Publications

How to cite?

• 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.

  https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-5-198

  PMID:22172142

Presentations

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

Publications that report contributions to SED-ML ecosystem

• Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König

  The simulation experiment description markup language (SED-ML): language specification for level 1 version 4

  Journal of Integrative Bioinformatics, vol. , no. , 2021, pp. 20210021. https://doi.org/10.1515/jib-2021-0021

  DOI: 10.1515/jib-2021-002

• 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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