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Derived Data Storage and Exchange Workflow for Large-Scale Neuroimaging Analyses on the BIRN Grid

David B. Keator
2009 Frontiers in Neuroinformatics  
BIRN) distributed environment to document and exchange derived data.  ...  The need to store and exchange data in meaningful ways in support of data analysis, hypothesis testing and future collaborative use is pervasive.  ...  presented here, and the FBIRN consortium members for the data collection and support of the scientists and engineers involved in the project.  ... 
doi:10.3389/neuro.11.030.2009 pmid:19826494 pmcid:PMC2759340 fatcat:cynqiogpbngihl7c36fmykl7p4

High-throughput neuroimaging-genetics computational infrastructure

Ivo D. Dinov, Petros Petrosyan, Zhizhong Liu, Paul Eggert, Sam Hobel, Paul Vespa, Seok Woo Moon, John D. Van Horn, Joseph Franco, Arthur W. Toga
2014 Frontiers in Neuroinformatics  
The INI/LONI infrastructure has been specifically designed to meet the big data storage and processing challenges as evident from large-scale, multi-site neuroimaging initiatives such as ADNI, the Autism  ...  For instance, Distributed Pipeline will enable dynamic decision making, branching, and looping based on the meta-data and on data derived in the analysis protocol itself.  ... 
doi:10.3389/fninf.2014.00041 pmid:24795619 pmcid:PMC4005931 fatcat:dcvv5nyiifg47mb33r67qjmf2q

Neuroimaging Data Provenance Using the LONI Pipeline Workflow Environment [chapter]

Allan J. MacKenzie-Graham, Arash Payan, Ivo D. Dinov, John D. Van Horn, Arthur W. Toga
2008 Lecture Notes in Computer Science  
The LONI Pipeline (http://pipeline.loni.ucla.edu) is a Java-based workflow environment for the construction and execution of data processing streams.  ...  We have developed a provenance framework for describing the current and retrospective data state integrated with the LONI Pipeline workflow environment.  ...  Within the neuroimaging community, the XCEDE (XML-based Clinical Experiment Data Exchange) schema [30] also provides for the storage of data provenance information.  ... 
doi:10.1007/978-3-540-89965-5_22 fatcat:3kobwveadjgnliynzohjgcapdi

Is it time to re-prioritize neuroimaging databases and digital repositories?

John Darrell Van Horn, Arthur W. Toga
2009 NeuroImage  
Finally, we suggest that, given these developments, now is the time for the neuroimaging community to re-prioritize large-scale databases as a valuable component of brain imaging science.  ...  A range of neuroimaging databasing approaches has streamlined the transmission, storage, and dissemination of data from such brain imaging studies.  ...  Acknowledgments The authors express their gratitude to our colleagues in the Laboratory of Neuro Imaging (LONI) and those collaborators at our partner laboratories who utilize LONI database and computational  ... 
doi:10.1016/j.neuroimage.2009.03.086 pmid:19371790 pmcid:PMC2754579 fatcat:qxjviytffrexbf7wrn2xfkrns4

Federated Web-accessible Clinical Data Management within an Extensible NeuroImaging Database

I. Burak Ozyurt, David B. Keator, Dingying Wei, Christine Fennema-Notestine, Karen R. Pease, Jeremy Bockholt, Jeffrey S. Grethe
2010 Neuroinformatics  
The Clinical Assessment Layout Manager (CALM) allows users to create on-line data entry forms for use within and across sites, through which data is pulled into the underlying database via the generic  ...  In this paper, an extensible data management system for clinical neuroimaging studies is introduced: The Human Clinical Imaging Database (HID) and Toolkit.  ...  Brown at the University of California, San Diego and Steven Potkin at the University of California, Irvine for their support on the work presented here, and the FBIRN consortium members for the data collection  ... 
doi:10.1007/s12021-010-9078-6 pmid:20567938 pmcid:PMC2974931 fatcat:tpy7px3etfdnnpd7nder22hgne

Provenance in neuroimaging

Allan J. MacKenzie-Graham, John D. Van Horn, Roger P. Woods, Karen L. Crawford, Arthur W. Toga
2008 NeuroImage  
Provenance, the description of the history of a set of data, has grown more important with the proliferation of research consortia-related efforts in neuroimaging.  ...  Knowledge about the origin and history of an image is crucial for establishing data and results quality; detailed information about how it was processed, including the specific software routines and operating  ...  Both workflows were then run on the LONI grid and the results were subtracted from one another. The same input data was used for both workflows.  ... 
doi:10.1016/j.neuroimage.2008.04.186 pmid:18519166 pmcid:PMC2664747 fatcat:ue56gsjx7bgqnk7dx4lfiky444

Human neuroimaging as a "Big Data" science

John Darrell Van Horn, Arthur W. Toga
2013 Brain Imaging and Behavior  
A range of neuroimaging databasing approaches has streamlined the transmission, storage, and dissemination of data from such brain imaging studies.  ...  sharing issues; infrastructural challenges for multi-site, multi-datatype archiving; and the means by which to explore and mine these data.  ...  RR021813, The Center for Computational Biology -CCB), and through an National Institute of Mental Health ARRA award (RC1 MH088194).  ... 
doi:10.1007/s11682-013-9255-y pmid:24113873 pmcid:PMC3983169 fatcat:vrbn7rrx2zbsvah6c5hssu5upa

1st INCF Workshop on Sustainability of Neuroscience Databases

Jack Van Horn, Jaap van Pelt
2008 Nature Precedings  
An example is the AstroWise project in Groningen that keeps track of a complete workflow for telescope data analysis in a large Oracle database. All derivations areline python programs.  ...  Matias Palva -Data Format and Interface Issues for Sustaining Multi-Scale Databases There is a need for process and data management tools to solve problems encountered in current data analysis workflow  ...  [ 21 ] A2 Minimum Information for Neuroimaging Description and Specification (MINDS) Several critical elements contributing towards MINDS include: 1 The raw data and full details for each MR acquisition  ... 
doi:10.1038/npre.2008.1983.1 fatcat:pfbpgf6pb5grfehdy6kvjq5hw4

Sharing brain mapping statistical results with the neuroimaging data model [article]

Camille Maumet, Tibor Auer, Alexander Bowring, Gang Chen, Samir Das, Guillaume Flandin, Satrajit Ghosh, Tristan Glatard, Krzysztof J. Gorgolewski, Karl G. Helmer, Mark Jenkinson, David Keator (+6 others)
2016 bioRxiv   pre-print
Only a tiny fraction of the data and metadata produced by an fMRI study is finally conveyed to the community.  ...  This lack of transparency not only hinders the reproducibility of neuroimaging results but also impairs future meta-analyses.  ...  XCEDE: an extensible schema for biomedical data. Neuroinformatics 10, . , D. B. et al. Derived Data Storage and Exchange Workflow for Large-Scale Neuroimaging Analyses on the BIRN Grid. Front.  ... 
doi:10.1101/041798 fatcat:b377pfynmzdj3al3kss6xpclsu

PLM as a strategy for the management of heterogeneous information in bio-medical imaging field

Marianne Allanic, Pierre Yves Hervé, Alexandre Durupt, Marc Joliot, Philippe Boutinaud, Benoît Eynard
2017 International Journal of Information Technology and Management  
Large-scale sharing and reusing of this information has become unavoidable.  ...  The generic, flexible and PLM-oriented data model called BMI-lifecycle management (BMI-LM) is described, as well as a neuroimaging classification which brings flexibility to the information management  ...  ANR-13-CORD-0007) for thematic axis no. 2 of the Contint 2013 Call for Proposal: from content to knowledge and big data.  ... 
doi:10.1504/ijitm.2017.080950 fatcat:ouzk5gymxvbcllaxi4afoqe4uq

PLM as a strategy for the management of heterogeneous information in bio-medical imaging field

Benoît Eynard, Marc Joliot, Philippe Boutinaud, Alexandre Durupt, Marianne Allanic, Pierre Yves Hervé
2017 International Journal of Information Technology and Management  
Large-scale sharing and reusing of this information has become unavoidable.  ...  The generic, flexible and PLM-oriented data model called BMI-lifecycle management (BMI-LM) is described, as well as a neuroimaging classification which brings flexibility to the information management  ...  ANR-13-CORD-0007) for thematic axis no. 2 of the Contint 2013 Call for Proposal: from content to knowledge and big data.  ... 
doi:10.1504/ijitm.2017.10001017 fatcat:7mxoqkraqrd7be2oqh2mbypj3i

Interactive exploration of neuroanatomical meta-spaces

Shantanu H. Joshi
2009 Frontiers in Neuroinformatics  
ACKNOWLEDGMENTS This research was partially supported by the National Institute of Health through the National Center for Research Resources (NCRR) for Center for Computational Biology (CCB), Grant U54  ...  This study utilized the LONI Pipeline environment (http://pipeline.loni.ucla.edu), which was developed by the Laboratory of Neuro Imaging and partially funded by NIH grants P41 RR013642, R01 MH71940 and  ...  The consensus on the archiving and sharing of primary neuroimaging data has fostered several large-scale initiatives: The Biomedical Informatics Resource Network (BIRN), the Morphometry and Function BIRN  ... 
doi:10.3389/neuro.11.038.2009 pmid:19915734 pmcid:PMC2776489 fatcat:6lnpptsmvfdmdmxbh6hxx2qzsi

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience

Luca Corradi, Ivan Porro, Andrea Schenone, Parastoo Momeni, Raffaele Ferrari, Flavio Nobili, Michela Ferrara, Gabriele Arnulfo, Marco M Fato
2012 BMC Medical Informatics and Decision Making  
Second, a repository implementing such a data structure has been deployed on a distributed Data Grid in order to provide scalability both in terms of data input and data storage and to exploit distributed  ...  This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of "meta" data model.  ...  The related processes and events could be defined depending on the analyses to be performed and the new results data to be stored.  ... 
doi:10.1186/1472-6947-12-115 pmid:23043673 pmcid:PMC3560115 fatcat:b2fdeetjpvdinmdmxwo5kdii2e

An XML-based System for Synthesis of Data from Disparate Databases

T. Kurc, D. A. Janies, A. D. Johnson, S. Langella, S. Oster, S. Hastings, F. Habib, T. Camerlengo, D. Ervin, U. V. Catalyurek, J. H. Saltz
2006 JAMIA Journal of the American Medical Informatics Association  
The application workflow requires the management and integration of genomic information and phenotypic data from external data repositories and from the results of phenotype-genotype correlation analyses  ...  Our implementation supports the process of carrying out a complex workflow that includes large-scale phylogenetic tree optimizations and application of Maddison's concentrated changes test to large phylogenetic  ...  This research was supported in part by the National Science Foundation under grants ACI-9619020 (UC Subcontract 10152408), EIA-0121177, ACI-0203846, ACI-0130437, ANI-0330612, ACI-9982087,  ... 
doi:10.1197/jamia.m1848 pmid:16501185 pmcid:PMC1513665 fatcat:kbwmnjy6wrc37aoiqye6hotbum

From the Wet Lab to the Web Lab: A Paradigm Shift in Brain Imaging Research

Anisha Keshavan, Jean-Baptiste Poline
2019 Frontiers in Neuroinformatics  
Here, we review the landscape of web technologies used in neuroimaging research, and discuss future applications, areas for improvement, and the limitations of using web technology in research.  ...  As the neuroimaging informatics research community amasses large datasets to answer complex neuroscience questions, we find that the web is the best medium to facilitate novel insights by way of improved  ...  The accessibility (FAIR-ness) of derived data is key to meta-and mega-analyses.  ... 
doi:10.3389/fninf.2019.00003 pmid:30881299 pmcid:PMC6405692 fatcat:k7x2llfff5hfrhr6igrt7hwhu4
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