Erratum to: The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism

Birkel, Garrett W.; Ghosh, Amit; Kumar, Vinay S.; Weaver, Daniel; Ando, David; Backman, Tyler W. H.; Arkin, Adam P.; Keasling, Jay D.; Martín, Héctor García

doi:10.1186/s12859-017-1631-y

Title: Erratum to: The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism

Abstract

Following publication of this article [1], it has come to our attention that an incomplete version of Fig. 7 was included in this article. The complete figure is shown below with the missing text included to the left of the chart.

Authors:

Birkel, Garrett W. ^[1]; Ghosh, Amit ^[2]; Kumar, Vinay S. ^[3]; Weaver, Daniel ^[3]; Ando, David ^[3]; Backman, Tyler W. H. ^[1]; Arkin, Adam P. ^[4]; Keasling, Jay D. ^[5]; Martín, Héctor García ^[6]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); DOE Agile BioFoundry, Emeryville, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Indian Institute of Technology (IIT), Kharagpur (India)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States); Technical Univ. of Denmark, Horsholm (Denmark)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); DOE Agile BioFoundry, Emeryville, CA (United States); BCAM, Basque Center for Applied Mathematics, Bilbao (Spain)

Publication Date:: Tue Apr 18 00:00:00 EDT 2017

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1510743

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: BMC Bioinformatics

Additional Journal Information:: Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1471-2105

Publisher:: BioMed Central

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Birkel, Garrett W., Ghosh, Amit, Kumar, Vinay S., Weaver, Daniel, Ando, David, Backman, Tyler W. H., Arkin, Adam P., Keasling, Jay D., and Martín, Héctor García. Erratum to: The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism.  United States: N. p., 2017. 
Web.  doi:10.1186/s12859-017-1631-y.

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                    Birkel, Garrett W., Ghosh, Amit, Kumar, Vinay S., Weaver, Daniel, Ando, David, Backman, Tyler W. H., Arkin, Adam P., Keasling, Jay D., & Martín, Héctor García. Erratum to: The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism.  United States.  https://doi.org/10.1186/s12859-017-1631-y

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                    Birkel, Garrett W., Ghosh, Amit, Kumar, Vinay S., Weaver, Daniel, Ando, David, Backman, Tyler W. H., Arkin, Adam P., Keasling, Jay D., and Martín, Héctor García. Tue .  
"Erratum to: The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism".  United States.  https://doi.org/10.1186/s12859-017-1631-y.  https://www.osti.gov/servlets/purl/1510743.

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@article{osti_1510743,

  title        = {Erratum to: The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism},

  author       = {Birkel, Garrett W. and Ghosh, Amit and Kumar, Vinay S. and Weaver, Daniel and Ando, David and Backman, Tyler W. H. and Arkin, Adam P. and Keasling, Jay D. and Martín, Héctor García},

  abstractNote = {Following publication of this article [1], it has come to our attention that an incomplete version of Fig. 7 was included in this article. The complete figure is shown below with the missing text included to the left of the chart.},

  doi          = {10.1186/s12859-017-1631-y},

  journal      = {BMC Bioinformatics},

  number       = 1,

  volume       = 18,

  place        = {United States},

  year         = {Tue Apr 18 00:00:00 EDT 2017},

  month        = {Tue Apr 18 00:00:00 EDT 2017}

}

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Journal Article:

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https://doi.org/10.1186/s12859-017-1631-y

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Figures / Tables:

Fig. 7 : Principal component analysis (PCA) of protein expression data

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Fig. 7 (p. 3)

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Title: Erratum to: The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism

Abstract

Citation Formats

Figures / Tables:

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism journal, April 2017

Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production: Targeted Proteomics-Based Correlation Analysis journal, May 2014

13 C-metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites journal, January 2010

13C Metabolic Flux Analysis journal, July 2001

The compatibility of potential bioderived fuels with Jet A-1 aviation kerosene journal, April 2014

Engineering Cellular Metabolism journal, March 2016

Redirecting carbon flux into malonyl-CoA to improve resveratrol titers: Proof of concept for genetic interventions predicted by OptForce computational framework journal, November 2013

High-throughput discovery metabolomics journal, February 2015

Sustainable consumption within a sustainable economy – beyond green growth and green economies journal, January 2014

Modeling soil metabolic processes using isotopologue pairs of position-specific 13C-labeled glucose and pyruvate journal, September 2011

Effect of temperature on metabolic activity of intact microbial communities: Evidence for altered metabolic pathway activity but not for increased maintenance respiration and reduced carbon use efficiency journal, October 2011

Systems biotechnology for strain improvement journal, July 2005

Elementary metabolite units (EMU): A novel framework for modeling isotopic distributions journal, January 2007

Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production journal, September 2013

A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins journal, November 2014

Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering journal, March 2015

Addressing the Need for Alternative Transportation Fuels: The Joint BioEnergy Institute journal, January 2008

Systems metabolic engineering of Escherichia coli for L ‐threonine production journal, January 2007

Engineering synergy in biotechnology journal, April 2014

The challenges of integrating multi-omic data sets journal, October 2010

Improved reproducibility by assuring confidence in measurements in biomedical research journal, August 2014

Synthetic and systems biology for microbial production of commodity chemicals journal, April 2016

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox journal, March 2007

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods journal, February 2012

Regulatory on/off minimization of metabolic flux changes after genetic perturbations journal, May 2005

Analysis of optimality in natural and perturbed metabolic networks journal, November 2002

13CFLUX2—high-performance software suite for 13C-metabolic flux analysis journal, October 2012

INCA: a computational platform for isotopically non-stationary metabolic flux analysis journal, January 2014

Proteome Analysis of Metabolically Engineered Escherichia coli Producing Poly(3-Hydroxybutyrate) journal, January 2001

Metabolic remodeling of white adipose tissue in obesity journal, August 2014

OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis journal, January 2009

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A Method to Constrain Genome-Scale Models with 13C Labeling Data journal, September 2015

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism
journal, April 2017

Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production: Targeted Proteomics-Based Correlation Analysis
journal, May 2014

¹³ C-metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites
journal, January 2010

13C Metabolic Flux Analysis
journal, July 2001

The compatibility of potential bioderived fuels with Jet A-1 aviation kerosene
journal, April 2014

Engineering Cellular Metabolism
journal, March 2016

Redirecting carbon flux into malonyl-CoA to improve resveratrol titers: Proof of concept for genetic interventions predicted by OptForce computational framework
journal, November 2013

High-throughput discovery metabolomics
journal, February 2015

Sustainable consumption within a sustainable economy – beyond green growth and green economies
journal, January 2014

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journal, September 2011

Effect of temperature on metabolic activity of intact microbial communities: Evidence for altered metabolic pathway activity but not for increased maintenance respiration and reduced carbon use efficiency
journal, October 2011

Systems biotechnology for strain improvement
journal, July 2005

Elementary metabolite units (EMU): A novel framework for modeling isotopic distributions
journal, January 2007

Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production
journal, September 2013

A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins
journal, November 2014

Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering
journal, March 2015

Addressing the Need for Alternative Transportation Fuels: The Joint BioEnergy Institute
journal, January 2008

Systems metabolic engineering of Escherichia coli for L ‐threonine production
journal, January 2007

Engineering synergy in biotechnology
journal, April 2014

The challenges of integrating multi-omic data sets
journal, October 2010

Improved reproducibility by assuring confidence in measurements in biomedical research
journal, August 2014

Synthetic and systems biology for microbial production of commodity chemicals
journal, April 2016

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
journal, March 2007

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
journal, February 2012

Regulatory on/off minimization of metabolic flux changes after genetic perturbations
journal, May 2005

Analysis of optimality in natural and perturbed metabolic networks
journal, November 2002

13CFLUX2—high-performance software suite for 13C-metabolic flux analysis
journal, October 2012

INCA: a computational platform for isotopically non-stationary metabolic flux analysis
journal, January 2014

Proteome Analysis of Metabolically Engineered Escherichia coli Producing Poly(3-Hydroxybutyrate)
journal, January 2001

Metabolic remodeling of white adipose tissue in obesity
journal, August 2014

OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis
journal, January 2009

Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells
journal, January 2012

COBRApy: COnstraints-Based Reconstruction and Analysis for Python
journal, January 2013

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
journal, August 2003

Bon-EV: an improved multiple testing procedure for controlling false discovery rates
journal, January 2017

A Method to Constrain Genome-Scale Models with 13C Labeling Data
journal, September 2015