2016 Whole-Cell Modeling Summer School

 描述（由申请人提供）：2016年全细胞建模暑期学校的目标是通过培训年轻研究人员和建立跨学科的全细胞建模社区来推进全细胞建模。这项建议的目的是提供旅行奖学金，使学生和博士后学者能够参加课程。这些目标推进了NIGMS生物医学技术，生物信息学和计算生物学部门的任务，即开发综合数据分析工具并培养未来的计算生物学家。尽管进行了数十年的研究，但对细胞生物学的综合理解仍然难以捉摸。需要新的计算方法来将日益丰富的数据整合到对细胞生物学的统一艾德理解中。全细胞建模是一种很有前途的技术，通过将单个细胞内通路的多个子模型（每个子模型使用不同的数学和数据描述）组合成一个基于物理的动力学模型，将数据整合到统一的艾德理解中。全细胞模型有可能加速生物科学，实现合理的微生物设计和精准医学。然而，要实现完整的全细胞模型，还有大量的工作要做，包括开发多算法建模的数学，组装构建全细胞模型所需的数据，建模途径，以及开发有效的模拟器。需要在系统生物学、实验生物学、物理学和计算机科学方面具有不同背景的新研究人员来推进全细胞建模。这个为期六天的课程将包括来自12个领先的教师如何实验表征和数学建模细胞内通路的讲座，以及动手教程，将教学生如何建模通路，联合收割机子模型，并通过建立自己的玩具全细胞模型进行计算机实验。该课程将强调全细胞建模所独有的方法，而不是任何其他课程所教授的方法，包括多算法建模，途径/基因组数据库和模型简化，以及教授全细胞建模的力量，以阐明途径相互作用如何决定行为。该课程还将为学生提供展示他们的研究并与其他研究人员建立联系的机会。课程组织者Jonathan Karr、Javier Carrera、Luis塞拉诺和Maria Lluch-Senar在全细胞建模方面拥有丰富的专业知识。Jonathan Karr和Javier Carrera是系统生物学家，他们开发了第一个全细胞模型。Luis塞拉诺和Maria Lluch-Senar是实验生物学家，他们对细菌进行了广泛的表征，以实现全细胞建模。该课程将由监管基因组学中心的教学和培训经理Elias Bechara协调。该课程将于2016年4月3日至8日在西班牙巴塞罗那的监管基因组学中心举行。该课程已在几个在线日历上做了广告。40-50名学生将根据他们的简历和参加课程的愿望通过竞争性的申请过程中选择。教程材料将在课程网站www.wholecell.org/school-2016上免费提供。我们将对学生进行调查，以了解如何改进未来课程的教程。

 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.