The future of whole-cell modeling

Area of Science:

• Systems biology
• Computational biology
• Bioengineering
• Biomedicine

Background:

• Integrated whole-cell modeling offers transformative potential for biological and medical research.
• Building comprehensive models of cellular systems is complex and requires addressing numerous challenges.

Purpose of the Study:

• To review and discuss the key challenges encountered in developing integrated whole-cell models.
• To identify critical areas for improvement to advance the field of whole-cell modeling.

Main Methods:

• Review of challenges based on experience with Mycoplasma genitalium whole-cell model construction.
• Categorization of challenges into seven key areas: experimental interrogation, data curation, model building/integration, computation, analysis/visualization, validation, and community development.

Main Results:

• Identified seven major challenge areas hindering the development of more complex whole-cell models.
• Highlighted the need for advancements in experimental data acquisition, data management, computational efficiency, and model validation.

Conclusions:

• Surmounting these challenges requires interdisciplinary collaboration.
• Increased accessibility of data, models, and simulations is crucial for community-wide progress in whole-cell modeling.