Details:

Alternative Title:
Database (Oxford)
Publisher's site:
http://dx.doi.org/10.1093/database/bau095
Personal Author:
Karr, Jonathan R. ; Phillips, Nolan C. ; Covert, Markus W.
Karr, Jonathan R. ; Phillips, Nolan C. ; Covert, Markus W. Less -
Description:
Mechanistic 'whole-cell' models are needed to develop a complete understanding of cell physiology. However, extracting biological insights from whole-cell models requires running and analyzing large numbers of simulations. We developed WholeCellSimDB, a database for organizing whole-cell simulations. WholeCellSimDB was designed to enable researchers to search simulation metadata to identify simulations for further analysis, and quickly slice and aggregate simulation results data. In addition, WholeCellSimDB enables users to share simulations with the broader research community. The database uses a hybrid relational/hierarchical data format architecture to efficiently store and retrieve both simulation setup metadata and results data. WholeCellSimDB provides a graphical Web-based interface to search, browse, plot and export simulations; a JavaScript Object Notation (JSON) Web service to retrieve data for Web-based visualizations; a command-line interface to deposit simulations; and a Python API to retrieve data for advanced analysis. Overall, we believe WholeCellSimDB will help researchers use whole-cell models to advance basic biological science and bioengineering.|http://www.wholecellsimdb.org SOURCE CODE REPOSITORY: URL: http://github.com/CovertLab/WholeCellSimDB.
Subject:
[+]
Cell Biology
Cells
Databases, Factual
Database Tool
Internet
Models, Biological
Software
User-Computer Interface

Source:
Database (Oxford). 2014; 2014.
Pubmed ID:
25231498
Pubmed Central ID:
PMC4165886
Document Type:
Journal Article
Funding:
1P50GM107615/GM/NIGMS NIH HHS/United States ; 5DP1LM01150-05/DP/NCCDPHP CDC HHS/United States ; DP1 LM011510/LM/NLM NIH HHS/United States ; DP1 OD006413/OD/NIH HHS/United States ; P50 GM107615/GM/NIGMS NIH HHS/United States
1P50GM107615/GM/NIGMS NIH HHS/United States ; 5DP1LM01150-05/DP/NCCDPHP CDC HHS/United States ; DP1 LM011510/LM/NLM NIH HHS/United States ; DP1 OD006413/OD/NIH HHS/United States ; P50 GM107615/GM/NIGMS NIH HHS/United States Less -
Collection(s):
CDC Public Access
Main Document Checksum:
[+]
urn:sha256:3a1cfef83797e67e8a1b021628de9b90518aec71e93c025aff80d82916048d30
File Type:

Supporting Files

• 	license.txt	txt
  	bau095.nxml	txt
  	bau095f1p.gif	gif
  	bau095f1p.jpg	jpeg
  	bau095f2p.gif	gif
  	bau095f2p.jpg	jpeg
  	bau095f3p.gif	gif
  	bau095f3p.jpg	jpeg

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