WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions

Karr, Jonathan R.; Phillips, Nolan C.; Covert, Markus W.

doi:10.1093/database/bau095

i

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions

Supporting Files

Sep 16 2014
By Karr, Jonathan R. ; Phillips, Nolan C. ; Covert, Markus W.

Details

Alternative Title:

Database (Oxford)
Personal Author:

Karr, Jonathan R. ; Phillips, Nolan C. ; Covert, Markus W.
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.
Subjects:

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
Volume:

2014
Collection(s):

CDC Public Access
Main Document Checksum:

urn:sha256:3a1cfef83797e67e8a1b021628de9b90518aec71e93c025aff80d82916048d30
Download URL:

https://stacks.cdc.gov/view/cdc/32168/cdc_32168_DS1.pdf
File Type:

[PDF - 768.26 KB ]

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