Toward reproducible disease models using the Systems Biology Markup Language. (October 2019)

• Record Type: Journal Article
• Authors: Watanabe, Leandro; Barhak, Jacob; Myers, Chris
• Is Part Of: Simulation. Volume 95:Number 10(2019)
• Page Start: 895
• Page End: 930
• Publication Date: 2019-10
• Subjects: Disease modeling -- microsimulation -- reproducibility -- SBML -- arrays package; Computer simulation -- Periodicals; 003.3
• DOI: 10.1177/0037549718793214
• Languages: English
• ISSNs: 0037-5497

Abstract

Disease modelers have been modeling progression of diseases for several decades using such tools as Markov models or microsimulation. However, they need to address a serious challenge; many models they create are not reproducible. Moreover, there is no proper practice that ensures reproducible models, since modelers rely on loose guidelines that change periodically, rather than well-defined machine-readable standards. The Systems Biology Markup Language (SBML) is one such standard that allows exchange of models between different software tools. Recently, the SBML Arrays package has been developed, which extends the standard to allow handling simulation of populations. This paper demonstrates through several abstract examples how microsimulation disease models can be encoded using the SBML Arrays package, enabling reproducible disease modeling.