Reproducibility of Model-Based Results in Systems Biology

  • Dagmar Waltemath
  • Ron Henkel
  • Felix Winter
  • Olaf Wolkenhauer

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.

Keywords

Reproducibility Simulation experiments Standards SED-ML SBML CellML Model management 

Acronyms

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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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Dagmar Waltemath
    • 1
  • Ron Henkel
    • 1
  • Felix Winter
    • 1
  • Olaf Wolkenhauer
    • 1
    • 2
  1. 1.Department of Systems Biology and BioinformaticsRostock UniversityRostockGermany
  2. 2.Stellenbosch Institute for Advanced Study (STIAS)Wallenberg Research Centre at Stellenbosch UniversityStellenboschSouth Africa

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