Search

Whole-cell (WC) models that predict phenotype from genotype have the potential to transform biology, bioengineering, and medicine. Achieving WC models will likely require collaboration among modelers, experimentalists, mathematicians, computer scientists, and engineers. In 2012, we and others began to build a WC community by organizing a central website, a primer, schools, hackathons, and challenges. This year, we have continued to build a WC community by developing a new website, expanding the primer, organizing a third school, and launching an online seminar. Here, we summarize these initiatives, their impact to date, and our plans to continue to build a WC community., These efforts were supported by National Science Foundation awards 1548123 and 1649014 to JRK, National Institutes of Health award R35 GM119771 to JRK, and National Institutes of Health award P41 EB023912 to Herbert Sauro. The 2019 school was also supported by an EMBO Practical Course award to JRK, MLS, and DK., {"references":["Tomita, M. Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol 19, 205–210 (2001).","Karr, J. R., Takahashi, K. & Funahashi, A. The principles of whole-cell modeling. Curr Opin Microbiol 27, 18–24 (2015).","Carrera, J. & Covert, M. W. Why build whole-cell models? Trends Cell Biol 25, 719–722 (2015).","Karr, J. R. et al. A whole-cell computational model predicts phenotype from genotype. Cell 150, 389–401 (2012).","Macklin, D. N., Ruggero, N. A. & Covert, M. W. The future of whole-cell modeling. Curr Opin Biotechnol 28, 111–115 (2014).","Goldberg, A. P. et al. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol 51, 97–102 (2018).","Szigeti, B. et al. A blueprint for human whole-cell modeling. Curr Opin Syst Biol 7, 8–15 (2018).","Karr, J. R. & Pochiraju, S. Whole-cell modeling https://www.wholecell.org (2019).","Karr, J. R. et al. Summary of the DREAM8 parameter estimation challenge: toward parameter identification for whole-cell models. PLoS Comput Biol 11, e1004096 (2015).","Hucka, M. et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524–531 (2003).","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. The 2016 Whole-Cell Modeling Summer School https://doi.org/10.5281/zenodo.1004027 (2016).","Karr, J. R., Lluch-Senar, M, Serrano, L & Carrera, J. The 2017 Whole-Cell Modeling Summer School https://doi.org/10.5281/zenodo.1004135 (2017).","Karr, J. R. & Goldberg, A. P. An introduction to whole-cell modeling https://intro-to- wc-modeling.readthedocs.io (2017).","Karr, J. R., Lluch-Senar, M, Kastelic, D & Serrano, L. 2019 EMBO whole-cell modeling sum- mer school http://meetings.embo.org/event/19-whole-cell-modelling (2019).","Roth, Y. D., Porubsky, V., Sauro, H. M. & Karr, J. R. Online whole-Cell modeling seminar https://reproduciblebiomodels.org/seminar (2019).","Medley, J. K., Goldberg, A. P. & Karr, J. R. Guidelines for reproducibly building and simu- lating systems biology models. IEEE Trans Biomed Eng 63, 2015–2020 (2016).","Watanabe, L., König, M. & Myers, C. Dynamic flux balance analysis models in SBML. BioRXiv, 245076 (2018).","Burke, P. E., de Campos, C. B. & Quiles, M. G. Whole-cell representation and analysis of My- coplasma genitalium organism using complex networks. ComplexNet. doi: 10.13140/2.1.3736.6084.","Rees, J. et al. Designing minimal genomes using whole-cell models. bioRxiv, 344564 (2019)."]}

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 September 2017, we organized the second Whole-Cell Modeling Summer School to continue to build a whole-cell community by training new researchers. The school created new whole-cell training materials; trained 18 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., The school was partly supported by ERASynBio award to JRK, LS, and MLS; Horizon 2020 award 634942 to LS; and National Science Foundation award 1649014 to JRK., {"references":["Tomita, M. Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol 19, 205–210 (2001).","Karr, J. R., Takahashi, K. & Funahashi, A. The principles of whole-cell modeling. Curr Opin Microbiol 27, 18–24 (2015).","Carrera, J. & Covert, M. W. Why build whole-cell models? Trends Cell Biol 25, 719–722 (2015).","Karr, J. R. et al. A whole-cell computational model predicts phenotype from genotype. Cell 150, 389–401 (2012).","Macklin, D. N., Ruggero, N. A. & Covert, M. W. The future of whole-cell modeling. Curr Opin Biotechnol 28, 111–115 (2014).","Goldberg, A. P. et al. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol (In submission).","Szigeti, B et al. A blueprint for human whole-cell modeling. Curr Opin Syst Biol (In submis- sion).","Karr, J. R., Lluch-Senar, M, Serrano, L & Carrera, J. The 2016 Whole-Cell Modeling Summer School http://www.karrlab.org/static/doc/papers/Karr2016.pdf (2016).","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 & Kastelic, D. 2017 Whole-Cell Modeling Summer School http://www.wholecell.org/school-2017 (2017).","Karr, J. R. & Goldberg, A. P. An introduction to whole-cell modeling http://intro-to-wc- modeling.readthedocs.io (2017).","European Molecular Biology Organization. Practical course funding http://www.embo.org/ funding-awards/courses-workshops/practical-courses (2017)."]}

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.