Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

  • Natalie J. Stanford
  • Martin Scharm
  • Paul D. Dobson
  • Martin Golebiewski
  • Michael Hucka
  • Varun B. Kothamachu
  • David Nickerson
  • Stuart Owen
  • Jürgen PahleEmail author
  • Ulrike Wittig
  • Dagmar Waltemath
  • Carole Goble
  • Pedro Mendes
  • Jacky Snoep
Part of the Methods in Molecular Biology book series (MIMB, volume 2049)


Computational systems biology involves integrating heterogeneous datasets in order to generate models. These models can assist with understanding and prediction of biological phenomena. Generating datasets and integrating them into models involves a wide range of scientific expertise. As a result these datasets are often collected by one set of researchers, and exchanged with others researchers for constructing the models. For this process to run smoothly the data and models must be FAIR—findable, accessible, interoperable, and reusable. In order for data and models to be FAIR they must be structured in consistent and predictable ways, and described sufficiently for other researchers to understand them. Furthermore, these data and models must be shared with other researchers, with appropriately controlled sharing permissions, before and after publication. In this chapter we explore the different data and model standards that assist with structuring, describing, and sharing. We also highlight the popular standards and sharing databases within computational systems biology.

Key words

Standards Metadata Databases Data storage Model storage FAIR Reproducible research 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Natalie J. Stanford
    • 1
  • Martin Scharm
    • 2
  • Paul D. Dobson
    • 1
  • Martin Golebiewski
    • 3
  • Michael Hucka
    • 4
  • Varun B. Kothamachu
    • 5
  • David Nickerson
    • 6
  • Stuart Owen
    • 1
  • Jürgen Pahle
    • 7
    Email author
  • Ulrike Wittig
    • 3
  • Dagmar Waltemath
    • 10
  • Carole Goble
    • 1
  • Pedro Mendes
    • 8
  • Jacky Snoep
    • 1
    • 9
  1. 1.School of Computer ScienceUniversity of ManchesterManchesterUK
  2. 2.Department of Systems Biology and BioinformaticsUniversity of RostockRostockGermany
  3. 3.Heidelberg Institute for Theoretical Studies (HITS)HeidelbergGermany
  4. 4.Computing and Mathematical SciencesCalifornia Institute of TechnologyPasadenaUSA
  5. 5.Signalling ISPThe Babraham InstituteCambridgeUK
  6. 6.Auckland Bioengineering InstituteUniversity of AucklandAucklandNew Zealand
  7. 7.BIOMS/BioQuantHeidelberg UniversityHeidelbergGermany
  8. 8.Centre for Quantitative MedicineUniversity of ConnecticutFarmingtonUSA
  9. 9.BiochemistryStellenbosch UniversityStellenboschSouth Africa
  10. 10.Medical InformaticsUniversity Medicine GreifswaldGreifswaldGermany

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