Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

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]
+ Show Author Affiliations
  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 Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). 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.
Copy to clipboard
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. https://doi.org/10.1093/nar/gks531
Copy to clipboard
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. https://doi.org/10.1093/nar/gks531. https://www.osti.gov/servlets/purl/1511340.
Copy to clipboard
@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 = {Mon Jun 18 00:00:00 EDT 2012},
month = {Mon Jun 18 00:00:00 EDT 2012}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1093/nar/gks531
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 126 works
Citation information provided by
Web of Science

Figures / Tables:

Figure 1 Figure 1: Screen shot of a typical search result, with pop-up preview shown.
All figures and tables (4 total)
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Essential information for synthetic DNA sequences
journal, January 2011

  • Peccoud, Jean; Anderson, J. Christopher; Chandran, Deepak
  • Nature Biotechnology, Vol. 29, Issue 1
  • DOI: 10.1038/nbt.1753

Writing DNA with GenoCADTM
journal, May 2009

  • Czar, M. J.; Cai, Y.; Peccoud, J.
  • Nucleic Acids Research, Vol. 37, Issue Web Server
  • DOI: 10.1093/nar/gkp361

Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria
journal, January 2006

  • Anderson, J. Christopher; Clarke, Elizabeth J.; Arkin, Adam P.
  • Journal of Molecular Biology, Vol. 355, Issue 4
  • DOI: 10.1016/j.jmb.2005.10.076

Measuring the activity of BioBrick promoters using an in vivo reference standard
journal, January 2009

  • Kelly, Jason R.; Rubin, Adam J.; Davis, Joseph H.
  • Journal of Biological Engineering, Vol. 3, Issue 1, Article No. 4
  • DOI: 10.1186/1754-1611-3-4

Engineering BioBrick vectors from BioBrick parts
journal, January 2008

  • Shetty, Reshma P.; Endy, Drew; Knight, Thomas F.
  • Journal of Biological Engineering, Vol. 2, Article No. 5
  • DOI: 10.1186/1754-1611-2-5

Construction of a genetic toggle switch in Escherichia coli
journal, January 2000

  • Gardner, Timothy S.; Cantor, Charles R.; Collins, James J.
  • Nature, Vol. 403, Issue 6767
  • DOI: 10.1038/35002131

TinkerCell: modular CAD tool for synthetic biology
journal, January 2009

  • Chandran, Deepak; Bergmann, Frank T.; Sauro, Herbert M.
  • Journal of Biological Engineering, Vol. 3, Issue 1
  • DOI: 10.1186/1754-1611-3-19

DNA assembly for synthetic biology: from parts to pathways and beyond
journal, January 2011

  • Ellis, Tom; Adie, Tom; Baldwin, Geoff S.
  • Integrative Biology, Vol. 3, Issue 2
  • DOI: 10.1039/c0ib00070a

A synthetic multicellular system for programmed pattern formation
journal, April 2005

  • Basu, Subhayu; Gerchman, Yoram; Collins, Cynthia H.
  • Nature, Vol. 434, Issue 7037
  • DOI: 10.1038/nature03461

Microbial production of fatty-acid-derived fuels and chemicals from plant biomass
journal, January 2010

  • Steen, Eric J.; Kang, Yisheng; Bokinsky, Gregory
  • Nature, Vol. 463, Issue 7280, p. 559-562
  • DOI: 10.1038/nature08721

Standard Biological Parts Knowledgebase
journal, February 2011

j5 DNA Assembly Design Automation Software
journal, December 2011

  • Hillson, Nathan J.; Rosengarten, Rafael D.; Keasling, Jay D.
  • ACS Synthetic Biology, Vol. 1, Issue 1, p. 14-21
  • DOI: 10.1021/sb2000116

Construction of a genetic toggle switch in Escherichia coli
journal, January 2000

  • Gardner, Timothy S.; Cantor, Charles R.; Collins, James J.
  • Nature, Vol. 403, Issue 6767
  • DOI: 10.1038/35002131

A synthetic multicellular system for programmed pattern formation
journal, April 2005

  • Basu, Subhayu; Gerchman, Yoram; Collins, Cynthia H.
  • Nature, Vol. 434, Issue 7037
  • DOI: 10.1038/nature03461

Microbial production of fatty-acid-derived fuels and chemicals from plant biomass
journal, January 2010

  • Steen, Eric J.; Kang, Yisheng; Bokinsky, Gregory
  • Nature, Vol. 463, Issue 7280, p. 559-562
  • DOI: 10.1038/nature08721

Self-sufficient control of urate homeostasis in mice by a synthetic circuit
journal, March 2010

  • Kemmer, Christian; Gitzinger, Marc; Daoud-El Baba, Marie
  • Nature Biotechnology, Vol. 28, Issue 4
  • DOI: 10.1038/nbt.1617

DNA assembly for synthetic biology: from parts to pathways and beyond
journal, January 2011

  • Ellis, Tom; Adie, Tom; Baldwin, Geoff S.
  • Integrative Biology, Vol. 3, Issue 2
  • DOI: 10.1039/c0ib00070a

Writing DNA with GenoCADTM
journal, May 2009

  • Czar, M. J.; Cai, Y.; Peccoud, J.
  • Nucleic Acids Research, Vol. 37, Issue Web Server
  • DOI: 10.1093/nar/gkp361

Measuring the activity of BioBrick promoters using an in vivo reference standard
journal, January 2009

  • Kelly, Jason R.; Rubin, Adam J.; Davis, Joseph H.
  • Journal of Biological Engineering, Vol. 3, Issue 1, Article No. 4
  • DOI: 10.1186/1754-1611-3-4

TinkerCell: Modular CAD Tool for Synthetic Biology
preprint, January 2009

    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases
    journal, May 2019

    • Barajas, Jesus F.; McAndrew, Ryan P.; Thompson, Mitchell G.
    • Journal of Industrial Microbiology & Biotechnology, Vol. 46, Issue 8
    • DOI: 10.1007/s10295-019-02189-z

    Technical Advances to Accelerate Modular Type I Polyketide Synthase Engineering towards a Retro-biosynthetic Platform
    journal, June 2019

    • Pang, Bo; Valencia, Luis E.; Wang, Jessica
    • Biotechnology and Bioprocess Engineering, Vol. 24, Issue 3
    • DOI: 10.1007/s12257-019-0083-9

    The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology
    journal, June 2014

    • Galdzicki, Michal; Clancy, Kevin P.; Oberortner, Ernst
    • Nature Biotechnology, Vol. 32, Issue 6
    • DOI: 10.1038/nbt.2891

    A robust gene-stacking method utilizing yeast assembly for plant synthetic biology
    journal, October 2016

    • Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim
    • Nature Communications, Vol. 7, Issue 1
    • DOI: 10.1038/ncomms13215

    Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development
    journal, April 2014

    • Paddon, Chris J.; Keasling, Jay D.
    • Nature Reviews Microbiology, Vol. 12, Issue 5
    • DOI: 10.1038/nrmicro3240

    Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer
    journal, March 2018

    An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals
    journal, June 2018

    • Carbonell, Pablo; Jervis, Adrian J.; Robinson, Christopher J.
    • Communications Biology, Vol. 1, Issue 1
    • DOI: 10.1038/s42003-018-0076-9

    Data model for biopart datasheets
    journal, March 2018

    • Sainz de Murieta, Iñaki; Bultelle, Matthieu; Kitney, Richard I.
    • Engineering Biology, Vol. 2, Issue 1
    • DOI: 10.1049/enb.2017.0020

    PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts
    journal, February 2018

    Sequence verification of synthetic DNA by assembly of sequencing reads
    journal, October 2012

    • Wilson, Mandy L.; Cai, Yizhi; Hanlon, Regina
    • Nucleic Acids Research, Vol. 41, Issue 1
    • DOI: 10.1093/nar/gks908

    SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities
    journal, November 2014

    • Martínez-García, Esteban; Aparicio, Tomás; Goñi-Moreno, Angel
    • Nucleic Acids Research, Vol. 43, Issue D1
    • DOI: 10.1093/nar/gku1114

    A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae
    journal, November 2016

    • Reider Apel, Amanda; d'Espaux, Leo; Wehrs, Maren
    • Nucleic Acids Research, Vol. 45, Issue 1
    • DOI: 10.1093/nar/gkw1023

    Better research by efficient sharing: evaluation of free management platforms for synthetic biology designs
    journal, January 2019

    • Urquiza-García, Uriel; Zieliński, Tomasz; Millar, Andrew J.
    • Synthetic Biology, Vol. 4, Issue 1
    • DOI: 10.1093/synbio/ysz016

    Characterization of an ECF56-family sigma factor from Streptomyces venezuelae reveals a highly conserved regulome
    posted_content, January 2020

    The plant glycosyltransferase clone collection for functional genomics
    journal, July 2014

    • Lao, Jeemeng; Oikawa, Ai; Bromley, Jennifer R.
    • The Plant Journal, Vol. 79, Issue 3
    • DOI: 10.1111/tpj.12577

    Fluorescent amplification for next generation sequencing (FA-NGS) library preparation
    journal, January 2020

    ATP citrate lyase mediated cytosolic acetyl-CoA biosynthesis increases mevalonate production in Saccharomyces cerevisiae
    journal, March 2016

    Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast
    journal, November 2016

    • Eudes, Aymerick; Mouille, Maxence; Robinson, David S.
    • Microbial Cell Factories, Vol. 15, Issue 1
    • DOI: 10.1186/s12934-016-0593-5

    Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae
    journal, December 2018

    End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis
    journal, February 2016

    • Linshiz, Gregory; Jensen, Erik; Stawski, Nina
    • Journal of Biological Engineering, Vol. 10, Issue 1
    • DOI: 10.1186/s13036-016-0024-5

    Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants
    journal, October 2016

    • Hollinshead, Whitney D.; Rodriguez, Sarah; Martin, Hector Garcia
    • Biotechnology for Biofuels, Vol. 9, Issue 1
    • DOI: 10.1186/s13068-016-0630-y

    Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts
    journal, October 2017

    Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass
    journal, January 2018

    • Aznar, Aude; Chalvin, Camille; Shih, Patrick M.
    • Biotechnology for Biofuels, Vol. 11, Issue 1
    • DOI: 10.1186/s13068-017-1007-6

    Increased drought tolerance in plants engineered for low lignin and low xylan content
    journal, July 2018

    A screening method to identify efficient sgRNAs in Arabidopsis, used in conjunction with cell-specific lignin reduction
    journal, May 2019

    An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism
    journal, June 2020

    • Thompson, Mitchell G.; Blake-Hedges, Jacquelyn M.; Pereira, Jose Henrique
    • Nature Communications, Vol. 11, Issue 1
    • DOI: 10.1038/s41467-020-16815-3

    Improving olefin tolerance and production in E. coli using native and evolved AcrB : Improving Olefin Tolerance and Production in
    journal, January 2015

    • Mingardon, Florence; Clement, Camille; Hirano, Kathleen
    • Biotechnology and Bioengineering, Vol. 112, Issue 5
    • DOI: 10.1002/bit.25511

    Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases
    journal, May 2019

    • Barajas, Jesus F.; McAndrew, Ryan P.; Thompson, Mitchell G.
    • Journal of Industrial Microbiology & Biotechnology, Vol. 46, Issue 8
    • DOI: 10.1007/s10295-019-02189-z

    Synbiological systems for complex natural products biosynthesis
    journal, December 2016

    A robust gene-stacking method utilizing yeast assembly for plant synthetic biology
    journal, October 2016

    • Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim
    • Nature Communications, Vol. 7, Issue 1
    • DOI: 10.1038/ncomms13215

    Engineering glucose metabolism of Escherichia coli under nitrogen starvation
    journal, January 2017

    • Chubukov, Victor; Desmarais, John James; Wang, George
    • npj Systems Biology and Applications, Vol. 3, Issue 1
    • DOI: 10.1038/npjsba.2016.35

    A machine learning Automated Recommendation Tool for synthetic biology
    journal, September 2020

    Isolation and characterization of novel mutations in the pSC101 origin that increase copy number
    journal, January 2018

    Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae
    journal, January 2016

    • Reider Apel, Amanda; Ouellet, Mario; Szmidt-Middleton, Heather
    • Scientific Reports, Vol. 6, Issue 1
    • DOI: 10.1038/srep19512

    Process-based design of dynamical biological systems
    journal, September 2016

    • Tanevski, Jovan; Todorovski, Ljupčo; Džeroski, Sašo
    • Scientific Reports, Vol. 6, Issue 1
    • DOI: 10.1038/srep34107

    BioPartsDB: a synthetic biology workflow web-application for education and research
    journal, July 2016

    Sequence verification of synthetic DNA by assembly of sequencing reads
    journal, October 2012

    • Wilson, Mandy L.; Cai, Yizhi; Hanlon, Regina
    • Nucleic Acids Research, Vol. 41, Issue 1
    • DOI: 10.1093/nar/gks908

    SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities
    journal, November 2014

    • Martínez-García, Esteban; Aparicio, Tomás; Goñi-Moreno, Angel
    • Nucleic Acids Research, Vol. 43, Issue D1
    • DOI: 10.1093/nar/gku1114

    GenoLIB: a database of biological parts derived from a library of common plasmid features
    journal, April 2015

    • Adames, Neil R.; Wilson, Mandy L.; Fang, Gang
    • Nucleic Acids Research, Vol. 43, Issue 10
    • DOI: 10.1093/nar/gkv272

    A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae
    journal, November 2016

    • Reider Apel, Amanda; d'Espaux, Leo; Wehrs, Maren
    • Nucleic Acids Research, Vol. 45, Issue 1
    • DOI: 10.1093/nar/gkw1023

    Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration
    journal, December 2016

    • Woodruff, Lauren B. A.; Gorochowski, Thomas E.; Roehner, Nicholas
    • Nucleic Acids Research
    • DOI: 10.1093/nar/gkw1226

    Better research by efficient sharing: evaluation of free management platforms for synthetic biology designs
    journal, January 2019

    • Urquiza-García, Uriel; Zieliński, Tomasz; Millar, Andrew J.
    • Synthetic Biology, Vol. 4, Issue 1
    • DOI: 10.1093/synbio/ysz016

    PartsGenie: an integrated tool for optimising and sharing synthetic biology parts
    journal, September 2017

    • Swainston, Neil; Dunstan, Mark; Jervis, Adrian J.
    • Bioinformatics
    • DOI: 10.1101/189357

    Development of a broad-host synthetic biology toolbox for ralstonia eutropha and its application to engineering hydrocarbon biofuel production
    journal, January 2013

    Fluorescent amplification for next generation sequencing (FA-NGS) library preparation
    journal, January 2020

    ATP citrate lyase mediated cytosolic acetyl-CoA biosynthesis increases mevalonate production in Saccharomyces cerevisiae
    journal, March 2016

    Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast
    journal, November 2016

    • Eudes, Aymerick; Mouille, Maxence; Robinson, David S.
    • Microbial Cell Factories, Vol. 15, Issue 1
    • DOI: 10.1186/s12934-016-0593-5

    Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae
    journal, December 2018

    End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis
    journal, February 2016

    • Linshiz, Gregory; Jensen, Erik; Stawski, Nina
    • Journal of Biological Engineering, Vol. 10, Issue 1
    • DOI: 10.1186/s13036-016-0024-5

    Increased drought tolerance in plants engineered for low lignin and low xylan content
    journal, July 2018

    A screening method to identify efficient sgRNAs in Arabidopsis, used in conjunction with cell-specific lignin reduction
    journal, May 2019

    SBOL Visual: A Graphical Language for Genetic Designs
    journal, December 2015

    Investigation of Proposed Ladderane Biosynthetic Genes from Anammox Bacteria by Heterologous Expression in E. coli
    journal, March 2016

    Ex vivo DNA Assembly
    journal, January 2013

    • Fisher, Adam B.; Canfield, Zachary B.; Hayward, Laura C.
    • Frontiers in Bioengineering and Biotechnology, Vol. 1
    • DOI: 10.3389/fbioe.2013.00012

    13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids
    journal, October 2016

    • Ghosh, Amit; Ando, David; Gin, Jennifer
    • Frontiers in Bioengineering and Biotechnology, Vol. 4
    • DOI: 10.3389/fbioe.2016.00076

    Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism
    journal, May 2017

    • Shymansky, Christopher M.; Wang, George; Baidoo, Edward E. K.
    • Frontiers in Bioengineering and Biotechnology, Vol. 5
    • DOI: 10.3389/fbioe.2017.00031

    Automated Robotic Liquid Handling Assembly of Modular DNA Devices
    journal, January 2017

    • Ortiz, Luis; Pavan, Marilene; McCarthy, Lloyd
    • Journal of Visualized Experiments, Issue 130
    • DOI: 10.3791/54703
      Sort by:
      [ × clear filter / sort ]

      Figures / Tables found in this record:

      Figure 1 (p. 5)figure
      Figure 2 (p. 5)figure
      Figure 3 (p. 6)figure
      Figure 4 (p. 6)figure
        [ × clear filter / sort ]
        Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.

        Similar Records in DOE PAGES and OSTI.GOV collections: