Work

Guidelines for Reproducibly Building and Simulating Systems Biology Models

Year: 2016

Type: article

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.

Source: IEEE Transactions on Biomedical Engineering

DOI: 10.1109/tbme.2016.2591960

Authors: J. Kyle Medley, Arthur P. Goldberg, Jonathan R. Karr

Institutions: University of Washington, Icahn School of Medicine at Mount Sinai

Language: English

Topic: Scientific Computing and Data Management

Subfield: Information Systems and Management

Field: Decision Sciences

Domain: Social Sciences

Open Access status: green

Funders: National Science Foundation, National Institutes of Health, National Institute of General Medical Sciences

Awards: ERASynBio: MiniCell - A Model-driven Approach to Minimal Cell Engineering, Collaborative: ABI Development: Synthetic Biology Open Language Resource, Continued Development and Maintenance of the Systems Biology Workbench, Toward whole-cell models for precision medicine and synthetic biology