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Title: Design, implementation and practice of JBEI-ICE: An open source biological part registry platform and tools

Abstract

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1]
  1. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division
OSTI Identifier:
1511340
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 40; Journal Issue: 18; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Ham, Timothy S., Dmytriv, Zinovii, Plahar, Hector, Chen, Joanna, Hillson, Nathan J., and Keasling, Jay D. Design, implementation and practice of JBEI-ICE: An open source biological part registry platform and tools. United States: N. p., 2012. Web. doi:10.1093/nar/gks531.
Ham, Timothy S., Dmytriv, Zinovii, Plahar, Hector, Chen, Joanna, Hillson, Nathan J., & Keasling, Jay D. Design, implementation and practice of JBEI-ICE: An open source biological part registry platform and tools. United States. doi:10.1093/nar/gks531.
Ham, Timothy S., Dmytriv, Zinovii, Plahar, Hector, Chen, Joanna, Hillson, Nathan J., and Keasling, Jay D. Mon . "Design, implementation and practice of JBEI-ICE: An open source biological part registry platform and tools". United States. doi:10.1093/nar/gks531. https://www.osti.gov/servlets/purl/1511340.
@article{osti_1511340,
title = {Design, implementation and practice of JBEI-ICE: An open source biological part registry platform and tools},
author = {Ham, Timothy S. and Dmytriv, Zinovii and Plahar, Hector and Chen, Joanna and Hillson, Nathan J. and Keasling, Jay D.},
abstractNote = {The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.},
doi = {10.1093/nar/gks531},
journal = {Nucleic Acids Research},
number = 18,
volume = 40,
place = {United States},
year = {2012},
month = {6}
}

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