eprintid: 20479
rev_number: 11
eprint_status: archive
userid: 1589
dir: disk0/00/02/04/79
datestamp: 2016-04-07 09:08:53
lastmod: 2024-04-18 00:25:47
status_changed: 2016-04-07 09:08:53
type: article
metadata_visibility: show
creators_name: Waltemath, Dagmar
creators_name: Adams, Richard
creators_name: Bergmann, Frank T.
creators_name: Hucka, Michael
creators_name: Kolpakov, Fedor
creators_name: Miller, Andrew K.
creators_name: Moraru, Ion I.
creators_name: Nickerson, David
creators_name: Sahle, Sven
creators_name: Snoep, Jacky L.
creators_name: Le Novère, Nicolas
title: Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language
subjects: ddc-570
divisions: i-716000
abstract: Background: The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools.   Results: In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions.   Conclusions: With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.
date: 2011
publisher: BioMed Central
id_scheme: DOI
ppn_swb: 165651608X
own_urn: urn:nbn:de:bsz:16-heidok-204791
language: eng
bibsort: WALTEMATHDREPRODUCIB2011
full_text_status: public
publication: BMC Systems Biology
volume: 5
number: 198
place_of_pub: London
pagerange: 1-10
issn: 1752-0509
citation:   Waltemath, Dagmar ; Adams, Richard ; Bergmann, Frank T. ; Hucka, Michael ; Kolpakov, Fedor ; Miller, Andrew K. ; Moraru, Ion I. ; Nickerson, David ; Sahle, Sven ; Snoep, Jacky L. ; Le Novère, Nicolas  (2011) Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language.  BMC Systems Biology, 5 (198).  pp. 1-10.  ISSN 1752-0509     
document_url: https://archiv.ub.uni-heidelberg.de/volltextserver/20479/1/12918_2011_Article_839.pdf