Sums:About

From Van Essen Lab

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* SumsDB and WebCaret on a Linux cluster housed in the Electronic Radiology Laboratory in the Washington University Department of Radiology.  * * Automatic data backup and recovery are handled through a Network Attached Storage system.
* SumsDB and WebCaret on a Linux cluster housed in the Electronic Radiology Laboratory in the Washington University Department of Radiology.  * * Automatic data backup and recovery are handled through a Network Attached Storage system.
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== Citing SumsDB ==
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Use of SumsDB and datasets contained within SumsDB can be referenced in several ways.
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=== Home page ===
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* URL for SumsDB: http://sumsdb.wustl.edu/sums
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=== Publications describing SumsDB ===
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* Van Essen, D.C., Harwell, J., Hanlon, D, and Dickson, J. (2005) Surface-Based Atlases and a Database of Cortical Structure and Function. In: Databasing the Brain: From Data to Knowledge (Neuroinformatics). S.H. Koslow and S. Subramaniam, eds., John Wiley & Sons, NJ, pp. 369-387
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* Dickson, J., Drury, H., and Van Essen, D.C. (2001) The surface management system (SuMS) database: A surface-based database to aid cortical surface reconstruction, visualization and analysis. Phil. Trans. Royal Soc, Ser B 356:1277-1292
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=== Links to Specific SumsDB Datasets ===
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* To find a specific dataset, link to the appropriate ‘archive_id’ or to the ‘directory_id’ containing the archive. 
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* An archive_id may represent a single data file or to a composite ‘tarball’ (e.g., *.tar.gz or *.zip).
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* 'Spec file’ archives receive special treatment:  each is a single file, but selecting a spec file allows its entire listing of files to be downloaded or viewed online.
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* '''Archive_id'''.  Any given data file can be identified using its archive_id with or without the archive_id appended.  For example, the following URL’s both link to the same archive:
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** http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6571220
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** http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6571220&archive_name=PALS_B12.BOTH-HEMS.STANDARD-SCENES.73730.spec
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* '''Directory_id links'''.  Any given directory can be identified using its directory_id with or without the directory_name appended.  For example, the following URL’s both link to the same directory:
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** http://sumsdb.wustl.edu/sums/directory.do?id=636032
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** http://sumsdb.wustl.edu/sums/directory.do?id=636032&dir_name=ATLAS_DATA_SETS

Revision as of 20:32, 11 April 2017

Contents

About SumsDB

Image:SumsAboutImage.jpg NITRC_logo_Listed_Small.jpg


SumsDB (the Surface Management System DataBase) provides access to a growing body of neuroimaging and related data. WebCaret software provides online data visualization for datasets in SumsDB.

Main Categories of Data Based on Data Type and Usage

Atlas Datasets

  • Surface and volume data
  • Structural and functional data
  • Data on cerebral cortex and cerebellar cortex
  • Human data – normal and neurological/psychiatric disorders
  • Nonhuman primate data: macaque, chimpanzee, gorilla
  • Rodent: mouse and rat data

Searchable Stereotaxic Foci and fMRI Maps

  • Published data, curated and customized for data mining
  • Over 25,000 sterotaxic foci from nearly 1,000 published studies

Publication Associated Datasets

  • Underlay key figures in specific online publications:
  • Individual subject data and population data mapped to atlases

Project-Related Datasets

  • From various ongoing projects that serve archival purposes and sharing with selected collaborators
  • Data from FreeSurfer, CIVET, and other brainmapping software besides Caret

Tutorials

  • Documents and associated datasets from tutorials for both SumsDB/WebCaret and Caret.

Data Access and Security

  • SumsDB provides multiple levels of data access and security
  • Free (public) access (e.g., for data associated with published studies)
  • Data access restricted to collaborators in different laboratories
  • Owner-only access for work in progress

Data Organization

  • Download data as individual files or as collections (‘spec files’) customized for offline analysis in Caret

WebCaret

  • WebCaret provides online ‘Caret-style’ visualization without software or data downloads:
  • WebCaret ‘scenes’ facilitate rapid visualization of complex combinations of data
  • Bi-directional links between online publications and WebCaret/SumsDB provide:
  • Links from figures in online journal article to corresponding scenes in WebCaret
  • Links from metadata in WebCaret directly to relevant online publications and figures

Searching and Data Mining

  • Searching and data mining options using SumsDB and WebCaret:
  • Search by data type, filename, associated metadata (text-based search)
  • Spatially based queries
    • Proximity to stereotaxic coordinates
    • Overlap with selected fMRI activations (metric files)
    • Overlap with identified cortical areas (paint files)
  • Searches can be applied to:
    • Currently loaded datasets
    • ‘Processed’ datasets
    • All public SumsDB data
    • Restricted access data
  • Search results can be:
    • Viewed in WebCaret
    • Combined with other loaded data sets
    • Downloaded directly

Hardware

  • SumsDB and WebCaret on a Linux cluster housed in the Electronic Radiology Laboratory in the Washington University Department of Radiology. * * Automatic data backup and recovery are handled through a Network Attached Storage system.


Citing SumsDB

Use of SumsDB and datasets contained within SumsDB can be referenced in several ways.

Home page

Publications describing SumsDB

  • Van Essen, D.C., Harwell, J., Hanlon, D, and Dickson, J. (2005) Surface-Based Atlases and a Database of Cortical Structure and Function. In: Databasing the Brain: From Data to Knowledge (Neuroinformatics). S.H. Koslow and S. Subramaniam, eds., John Wiley & Sons, NJ, pp. 369-387
  • Dickson, J., Drury, H., and Van Essen, D.C. (2001) The surface management system (SuMS) database: A surface-based database to aid cortical surface reconstruction, visualization and analysis. Phil. Trans. Royal Soc, Ser B 356:1277-1292

Links to Specific SumsDB Datasets

Personal tools
Sums Database