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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. [ABSTRACT FROM PUBLISHER]

Objective: Only reproducible results are of significance to science. The lack of suitable standards and appropriate support of standards in software tools has led to numerous publications with irreproducible results. Our objectives are to identify the key challenges of reproducible research and to highlight existing solutions. Results: In this paper, we summarize problems concerning reproducibility in systems biology and systems medicine. We focus on initiatives, standards, and software tools that aim to improve the reproducibility of simulation studies. Conclusions: The long-term success of systems biology and systems medicine depends on trustworthy models and simulations. This requires openness to ensure reusability and transparency to enable reproducibility of results in these fields. [ABSTRACT FROM PUBLISHER]