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Providing traceability for neuroimaging analyses

Richard McClatchey, Andrew Branson, Ashiq Anjum, Peter Bloodsworth, Irfan Habib, Kamran Munir, Jetendr Shamdasani, Kamran Soomro
2013 International Journal of Medical Informatics  
It introduces the use of the CRISTAL software to provide provenance management as one of a number of services delivered on a SOA, deployed to manage neuroimaging projects that have been studying biomarkers  ...  Over the past decade, we have been working with mammographers, paediatricians and neuroscientists in three generations of projects to provide the data management and provenance services now required for  ...  Acknowledgements The authors wish to thank their institutes and the European Commission for their support and to  ... 
doi:10.1016/j.ijmedinf.2013.05.005 pmid:23763909 fatcat:c3yyjdxqizgp7hlowa32zfthny

Intelligent grid enabled services for neuroimaging analysis

Richard McClatchey, Irfan Habib, Ashiq Anjum, Kamran Munir, Andrew Branson, Peter Bloodsworth, Saad Liaquat Kiani
2013 Neurocomputing  
This paper reports our work in the context of the neuGRID project in the development of intelligent services for a robust and efficient Neuroimaging analysis environment. neuGRID is an EC-funded project  ...  required for the study of degenerative brain diseases.  ...  Acknowledgement The authors would like to thank Professor Nik Bessis, University of Derby, for his valuable contributions to the article.  ... 
doi:10.1016/j.neucom.2013.01.042 fatcat:2zqnqim5o5dlrgojdn4dewctba

Research Traceability using Provenance Services for Biomedical Analysis [article]

Ashiq Anjum, Peter Bloodsworth, Andrew Branson, Irfan Habib, Richard McClatchey, Tony Solomonides, the neuGRID Consortium
2012 arXiv   pre-print
We outline the approach being developed in the neuGRID project to use provenance management techniques for the purposes of capturing and preserving the provenance data that emerges in the specification  ...  approach for provenance management could emerge for more generic application to the (Health)Grid community.  ...  In this paper we outline the approach being developed in the neuGRID project [6] to use provenance management approaches (to be based on the OPM) for the purposes of capturing and preserving the provenance  ... 
arXiv:1202.5517v1 fatcat:zhkhowd2pzccdjwkx56ts6emli

Traceability and Provenance in Big Data Medical Systems

Richard McClatchey, Jetendr Shamdasani, Andrew Branson, Kamran Munir, Zsolt Kovacs, Giovanni Frisoni
2015 2015 IEEE 28th International Symposium on Computer-Based Medical Systems  
The use of CRISTAL has provided a rich environment for neuroscientists to track and manage the evolution of data and workflow usage over time in neuGRID and N4U.  ...  To facilitate the orchestration of complex, large-scale analyses in these projects we have adapted CRISTAL, a workflow and provenance tracking solution.  ...  In this article we outline the provenance management approach developed in the neuGRID [9] and neuGRIDforUsers (N4U) projects to preserve the data collected in the execution of neuroimaging analysis  ... 
doi:10.1109/cbms.2015.10 dblp:conf/cbms/McClatcheySBMKF15 fatcat:m2y6utkz6jcadetkcktudui3um

Research Traceability using Provenance Services for Biomedical Analysis [article]

Ashiq Anjum, Peter Bloodsworth, Andrew Branson, Irfan Habib, Richard McClatchey, Tony Solomonides, the neuGRID Consortium
2014 arXiv   pre-print
We outline the approach being developed in the neuGRID project to use provenance management techniques for the purposes of capturing and preserving the provenance data that emerges in the specification  ...  approach for provenance management could emerge for more generic application to the (Health)Grid community.  ...  In this paper we outline the approach being developed in the neuGRID project [6] to use provenance management approaches (to be based on the OPM) for the purposes of capturing and preserving the provenance  ... 
arXiv:1403.0230v1 fatcat:xfhuf4mghvakfl4cyhkc5mjxm4

Towards Provenance and Traceability in CRISTAL for HEP

Jetendr Shamdasani, Andrew Branson, Richard McClatchey
2014 Journal of Physics, Conference Series  
This paper discusses the CRISTAL object lifecycle management system and its use in provenance data management and the traceability of system events.  ...  From these examples, applications are drawn for the High Energy Physics domain and some initial ideas for its use in data preservation HEP are outlined in detail in this paper.  ...  For example in the neuGRID project the CRISTAL provenance service captured: -Workflow specifications -These were XML based specifications of workflow descriptions which were external to CRISTAL.  ... 
doi:10.1088/1742-6596/513/3/032091 fatcat:425xcbkhrzbolfycwxkx2t5xee

Towards Semantic Provenance in CRISTAL

Jetendr Shamdasani, Richard McClatchey, Andrew Branson
2012 Extended Semantic Web Conference  
Traceability is an important feature of workflow based systems, and is a key source of provenance data.  ...  In this paper we summarize some initial work towards the adaptation of CRISTAL to a more semantic orientation, in particular compliance with the Open Provenance Model.  ...  For example in the neuGRID project the CRISTAL provenance service captured: Provenance in CRISTAL -Workflow specifications -These were XML based specifications of workflow descriptions which were external  ... 
dblp:conf/esws/ShamdasaniMB12 fatcat:bqajaiuufnfrdkuutk6escsw6m

Position Paper: Provenance Data Visualisation for Neuroimaging Analysis [article]

Bilal Arshad, Kamran Munir, Richard McClatchey, Saad Liaquat
2015 arXiv   pre-print
We present an account for the need to visualise provenance information in order to aid the process of verification of scientific outputs, comparison of analyses,progression and evolution of results for  ...  neuroimaging analysis.  ...  Most workflow provenance management systems are designed for data-flow oriented workflows and researchers are now realising that tracking data alone is insufficient to support the scientific process (for  ... 
arXiv:1502.01556v1 fatcat:t44kjzyiobhond67kn76ezvs7y

An Integrated e-Science Analysis Base for Computation Neuroscience Experiments and Analysis

Kamran Munir, Saad Liaquat Kiani, Khawar Hasham, Richard McClatchey, Andrew Branson, Jetendr Shamdasani
2013 Procedia - Social and Behavioral Sciences  
Recent developments in data management and imaging technologies have significantly affected diagnostic and extrapolative research in the understanding of neurodegenerative diseases.  ...  The EU's neuGRID for Users (N4U) is a follow-on project to neuGRID, which aims to provide an integrated environment to carry out computational neuroscience experiments.  ...  The Provenance service exposes interfaces to record provenance information of a pipeline and record it along with the output and error logs in analysis base via Storage Manager.  ... 
doi:10.1016/j.sbspro.2013.02.026 fatcat:bnqtqmkvcfaynjsyftz332y54u

Data provenance tracking as the basis for a biomedical virtual research environment [article]

Richard McClatchey
2018 arXiv   pre-print
Furthermore most workflow provenance management services are designed only for data-flow oriented workflows and researchers are now realising that tracking data or workflows alone or separately is insufficient  ...  We have extended the work carried out in the neuGRID and N4U projects in providing a so-called Virtual Laboratory to provide the foundation for a generic VRE in which sets of biomedical data (images, laboratory  ...  ") and n. 283562 ("neuGRID for users") with special thanks to the N4U consortium.  ... 
arXiv:1803.07433v1 fatcat:5pe5trly6fesjb4rmx3npnwbdu

Provision of an integrated data analysis platform for computational neuroscience experiments

Kamran Munir, Saad Liaquat Kiani, Khawar Hasham, Richard McClatchey, Andrew Branson, Jetendr Shamdasani, Professor Georgios Giannakopoulos and Profess
2014 Journal of Systems and Information Technology  
Provision of an integrated data analysis platform for computational neuroscience experiments. Journal of Systems and Information Technology, 16 (3). pp. 150-169.  ...  The authors take this opportunity to acknowledge the contribution of all the partner institutions in the N4U project to this paper.  ...  FBIRN (Burak et al., 2010) presents an extensible data management system for clinical neuroimaging studies.  ... 
doi:10.1108/jsit-01-2014-0004 fatcat:ppnacijscvfq3lecxsla5uiezq

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research

Tarek Sherif, Pierre Rioux, Marc-Etienne Rousseau, Nicolas Kassis, Natacha Beck, Reza Adalat, Samir Das, Tristan Glatard, Alan C. Evans
2014 Frontiers in Neuroinformatics  
CBRAIN leverages remote computing cycles and facilitates resource-interoperability in a transparent manner for the end-user.  ...  The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research  ...  In addition to the authors, we would like to thank Mathieu Desrosiers for contributing sustained development efforts and site project coordination.  ... 
doi:10.3389/fninf.2014.00054 pmid:24904400 pmcid:PMC4033081 fatcat:67qhzkijujg4hgabntljsewq3m

A Virtual Imaging Platform for Multi-Modality Medical Image Simulation

T. Glatard, C. Lartizien, B. Gibaud, Rafael Ferreira da Silva, G. Forestier, F. Cervenansky, M. Alessandrini, H. Benoit-Cattin, O. Bernard, S. Camarasu-Pop, N. Cerezo, P. Clarysse (+8 others)
2013 IEEE Transactions on Medical Imaging  
A complete overview is presented, describing the ontologies designed to share models in a common repository, the workflow template used to integrate simulators, and the tools and strategies used to exploit  ...  The platform currently has 200 registered users who consumed 33 years of CPU time in 2011.  ...  This formalism not only provides a frame for the design of new workflows, but it also assists users in workflow creation and validation.  ... 
doi:10.1109/tmi.2012.2220154 pmid:23014715 fatcat:rrlkowdhxvcyzhol6mlmpz6x2i

Development of a large-scale neuroimages and clinical variables data atlas in the neuGRID4You (N4U) project

Kamran Munir, Khawar Hasham Ahmad, Richard McClatchey
2015 Journal of Biomedical Informatics  
The EU FP7 neuGRID and its follow on neuGRID4You (N4U) project is a leading e-Infrastructure where neuroscientists can find core services and resources for brain image analysis.  ...  the EU FP7 N4U project in the light of user requirements.  ...  Acknowledgments The authors would like to acknowledge the support of the European Union in funding this work via the neuGRID4You (N4U) project (Grant agreement no. 283562, 2011-2014), with special thanks  ... 
doi:10.1016/j.jbi.2015.08.004 pmid:26277116 fatcat:wsouwjhuxrhudb6q4ixdzlkdtq

MRI analysis for hippocampus segmentation on a distributed infrastructure

S. Tangaro, N. Amoroso, M. Antonacci, M. Boccardi, M. Bocchetta, A. Chincarini, D. Diacono, G. Donvito, R. Errico, G. B. Frisoni, T. Maggipinto, A. Monaco (+3 others)
2016 2016 IEEE International Symposium on Medical Measurements and Applications (MeMeA)  
One of the most used workflow manager for medical image processing is the LONI pipeline (LP), a graphical workbench developed by the Laboratory of Neuro Imaging (http://pipeline.loni.usc.edu).  ...  a Data used in preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database (adni.loni.usc.edu).  ...  In this study the LONI Pipeline processing environment was used, a user-friendly and efficient workflow manager for complex analysis pipeline.  ... 
doi:10.1109/memea.2016.7533716 dblp:conf/memea/TangaroAABBCDDE16 fatcat:yvd6ddajyfawdej6nzmwjthepe
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