data center and is being resurrected during 2017, on the company data center systems.
Title CARMEN software platform 
Description The CARMEN system is a platform for sharing software and data world wide. It combines a cloud/Grid platform with the ability to upload both data and software. the user is able to control who can update, read, download data. It links to papers published and other artifacts. Provides workflows, libraries of software and data. 
Type Of Technology Grid Application 
Year Produced 2013 
Impact The impact in the academic community is large. There have been over a 1000 users and over 150Tb of data and software is now on the system. The spin out Cybula ltd is commissioning the use of the system on a wide basis. It has been used in Cybula on at least two commercial projects.