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3 Summary of Key Points More than two dozen experts from across the country met at the National Academies to discuss the promise of systems microbiology and to identify the multiple strategies and novel experimental tools needed to explore these systems. Although formal conclusions and recom- mendations will not come from this workshop, many insights into the future of the field can be gleaned from the discussion described here. The major points are summarized below. APPLICATION OF THE SYSTEMS APPROACH · The study of single-organism and multiorganism microbial commu- nities, as illustrated by the two case studies, can greatly benefit from appli- cation of systems biology. To apply that approach successfully, we need to define systems with closed boundaries and identify the goals of studies. MODELING · Modeling can play a major role in helping us to understand biological systems. Software infrastructure and other interoperable tools for systems microbiology are needed to facilitate modeling. · Successful modeling requires defined multiple goals. If the goal of modeling is to understand biological processes, modelers can help biolo- gists to identify key components that reveal biological structure. For predictive modeling, modelers can help biologists to identify parameters that exert the most influence and the governing principles that place con- 27
28 PROMISE AND CHALLENGES IN SYSTEMS MICROBIOLOGY straints on the variables to be modeled. Mode! parameters should be those that have a large influence on the predicted outcome. TOOLS · Having commercial access to assays, gene chips, and other novel tools of biotechnology would streamline scientific research by allowing biologists to concentrate on fundamental questions, rather than preparing the actual tools. Access to inexpensive tools, such as the affordable gene chips provided by the Cystic Fibrosis Foundation, would also encourage increased research. · Although databases on microorganisms exist, they are not connected to each other, so microbiologists cannot move from one database to another easily. To conduct a comprehensive search, they must be aware of various databases. Furthermore, information in some databases is outdated, and nomenclature is not uniform among databases. Effort is required to update the databases, and software engineers are needed to design technologic infrastructure that will link databases seamiessly. EDUCATION AND RESEARCH · Biologists need to learn more about systems approaches and learn enough mathematics and computing knowledge to communicate with systems engineers who design software and computational technologies. Systems engineers could benefit from learning more about biology and the interesting questions that could be answered by their discipline. · Interdisciplinary research projects would be encouraged by increased long-term funding opportunities. Scientists can facilitate collaboration not only by learning a common language but by designing projects that are of interest to scientists working in different fields. · Training people with enough overlap of various disciplines will allow them to communicate with one another. New graduate and undergraduate curricula could be developed to facilitate such training. · Experienced scientists can take advantage of short courses offered by various research centers to learn more about other disciplines. · Focusing systems microbiology too narrowly around microbiology, modeling, and computational biology could exclude important fields of knowledge that are essential for the understanding of the complexities of systems. Biochemistry, organic and inorganic chemistry, physics, economics, and other disciplines should all play a role in the exploration of microbial ecosystems.
