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Computational models in systems biology: standards, dissemination, and best practices
Luis Sordo Vieira1, Reinhard C Laubenbacher2
1Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Florida, Gainesville, FL 32610, United States; Department of Psychiatry, University of Florida, Gainesville, FL 32610, United States.
Current Opinion in Biotechnology
|February 26, 2022
Summary
Clear standards are essential for reproducible systems biology models. This review examines current standards and identifies needs, especially for agent-based models.
Area of Science:
- Systems biology
- Computational modeling
- Mathematical modeling
Background:
- Mathematical and computational models are crucial for advancing systems biology.
- Replicability and reproducibility of these models are vital for scientific progress.
- Lack of standardized specifications hinders model sharing and validation.
Purpose of the Study:
- To review existing standards for model specification and dissemination in systems biology.
- To identify key areas requiring further development in modeling standards.
- To address the specific needs for standardizing agent-based models.
Main Methods:
- Literature review of current standards in computational systems biology.
- Analysis of existing frameworks for model specification.
- Identification of gaps and challenges in current standards.
Main Results:
- Several standards exist for model specification and dissemination.
- Significant areas for improvement were identified.
- The specification of agent-based models requires particular attention and standardization.
Conclusions:
- Establishing clear standards is paramount for ensuring the reliability of systems biology models.
- Further work is needed to refine and expand existing standards.
- Standardization of agent-based models is a critical next step for the field.
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