Evidence map›Paper›PMID 30787451›Full record

ArticleNature protocols2019

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

Laurent Heirendt, Sylvain Arreckx, Thomas Pfau, Sebastián N Mendoza, Anne Richelle, Almut Heinken, Hulda S Haraldsdóttir, Jacek Wachowiak, Sarah M Keating, Vanja Vlasov and 45 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature protocols, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 673 papers.

0numbers the graph read from it
0cells of the map it votes in
673citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

673 citing papers in PubMed.

  1. Trial
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Review
  10. Article
  11. Review
  12. Review
  13. Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. EHMN2026Metabolites · 2026
    Article

613 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

55 authors.

Laurent Heirendt *Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Sylvain Arreckx *Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Thomas PfauLife Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg.ORCID http://orcid.org/0000-0001-5048-2923
Sebastián N MendozaCenter for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile.ORCID http://orcid.org/0000-0002-2192-5569
Anne RichelleDepartment of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, USA.
Almut HeinkenLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Hulda S HaraldsdóttirLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Jacek WachowiakLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Sarah M KeatingEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK.
Vanja VlasovLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Stefania MagnusdóttirLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Chiam Yu NgDepartment of Chemical Engineering, The Pennsylvania State University, State College, PA, USA.
German PreciatLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Alise ŽagareLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Siu H J ChanDepartment of Chemical Engineering, The Pennsylvania State University, State College, PA, USA.
Maike K AurichLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Catherine M ClancyLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Jennifer ModamioLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
John T SaulsDepartment of Physics, and Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA.
Alberto NoronhaLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Aarash BordbarSinopia Biosciences, San Diego, CA, USA.
Benjamin CousinsAlgorithms and Randomness Center, School of Computer Science, Georgia Institute of Technology, Atlanta, GA, USA.
Diana C El AssalLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Luis V ValcarcelBiomedical Engineering and Sciences Department, TECNUN, University of Navarra, San Sebastián, Spain.ORCID http://orcid.org/0000-0003-3769-5419
Iñigo ApaolazaBiomedical Engineering and Sciences Department, TECNUN, University of Navarra, San Sebastián, Spain.ORCID http://orcid.org/0000-0002-8961-4513
Susan GhaderiLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Masoud AhookhoshLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Marouen Ben GuebilaLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Andrejs KostrominsInstitute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia.
Nicolas SompairacInstitut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, Paris, France.
Hoai M LeLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Ding MaDepartment of Management Science and Engineering, Stanford University, Stanford, CA, USA.
Yuekai SunDepartment of Statistics, University of Michigan, Ann Arbor, MI, USA.
Lin WangDepartment of Chemical Engineering, The Pennsylvania State University, State College, PA, USA.
James T YurkovichDepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-9403-509X
Miguel A P OliveiraLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Phan T VuongLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Lemmer P El AssalLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Inna KupersteinInstitut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, Paris, France.ORCID http://orcid.org/0000-0001-8086-8915
Andrei ZinovyevInstitut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, Paris, France.
H Scott HintonUtah State University Research Foundation, North Logan, UT, USA.
William A BryantCentre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK.
Francisco J Aragón ArtachoDepartment of Mathematics, University of Alicante, Alicante, Spain.
Francisco J PlanesBiomedical Engineering and Sciences Department, TECNUN, University of Navarra, San Sebastián, Spain.
Egils StalidzansInstitute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia.
Alejandro MaassCenter for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile.
Santosh VempalaAlgorithms and Randomness Center, School of Computer Science, Georgia Institute of Technology, Atlanta, GA, USA.
Michael HuckaDepartment of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
Michael A SaundersDepartment of Management Science and Engineering, Stanford University, Stanford, CA, USA.
Costas D MaranasDepartment of Chemical Engineering, The Pennsylvania State University, State College, PA, USA.
Nathan E LewisDepartment of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-7700-3654
Thomas SauterLife Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg.
Bernhard Ø PalssonDepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
Ines ThieleLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
Ronan M T FlemingLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg. ronan.mt.fleming@gmail.com.

Funding

Continued Support of Essential SBML Software and Community ResourcesR01GM070923 · NIGMS · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI HUCKA, MICHAEL · 2004 to 2018
$8.0M
Unraveling the mammalian secretory pathway through systems biology and algorithm developmentR35GM119850 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI LEWIS, NATHAN ENOCH · 2016 to 2025
$4.3M
NIGMS NIH HHS R01 GM070923NIGMS NIH HHS R35 GM119850
6 · The paper itself

Abstract

Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. It has found widespread application in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. This protocol is an update to the COBRA Toolbox v.1.0 and v.2.0. Version 3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimization solvers for multi-scale, multi-cellular, and reaction kinetic modeling, respectively. This protocol provides an overview of all these new features and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios. The COBRA Toolbox v.3.0 provides an unparalleled depth of COBRA methods.

Indexed as

Models, BiologicalSoftwareGenomeMetabolic Networks and PathwaysSystems Biology

Identifiers

PMID30787451
PMCPMC6635304

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.