Evidence map›Paper›PMID 26079347›Full record

ArticleBioinformatics (Oxford, England)2015

JSBML 1.0: providing a smorgasbord of options to encode systems biology models.

Nicolas Rodriguez, Alex Thomas, Leandro Watanabe, Ibrahim Y Vazirabad, Victor Kofia, Harold F Gómez, Florian Mittag, Jakob Matthes, Jan Rudolph, Finja Wrzodek and 12 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.

0numbers the graph read from it
0cells of the map it votes in
18citing 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

18 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Review
  5. Article
  6. High-Quality Genome-Scale Reconstruction ofFrontiers in microbiology · 2021
    Article
  7. Article
  8. Article
  9. Review
  10. Article
  11. Article
  12. Review
  13. Review
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
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

22 authors.

Nicolas RodriguezEuropean Bioinformatics Institute (EBI), Hinxton, UK, Babraham Institute, Babraham Research Campus, Cambridge, UK.
Alex ThomasUniversity of California, San Diego, La Jolla, CA, USA, Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA.
Leandro WatanabeThe University of Utah, Salt Lake City, UT, USA.
Ibrahim Y VazirabadMarquette University, Milwaukee, WI, USA.
Victor KofiaThe University of Toronto, Toronto, ON, Canada.
Harold F GómezBoston University, Boston, MA, USA.
Florian MittagEuropean Bioinformatics Institute (EBI), Hinxton, UK, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
Jakob MatthesCenter for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
Jan RudolphCenter for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany, Tel Aviv University, Tel Aviv, Israel.
Finja WrzodekEuropean Bioinformatics Institute (EBI), Hinxton, UK, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
Eugen NetzCenter for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
Alexander DiamantikosCenter for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
Johannes EichnerCenter for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
Roland KellerCenter for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
Clemens WrzodekCenter for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany, Roche Pharmaceutical Research and Early Development, pRED Informatics, Roche Innovation Center, Penzberg, Germany.
Sebastian FröhlichLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany and.
Nathan E LewisUniversity of California, San Diego, La Jolla, CA, USA, Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA.
Chris J MyersThe University of Utah, Salt Lake City, UT, USA.
Nicolas Le NovèreEuropean Bioinformatics Institute (EBI), Hinxton, UK, Babraham Institute, Babraham Research Campus, Cambridge, UK.
Bernhard Ø PalssonUniversity of California, San Diego, La Jolla, CA, USA, Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA.
Michael HuckaThe California Institute of Technology, Pasadena, CA, USA.
Andreas DrägerUniversity of California, San Diego, La Jolla, CA, USA, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.

Funding

Continued Support of Essential SBML Software and Community ResourcesR01GM070923 · NIGMS · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI HUCKA, MICHAEL · 2004 to 2018
$8.0M
Biotechnology and Biological Sciences Research Council BBS/E/B/000C0419NIAID NIH HHS HHSN272201000053CNIGMS NIH HHS GM070923
6 · The paper itself

Abstract

unlabelledJSBML, the official pure Java programming library for the Systems Biology Markup Language (SBML) format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users. AVAILABILITY AND IMPLEMENTATION: Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML. More information about JSBML can be found in the user guide at http://sbml.org/Software/JSBML/docs/. CONTACT: jsbml-development@googlegroups.com or andraeger@eng.ucsd.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

Models, BiologicalSoftwareSystems BiologyComputer SimulationProgramming Languages

Identifiers

PMID26079347
PMCPMC4595895

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.