Publications

How to cite?

Presentations

Date Author Title
pdf 2016 Martin Peters, Jacky Snoep, Dagmar Waltemath SED-ML support in JWS Online - Using SED-ML and COMBINE archives to reproduce simulation results
pdf 2014 David Nickerson Introduction to SED-ML
pdf 2010 Frank Bergmann, Dagmar Waltemath The Simulation Experiment Description Language (SED-ML)
pdf 2010 Frank Bergmann SED-ML
pdf 2010 Dagmar Waltemath Biomodels Meta Information and SED-ML

Publications that report contributions to SED-ML ecosystem

  • Shaikh B, Marupilla G, Blinov ML, Moraru II, Karr JR
    RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats
    bioRxiv. 2021.03.05.433787v1.
    DOI: 10.1101/2021.03.05.433787
  • Bergmann FT, Cooper J, König M, Moraru I, Nickerson D, Le Novère N, Olivier BG, Sahle S, Smith L, Waltemath D
    Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)
    Integr Bioinform. 2018;15(1):20170086.
    DOI: 10.1515/jib-2017-0086
    PMID: 29550789
  • Bergmann FT, Nickerson D, Waltemath D, Scharm M.
    SED-ML web tools: generate, modify and export standard-compliant simulation studies.
    Bioinformatics. 2017 Apr 15;33(8):1253-1254.
    DOI: 10.1093/bioinformatics/btw812
    PMID: 28049131
  • Scharm M, Waltemath D.
    A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos
    F1000Research 2016, 5:2421
    DOI: 10.12688/f1000research.9379.1
  • Choi K, Smith LP, Medley JK, Sauro HM.
    phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.
    J Bioinform Comput Biol. 2016 Dec;14(6):1650035.
    DOI: 10.1142/S0219720016500359
    PMID: 27774871
  • Henkel R, Wolkenhauer O, Waltemath D
    Combining computational models, semantic annotations and simulation experiments in a graph database.
    Database (Oxford). 2015 Mar 8;2015. pii: bau130.
    DOI: 10.1093/database/bau130
    PMID: 25754863
  • Bergmann FT, Cooper J, Le Novère N, Nickerson D, Waltemath D.
    Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.
    J Integr Bioinform. 2015 Sep 4;12(2):262.
    DOI: 10.2390/biecoll-jib-2015-262
    PMID: 26528560
  • Adams RR.
    SED-ED, a workflow editor for computational biology experiments written in SED-ML.
    Bioinformatics. 2012 Apr 15;28(8):1180-1.
    DOI: 10.1093/bioinformatics/bts101
    PMID: 22368254
  • Miller AK, Britten RD, Nielsen PM.
    Declarative representation of uncertainty in mathematical models.
    PLoS One. 2012;7(7):e39721.
    DOI: 10.1371/journal.pone.0039721
    PMID: 22802941
  • Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, Moraru II, Nickerson D, Sahle S, Snoep JL, Le Novère N.
    Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.
    BMC Syst Biol. 2011 Dec 15;5:198.
    DOI: 10.1186/1752-0509-5-198
    PMID: 22172142
  • Waltemath D, Bergmann FT, Adams R, LeNovère N
    Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1
    Nature Precedings.
    DOI: 10.1038/npre.2011.5846.1
  • Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N.
    Minimum Information About a Simulation Experiment (MIASE).
    PLoS Comput Biol. 2011 Apr;7(4):e1001122.
    DOI: 10.1371/journal.pcbi.1001122
    PMID: 21552546
  • Bergmann FT.
    A simple nested simulation for SED-ML.
    Nature Precedings (2010): 1-1.
    DOI: 10.1038/npre.2010.4257.1
  • Dagmar Köhn, Nicolas Le Novère
    SED-ML – An XML Format for the Implementation of the MIASE Guidelines.
    Lecture Notes in Computer Science, Computational Methods in Systems Biology 2008
    DOI: 10.1007/978-3-540-88562-7_15

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