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Model Reproducibility: Overview

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  • First Online:
Encyclopedia of Computational Neuroscience
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Definition

The ability to reproduce an experimental result is the foundation of scientific inquiry; however, computational scientists find it difficult to reproduce many published results. Here we provide an overview of efforts to support model reproducibility in computational neuroscience.

Detailed Description

Reproducing the simulation results of computational models and establishing the provenance of results should be straightforward given that computational studies do not suffer from the measurement errors seen in the experimental sciences. However, computational science has its own challenges for reproducibility, which are described well by Crook et al. (2013). In particular, issues such as the sensitivity of a model to numerics or the publication of models that are computationally under-specified lead to the need for criteria for successful model reproduction in many cases. These authors also make distinctions among:

  • Replicability, where the same code and tools are used to...

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References

  • Bray T, Paoli J, Sperberg-McQueen C (1998) Extensible markup language (XML) 1.0. http://www.w3.org/TR/REC-xml

  • Crook S, Gleeson P, Howell F, Svitak J, Silver RA (2007) MorphML: level 1 of the NeuroML standards for neuronal morphology data and model specification. Neuroinformatics 5:96–104

    PubMed  Google Scholar 

  • Crook S, Davison AP, Plesser HE (2013) Learning from the past: approaches for reproducibility in computational neuroscience. In: Bower JM (ed) 20 Years of computational neuroscience, vol 9, Springer series in computational neuroscience. Springer, New York, pp 73–102

    Google Scholar 

  • Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, Silver RA (2010a) NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput Biol 6(6):e1000815

    PubMed Central  PubMed  Google Scholar 

  • Gleeson P, Piasini E, Crook S, Cannon R, Steuber V, Jaeger D, Solinas S, D’Angelo E, Silver RA (2010b) The open source brain initiative: enabling collaborative modelling in computational neuroscience. BMC Neurosci 13(1):1–2

    Google Scholar 

  • Goddard N, Hucka M, Howell F, Cornelis H, Shankar K, Beeman D (2001) NeuroML: model description methods for collaborative modeling in neuroscience. Philos Trans R Soc Lond B Biol Sci 356:1209–1228

    PubMed Central  CAS  PubMed  Google Scholar 

  • Lloyd CM, Halstead MDB, Nielsen PF (2004) CellML: its future, present and past. Progress in Biophysics and Molecular Biology 85(2–3):433–450

    CAS  PubMed  Google Scholar 

  • Hucka M, Finney A, Sauro H, Bolouri H, Doyle J, Kitano H, Arkin A (2003) The systems biology markup language (SMBL): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524–531

    CAS  PubMed  Google Scholar 

  • Köhn D, Le Novère N (2008) SED-ML – an XML format for the implementation of the MIASE guidelines. In: Heiner M, Uhrmacher A (eds) Computational methods in systems biology, vol 5307, Lecture notes in computer science. Springer, Berlin, pp 176–190

    Google Scholar 

  • Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Callado-Vides J, Crampin E, Halstead M et al (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 23(12):1509–1515

    PubMed  Google Scholar 

  • Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novere N, Laibe C (2010) BioModels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 4:92

    PubMed Central  PubMed  Google Scholar 

  • Migliore M, Morse TM, Davison AP, Marenco L, Shepherd GM, Hines M (2003) ModelDB. Neuroinformatics 1(1):135–139

    PubMed Central  PubMed  Google Scholar 

  • Nordlie E, Gewaltig MO, Plesser HE (2009) Towards reproducible descriptions of neuronal network models. PLoS Comput Biol 5(8):e1000456

    PubMed Central  PubMed  Google Scholar 

  • Vijayalakshmi C, Laibe C, Le Novere N (2013) Biomodels database: a repository of mathematical models of biological processes. Methods Mol Biol 1021:189–199

    Google Scholar 

  • Yu T, Lloyd CM, Nickerson DP, Cooling MT, Miller AK, Garny A, Terk-ildsen JR, Lawson J, Britten RD, Hunter PJ, Nielsen PM (2011) The physiome model repository 2. Bioinformatics 27(5):743–744

    CAS  PubMed  Google Scholar 

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Correspondence to Sharon Crook .

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Crook, S. (2015). Model Reproducibility: Overview. In: Jaeger, D., Jung, R. (eds) Encyclopedia of Computational Neuroscience. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6675-8_763

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