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(种群、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是回答生物学问题的有用方法。可以说，这些努力产生了有趣的数学、统计学和量化进步。然而，在比DNA更大但比种群更小的规模上，生物和数学社区未能充分利用彼此的优势。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在更大规模的集成中产生适应性行为。我们将系统生物学广义地解释为包括以下领域：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的动态平衡，神经网络中高级认知功能的出现，以及通过个体有机体的运动和相互作用来组织社会系统。这些问题显然可以从数学、统计、计算和工程分析方面的进步中受益。加强系统生物学的数学和计算部分有几个原因。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，已经有了许多科学成果，因此调查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，越来越多地成功地强调数学和计算方法，如果系统生物学不也采用这些分析方法，那么它将减少资助机会。如果我们不利用数学和计算科学的进步，我们可能会失去更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，以帮助绘制出数学、统计和计算方法在综合生物学或系统生物学中最有可能有用的图表，存在哪些绊脚石，以及如何在这些被忽视的尺度上促进定量方法的更多利用以及数学和计算专家在生物学中的参与。通过一组主要研究人员和教育工作者的直接讨论，研讨会将：i)确定定量分析能够从根本上加强综合生物学的研究和教育的最有效的方法；ii)确定近期和长期的教育需求[要求]，以发展那些将促进未来在综合生物学中使用定量方法的多学科技能；iii)概述目标和战略，以支持在这些被忽视的尺度上更多地使用系统生物学中的定量方法。拟议活动的智力价值是什么？组织这次研讨会是为了解决在系统一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种方法，使用这些方法的所有关键部分都到位了吗？必须开发哪些技术和培训才能充分利用这些技术？通过审查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。拟议活动的更广泛影响是什么？系统生物学本质上是综合性的，有助于增进对较小规模系统之间关系的理解。特别是当通过模型增强时，这样的理解往往会使知识系统化，从而有助于一般教学和教育。更具体地说，研讨会的目标之一是讨论需要哪些培训来促进数学和计算在综合生物学中的作用。这很可能涉及到所有相关领域的各级教育问题：生物、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.