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

Jonathan R Karr; Nolan C Phillips; Markus W Covert

doi:10.1093/database/bau095

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

Database (Oxford). 2014 Sep 16:2014:bau095. doi: 10.1093/database/bau095. Print 2014.

Authors

Jonathan R Karr¹, Nolan C Phillips¹, Markus W Covert²

Affiliations

¹ Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
² Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and Department of Bioengineering, Stanford University, Stanford, CA 94305, USA mcovert@stanford.edu.

Abstract

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.

Database url: http://www.wholecellsimdb.org SOURCE CODE REPOSITORY: URL: http://github.com/CovertLab/WholeCellSimDB.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Cell Biology*
Cells / cytology
Databases, Factual*
Internet
Models, Biological*
Software*
User-Computer Interface

Abstract

Publication types

MeSH terms

Grants and funding