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Reproducibility of Model-Based Results in Systems Biology

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Book cover Systems Biology

Abstract

Science requires that results are reproducible. This is naturally expected for wet-lab experiments and it is equally important for model-based results published in the literature. Reproducibility, in general, requires standards that provide the information necessary and tools that enable others to re-use this information. In computational biology, reproducibility requires not only a coded form of the model but also a coded form of the experimental setup to reproduce the analysis of the model. Well-established databases and repositories store and provide mathematical models. Recently, these databases started to distribute simulation setups together with the model code. These developments facilitate the reproduction of results. In this chapter, we outline the necessary steps towards reproducing model-based results in computational biology. We exemplify the workflow using a prominent example model of the Cell Cycle and state-of-the-art tools and standards.

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Notes

  1. 1.

    A limit cycle is “a closed orbit which is isolated, i.e. neighboring orbits are not closed”. (Definition: TEDDY ontology, http://www.biomodels.net/teddy)

  2. 2.

    http://www.ebi.ac.uk/biomodels-main/BIOMD0000000005

  3. 3.

    Please refer to Bellinger et al. [14] for an overview about the distinction between data, information, and knowledge

  4. 4.

    http://co.mbine.org/

  5. 5.

    http://www.ebi.ac.uk/miriam/main

  6. 6.

    http://www.uniprot.org/

  7. 7.

    www.ebi.ac.uk/biomodels-main/

  8. 8.

    http://www.cellml.org/models

  9. 9.

    http://jjj.biochem.sun.ac.za/database

  10. 10.

    http://senselab.med.yale.edu/modeldb/

  11. 11.

    http://www.ebi.ac.uk/biomodels-demo/search

  12. 12.

    http://sed-ml.org

  13. 13.

    http://libsedml.sourceforge.net/libSedML/SedMLScript.html

  14. 14.

    http://sysbioapps.dyndns.org/SED-ML_Web_Tools/

Abbreviations

SBML:

Systems Biology Markup Language

ChEBI:

Chemical Entities of Biological Interest

RDF:

Resource Description Framework

GO:

Gene Ontology

TEDDY:

TErminology for the Description of DYnamics

COMBINE:

The COmputational Modeling in BIology NEtwork

XML:

Extensible Markup Language

OWL:

Web Ontology Language

MIRIAM:

Minimum Information Required in the Annotation of Models

URN:

Uniform Resource Name

PMR2:

Physiome Model Repository

COPASI:

Complex Pathway SImulator

SED-ML:

Simulation Experiment Description Markup Language

MIASE:

Minimum Information About a Simulation Experiment

IR:

Information Retrieval

DDMoRe:

Drug Disease Model Resources

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Author information

Authors and Affiliations

  1. Department of Systems Biology and Bioinformatics, Rostock University, 18051, Rostock, Germany

    Dagmar Waltemath, Ron Henkel, Felix Winter & Olaf Wolkenhauer

  2. Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Marais Street, Stellenbosch, 7600, South Africa

    Olaf Wolkenhauer

Authors
  1. Dagmar Waltemath
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  2. Ron Henkel
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  3. Felix Winter
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  4. Olaf Wolkenhauer
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Corresponding author

Correspondence to Dagmar Waltemath .

Editor information

Editors and Affiliations

  1. Chemical and Biological Engineering, Vanderbilt University, Nashville, TN, USA

    Aleš Prokop

  2. Research Group on Process Network Engineering, Kaposvár University, Kaposvár, Hungary

    Béla Csukás

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Waltemath, D., Henkel, R., Winter, F., Wolkenhauer, O. (2013). Reproducibility of Model-Based Results in Systems Biology. In: Prokop, A., Csukás, B. (eds) Systems Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6803-1_10

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