Workshop: The Roles of Mathematics and Computation in Systems and Integrative Biology, USU Campus, Logan, Utah, Spring 2003

数学和计算在系统和综合生物学中的作用无论是大尺度（人口、群落、生态系统）还是小尺度（化学和染色体）定量技术都被广泛认为在回答生物学问题方面是有用的。可以说，这些努力产生了有趣的数学、统计学和定量方面的进步。然而，在比DNA大但比人口小的尺度上，生物学和数学社区未能充分利用彼此。在系统或综合生物学中，这种失败尤其能说明问题。系统生物学主要关注生物成分如何相互作用以产生更大规模的适应性行为。我们广泛地解释系统生物学，包括发育过程中的细胞内遗传和蛋白质网络动力学，组织反应的整合以在生物体水平上创造动态稳态，神经网络中更高认知功能的出现，以及通过个体生物的运动和相互作用组织社会系统。这些问题显然可以从数学、统计、计算和工程分析的进步中受益。加强系统生物学的数学和计算成分有几个原因。作为一个积极的好处，由于基因组学、生物信息学和环境生物学在很大程度上采用了定量方法，因此研究系统生物学中存在哪些类似的机会以及需要解决哪些关键问题来实现这些机会似乎是很自然的。第二个原因是，在医学、基因组学和蛋白质组学等相互竞争的学科中，对数学和计算方法的成功强调将减少系统生物学的资助机会，如果它不接受这些分析方法的话。如果我们不能利用数学和计算科学的进步，就可能失去深入了解综合生命系统的机会。我们建议组织一个小型研讨会，以帮助绘制数学、统计和计算方法如何最有可能在综合或系统生物学中有用，存在哪些绊脚石，以及如何在这些被忽视的尺度上激励定量方法的更多利用和数学和计算专家在生物学中的参与。通过一组领先的研究人员和教育工作者之间的直接讨论，研讨会将i)确定定量分析可以从根本上增强综合生物学研究和教育的最有效方法，ii)确定发展这些多学科技能的当前和长期教育需求[要求]，这些技能将促进未来在综合生物学中使用定量方法。iii)概述目标和策略，以支持在这些被忽视的尺度上增加系统生物学中定量方法的使用。所提议的活动的智力价值是什么？这次研讨会的目的是解决在系统级生物学中多学科使用定量方法的紧迫问题：如何最有效地使用这些方法，是否所有的关键部分都已到位，以及必须开发哪些技术和培训才能充分利用这些技术？通过研究这些问题并提出答案，希望研讨会将促进一种全新的科学突破。建议的活动有何更广泛的影响？系统生物学，就其本质而言，是综合的，并有助于增加对较小规模系统之间关系的理解。特别是在模型的帮助下，这样的理解往往会使知识系统化，从而有助于一般的指导和教育。更具体地说，研讨会的目标之一是讨论什么训练是必要的，以促进数学和计算在综合生物学中的作用。这可能涉及到所有领域的各级教育问题：生物学、数学、统计学、计算机科学和工程学。

The Roles of Mathematics and Computation in Systems and Integrative BiologyAt both the large (population, community, ecosystem) and small scales (chemical and chromosomal) quantitative techniques are widely acknowledged to be useful in answering biological questions. Arguably, these efforts have produced interesting mathematics, statistics, and quantitative advances. However, at scales larger than DNA but smaller than populations, the biological and mathematical communities have failed to take full advantage of one another. In systems or integrative biology this failure is particularly telling. Systems biology is primarily concerned with how biological components interact to produce adaptive behavior at a larger scale of integration. We interpret systems biology broadly to encompass areas such as intracellular genetic and protein network dynamics during development, integration of tissue responses to create dynamic homeostasis at the organism level, the emergence of higher cognitive function from neural networks, as well as the organization of social systems by the movement and interaction of individual organisms. Such questions can clearly benefit from advances in mathematical, statistical, computational, and engineering analysis. There are several reasons for enhancing the mathematical and computational components of systems biology. As a positive benefit, since there have been many scientific payoffs in genomics, bioinformatics and environmental biology, which have largely embraced quantitative methodology, it seems natural to investigate what similar opportunities exist in systems biology and what key issues need to be addressed to achieve these opportunities. A second reason is that the increased successful emphasis on mathematical and computational approaches in competing disciplines such as medicine, genomics, and proteomics, will reduce funding opportunities for systems biology if it does not also embrace these analytical methods. An opportunity for deeper understanding of integrated living systems may be lost if we fail to exploit advances in the mathematical and computational sciences. We propose to organize a small workshop to help chart how mathematical, statistical and computational methods are most likely to be useful in integrative or systems biology, what stumbling blocks exist, and how to motivate increased utilization of quantitative methods and participation of mathematical and computational specialists in biology at these neglected scales. Through directed discussion among a group of leading researchers and educators, the workshop will i) identify the most effective ways that quantitative analysis can fundamentally enhance research and education in Integrative Biology, ii) identify immediate and long-term educational needs [requirements] for developing those multidisciplinary skills that will facilitate the future use of quantitative approaches in Integrative Biology, and iii) outline goals and strategies to support increased use of quantitative methods in systems biology at these neglected scales.What is the intellectual merit of the proposed activity? The workshop is organized to address pressing questions on the multidisciplinary use of quantitative methodologies in systems-level biology: how may such approaches most fruitfully be used, are all the keystone pieces in place for their use, and what technologies and training must be developed to fully utilize these technologies? By examining these questions and proposing answers it is hoped that the workshop will facilitate a whole new vein of scientific breakthroughs.What are the broader impacts of the proposed activity? Systems biology, by its nature, is integrative and serves to increase understanding of relationships among smaller-scale systems. Particularly when enhanced with models, such understandings tend to systematize knowledge, therefore aiding with general instruction and education. More specifically, one of the objectives of the workshop is to discuss what training is necessary to facilitate advancing the role of mathematics and computation in integrative biology. This is likely to involve educational issues at all levels in all fields involved: biology, math, statistics, computer science, and engineering.