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Whole-cell models that predict phenotype from genotype by representing all of the biochemical activity inside cells are needed to advance biology, bioengineering, and medicine. Achieving whole-cell models will require a strong community of modelers, experimentalists, mathematicians, computer scientists, and software engineers. The EMBO Practical Course on Whole-Cell Modeling will teach students the fundamentals of whole-cell modeling and provide them opportunities to network with other promising whole-cell modelers. The school will be held April 7–13, 2019 at the Center for Genomic Regulation in Barcelona, Spain. The course will consist of two introductory lectures, tutorials on the fundamentals of whole-cell modeling, group discussions about the future of whole-cell modeling, two keynote talks, and two networking activities. The tutorials will teach the students how to aggregate and integrate data for modeling, build large models by combining smaller models, use rules to represent models, simulate hybrid models, and experimentally validate models, as well as teach the students critical software engineering skills. Each tutorial will include a brief lecture followed by hands-on exercises in which the students will work in small groups with guidance from an instructor to build, simulate, and test toy models.