Integrative Modeling
Published October 6, 2017 | Version v1
Report Open

The 2016 Whole-Cell Modeling Summer School

Creators

  • 1. Icahn School of Medicine at Mount Sinai, New York, NY, USA
  • 2. Centre for Genomic Regulation, Barcelona, Spain
  • 3. Stanford University, Stanford, CA, USA

Description

Whole-cell models that predict phenotype from genotype are needed to advance biology, bioengineering, and medicine. Achieving whole-cell models will require extensive collaboration among modelers, experimentalists, mathematicians, computer scientists, and software engineers. In April 2016, we organized the first Whole-Cell Modeling Summer School to begin to build a whole-cell community by training new researchers. The school created the first whole-cell training materials; trained 21 graduate students, postdoctoral scholars, and faculty; and generated ideas about how to better teach whole-cell modeling. To build a whole-cell modeling community, we plan to continue to organize schools, continue to improve these schools based on the lessons that we learned this year, and initiate an annual workshop and/or online seminar series to facilitate sustained discussion about whole-cell modeling.

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Additional details

Funding

ERASynBio: MiniCell - A Model-driven Approach to Minimal Cell Engineering 1548123
National Science Foundation
MINICELL – Building minimal cells to understand active cell shape control 335672
European Commission
MycoSynVac – Engineering of Mycoplasma pneumoniae as a broad-spectrum animal vaccine 634942
European Commission

References

  • Karr, J. R., Takahashi, K. & Funahashi, A. The principles of whole-cell modeling. Curr Opin Microbiol 27, 18–24 (2015).
  • Tomita, M. Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol 19, 205–210 (2001).
  • Carrera, J. & Covert, M. W. Why build whole-cell models? Trends Cell Biol 25, 719–722 (2015).
  • Macklin, D. N., Ruggero, N. A. & Covert, M. W. The future of whole-cell modeling. Curr Opin Biotechnol 28, 111–115 (2014).
  • Karr, J. R. et al. A whole-cell computational model predicts phenotype from genotype. Cell 150, 389–401 (2012).
  • Waltemath, D. et al. Toward community standards and software for whole-cell modeling. IEEE Trans Biomed Eng 63, 2007–2014 (2016).
  • Karr, J. R., Lluch-Senar, M, Serrano, L & Carrera, J. 2016 Whole-Cell Modeling Summer School http://www.wholecell.org/school-2016 (2017).