Guidelines for Reproducibly Building and Simulating Systems Biology Models

Overview

Journal IEEE Trans Biomed Eng

Specialties Biomedical Engineering
Biophysics

Date 2016 Jul 19

PMID 27429432

Citations 17

Authors

J Kyle Medley

Arthur P Goldberg

Jonathan R Karr

Affiliations

Soon will be listed here.

Abstract

Objective: Reproducibility is the cornerstone of the scientific method. However, currently, many systems biology models cannot easily be reproduced. This paper presents methods that address this problem.

Methods: We analyzed the recent Mycoplasma genitalium whole-cell (WC) model to determine the requirements for reproducible modeling.

Results: We determined that reproducible modeling requires both repeatable model building and repeatable simulation.

Conclusion: New standards and simulation software tools are needed to enhance and verify the reproducibility of modeling. New standards are needed to explicitly document every data source and assumption, and new deterministic parallel simulation tools are needed to quickly simulate large, complex models.

Significance: We anticipate that these new standards and software will enable researchers to reproducibly build and simulate more complex models, including WC models.

Citing Articles

A Practical Guide to Reproducible Modeling for Biochemical Networks.

Porubsky V, Sauro H Methods Mol Biol. 2023; 2634:107-138.

PMID: 37074576 DOI: 10.1007/978-1-0716-3008-2_5.

VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models.

Parker C, Nelson E, Zhang T Entropy (Basel). 2022; 24(12).

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Reproducible parallel inference and simulation of stochastic state space models using odin, dust, and mcstate.

FitzJohn R, Knock E, Whittles L, Perez-Guzman P, Bhatia S, Guntoro F Wellcome Open Res. 2021; 5:288.

PMID: 34761122 PMC: 8552050. DOI: 10.12688/wellcomeopenres.16466.2.

Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node.

Scholzel C, Blesius V, Ernst G, Goesmann A, Dominik A PLoS One. 2021; 16(7):e0254749.

PMID: 34280231 PMC: 8289093. DOI: 10.1371/journal.pone.0254749.

Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective.

Scholzel C, Blesius V, Ernst G, Dominik A NPJ Syst Biol Appl. 2021; 7(1):27.

PMID: 34083542 PMC: 8175692. DOI: 10.1038/s41540-021-00182-w.

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