2016 Whole-Cell Modeling Summer School



 DESCRIPTION (provided by applicant): The goal of the 2016 Whole-Cell Modeling Summer School is to advance whole-cell modeling by training young researchers and by building an interdisciplinary whole-cell modeling community. The goal of this proposal is to provide travel scholarships to enable students and postdoctoral scholars to participate in the course. These goals advance the NIGMS Division of Biomedical Technology, Bioinformatics, & Computational Biology's missions to develop integrative data analysis tools and to train future computational biologists. Despite decades of research, an integrated understanding of cell biology remains elusive. New computational methods are needed to integrate the growing wealth of data into a unified understanding of cell biology. Whole-cell modeling is a promising technique for integrating data into a unified understanding by combining multiple sub-models of individual intracellular pathways, each described using different mathematics and data, into a single physics-based dynamical model. Whole-cell models have the potential to accelerate biological science and enable rational microorganism design and precision medicine. However, significant work remains to achieve complete whole-cell models including developing the mathematics of multi-algorithm modeling, assembling the data needed to build whole-cell models, modeling pathways, and developing efficient simulators. New researchers with diverse backgrounds in systems biology, experimental biology, physics, and computer science are needed to advance whole-cell modeling. This six-day course will include lectures from 12 leading faculty on how to experimentally characterize and mathematically model intracellular pathways, as well as hands-on tutorials which will teach students how to model pathways, combine sub-models, and conduct in silico experiments by building their own toy whole-cell models. The course will emphasize methods that are unique to whole-cell modeling and not taught by any other class including multi- algorithm modeling, pathway/genome databases, and model reduction, as well as teach the power of whole-cell modeling to elucidate how pathway interactions determine behavior. The course will also provide students opportunities to present their research and to network with other researchers. The course organizers, Jonathan Karr, Javier Carrera, Luis Serrano, and Maria Lluch-Senar have extensive expertise in whole-cell modeling. Jonathan Karr and Javier Carrera are systems biologists who have developed the first whole-cell models. Luis Serrano and Maria Lluch-Senar are experimental biologists who extensively characterize bacteria to enable whole-cell modeling. The course will be coordinated by Elias Bechara, the Manager of Teaching and Training at the Center for Regulatory Genomics. The course will take place April 3-8, 2016 at the Center for Regulatory Genomics in Barcelona, Spain. The course has been advertised on several online calendars. 40-50 students will be selected through a competitive application process based on their CV and desire to participate in the course. The tutorial materials will be freely available on the course website, www.wholecell.org/school-2016. We will survey the students to learn how to improve the tutorials for future courses.