Reproducible computational biology experiments with SED-ML-the Simulation Experiment Description Markup Language

Dagmar Waltemath; Richard Adams; Frank T Bergmann; Michael Hucka; Fedor Kolpakov; Andrew K Miller; Ion I Moraru; David Nickerson; Sven Sahle; Jacky L Snoep; Nicolas Le Novère

doi:10.1186/1752-0509-5-198

Reproducible computational biology experiments with SED-ML-the Simulation Experiment Description Markup Language

Dagmar Waltemath, Richard Adams, Frank T Bergmann, Michael Hucka, Fedor Kolpakov, Andrew K Miller, Ion I Moraru, David Nickerson, Sven Sahle, Jacky L Snoep, Nicolas Le Novère

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English
Article number	198
Journal	BMC Systems Biology
Volume	5
DOIs	https://doi.org/10.1186/1752-0509-5-198
Publication status	Published - 2011

Keywords / Materials (for Non-textual outputs)

Computational Biology
Computer Simulation
Programming Languages
Reproducibility of Results
Software

Access to Document

10.1186/1752-0509-5-198

1752-0509-5-198
© 2011 Waltemath et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Final published version, 1.87 MB

SynthSys; formerly CSBE: Centre for Systems Biology at Edinburgh
Millar, A. (Principal Investigator), Beggs, J. (Co-investigator), Ghazal, P. (Co-investigator), Goryanin, I. (Co-investigator), Hillston, J. (Co-investigator), Plotkin, G. (Co-investigator), Tollervey, D. (Co-investigator), Walton, A. (Co-investigator) & Robertson, K. (Researcher)
Biotechnology and Biological Sciences Research Council
8/01/07 → 31/12/12
Project: Research

Cite this

@article{1b2fc55bd3b04e6b8b606614254b020a,

title = "Reproducible computational biology experiments with SED-ML-the Simulation Experiment Description Markup Language",

abstract = "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.",

keywords = "Computational Biology, Computer Simulation, Programming Languages, Reproducibility of Results, Software",

author = "Dagmar Waltemath and Richard Adams and Bergmann, \{Frank T\} and Michael Hucka and Fedor Kolpakov and Miller, \{Andrew K\} and Moraru, \{Ion I\} and David Nickerson and Sven Sahle and Snoep, \{Jacky L\} and \{Le Nov{\`e}re\}, Nicolas",

year = "2011",

doi = "10.1186/1752-0509-5-198",

language = "English",

volume = "5",

journal = "BMC Systems Biology",

issn = "1752-0509",

publisher = "BioMed Central",

}

TY - JOUR

T1 - Reproducible computational biology experiments with SED-ML-the Simulation Experiment Description Markup Language

AU - Waltemath, Dagmar

AU - Adams, Richard

AU - Bergmann, Frank T

AU - Hucka, Michael

AU - Kolpakov, Fedor

AU - Miller, Andrew K

AU - Moraru, Ion I

AU - Nickerson, David

AU - Sahle, Sven

AU - Snoep, Jacky L

AU - Le Novère, Nicolas

PY - 2011

Y1 - 2011

N2 - 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.

AB - 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.

KW - Computational Biology

KW - Computer Simulation

KW - Programming Languages

KW - Reproducibility of Results

KW - Software

U2 - 10.1186/1752-0509-5-198

DO - 10.1186/1752-0509-5-198

M3 - Article

C2 - 22172142

SN - 1752-0509

VL - 5

JO - BMC Systems Biology

JF - BMC Systems Biology

M1 - 198

ER -

Reproducible computational biology experiments with SED-ML-the Simulation Experiment Description Markup Language

Abstract

Keywords / Materials (for Non-textual outputs)

Access to Document

Fingerprint

Projects

SynthSys; formerly CSBE: Centre for Systems Biology at Edinburgh

Cite this