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Name of Collaboratory :

 

Code Analysis, Repository, & Modelling for E-Neuroscience (CARMEN)

 
 

URL :

  http://www.carmen.org.uk/  
 

Collaboratory Status :

 
In Development   Start Date : 2006 End Date : Info Last Updated : Wed, Dec 8 2010 3:01pm PST
 
 

Primary Collaboratory Function :

  Community Data Systems  
 

Secondary Collaboratory Functions :

  Expert Consultation, Virtual Community of Practice, Distributed Research Center  
 

Domain(s) :

  BIOLOGICAL/AGRICULTURAL SCIENCES >Biological Sciences >Neuroscience  
 

Brief Description of the Collaboratory :

 

The CARMEN (Code, Analysis, Repository and Modelling for e-Neuroscience) system provides a web based portal platform through which users can share and collaboratively exploit data, analysis code and expertise in neuroscience. The system has been been developed in the UK and currently supports 200 hundred neuroscientists working in a Virtual Environment with an initial focus on electrophysiology data. CARMEN has been built by York and Newcastle Universities and is based on over 10 years experience in the construction of eScience based distributed technology. CARMEN started four years ago involving 20 scientific investigators (neuroscientists and computer scientists) at 11 UK Universities. The project is supported for another 4 years at York and Newcastle, along with a sister project to take the underlying technology and pilot it as a UK platform for supporting the sharing of research outputs in a generic way. An entirely natural extension to the CARMEN system would be its alignment with a publications repository.

Particular work packages are as follows:

WP0. Virtual laboratory infrastructure. User requirements gathering and support.
WP1. Spike detection and sorting. WP2. Information theory methods for spike trains,
continuous waveforms and image series.
WP3. Search algorithms for ion channel conductance parameter determination in cellular membrane models.
WP4. High performance template and context based signal data search.
WP5. Synchronous neural activation in motor disorders. Causality analysis and visualisation. Real-time data streaming.
WP6. Neural activity dynamics in the neonate retina. Models of activity spreading in epilepsy. Bayesian correlation methods.

 
 

Access to Instruments :

   
 

Access to Information Resources :

  The virtual laboratory is a federation of server nodes which allow distributed data to be stored local to acquisition. Analysis codes can be uploaded and executed on the nodes so that derived datasets need not be transported over low bandwidth connections. Data and analysis codes are described by structured metadata, providing an index for search, annotation and audit over workflows leading to scientific outcomes. Users access the distributed resources through a web portal emulating a PC desktop.

CARMEN provides researchers with a virtual research environment which facilitates collaboration and interaction with four mains types of assets: data, metadata, services and workflows. Data and metadata are currently structured for neurophysiology, but the mechanisms for data and metadata management are generic and hence the platform is applicable for any science domain. Services, in CARMEN terms, are stand alone software applications that are hosted on the platform and which can be executed on the underpinning compute resource using any appropriate data assets on the system. Services are exposed by a simple execution GUI inside the portal, which prompts the user to input the relevant operating parameters and input files/variables. Workflows provide the means to orchestrate services into an execution pipeline.

The CARMEN system is operational on the domain https://portal.CARMEN.org.uk, where it is possible to request a login to try out the system.
 
 

Access to People as Resources :

  They have a yearly consortium meeting.  
 

Funding Agency or Sponsor :

 
Engineering and Physical Sciences Research Council (EPSRC)
 
 
 

Notes on Funding Agencies/Sponsors:
$10M was committed to 20 scientific investigators at 11 UK universities from 2006-2010.

 
 
 
Organizations with Funded Participants:
 
Organization name:
Approx # of participants:
Description of organization's role(s):
Albert-Ludwigs-Universit├Ąt Freiburg
1
Consortium Member
Cambridge Electronic Design
1
Consortium Member
Cybula
1
Consortium Member
European Molecular Biology Laboratory (EMBL)
   European Bioinformatics Institute (EBI)
2
Consortium Member
Glaxo Smith Kline
1
Consortium Member
Imperial College London
1
Consortium Member
Lectus Therapeutics
1
Consortium Member
Microsoft
1
Consortium Member
Neuralynx, Inc.
1
Consortium Member
Newcastle University
20
Consortium Member
University of Oxford
   Oxford e-Research Centre (OeRC)
1
Consortium Member
University of Tokyo, RIKEN
   RIKEN Brain Science Institute
1
Consortium Member
University of Edinburgh
2
Consortium Member
University of Leicester
2
Consortium Member
University of Manchester
2
Consortium Member
University of Plymouth
2
Consortium Member
University of Sheffield
2
Consortium Member
University of St. Andrews
1
Consortium Member
University of Stirling
2
Consortium Member
University of Warwick
1
Consortium Member
University of York
6
Consortium Member
 
TOTAL PARTICIPANTS:
51
 

Notes on Participants/Organizations:

   
     
 
 

Communications Technology Used :

   
 

Technical Capabilities :

   
  Key Articles :    
 

Project-reported performance data :

   
 
         
    
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