title: The future of whole-cell modeling.
abstract: Integrated whole-cell modeling is poised to make a dramatic impact on molecular and systems biology, bioengineering, and medicine--once certain obstacles are overcome. From our group's experience building a whole-cell model of Mycoplasma genitalium, we identified several significant challenges to building models of more complex cells. Here we review and discuss these challenges in seven areas: first, experimental interrogation; second, data curation; third, model building and integration; fourth, accelerated computation; fifth, analysis and visualization; sixth, model validation; and seventh, collaboration and community development. Surmounting these challenges will require the cooperation of an interdisciplinary group of researchers to create increasingly sophisticated whole-cell models and make data, models, and simulations more accessible to the wider community.
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, USA.
authors.forename: Derek N
authors.initials: DN
authors.lastname: Macklin
authors.affiliation: Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Ruggero
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, USA. Electronic address: mcovert@stanford.edu.
authors.forename: Markus W
authors.initials: MW
authors.lastname: Covert
mesh_terms: D002477:Cells; D019295:Computational Biology; D016208:Databases, Factual; D008954:Models, Biological; D045686:Mycoplasma gallisepticum / Q000235:genetics / Q000378:metabolism