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Lighting the Way for Researchers Everywhere Foreword This booklet tells the story of an extraordinary community of scientists, educators and administrators brought together by a remarkable initiative on the part of the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH). From the outset, the National Centers for Systems Biology program tapped into the very heart of a movement that was rapidly sweeping through the biomedical research establishment. In retrospect, many may argue that the Systems Biology “revolution” was an inevitable consequence of the successes of the molecular biology revolution, which brought us (and continues to bring us) deep knowledge of biological mechanism, but provides only limited insight into the underlying principles of biological organization. Systems Biology seeks to remedy this deficiency, exploiting quantitative approaches and tools from Mathematics, Physics, Computer Science, and Engineering to unravel the complex relationships between molecular mechanism and organismal function. What could not be seen as inevitable, however, was that one institute of the NIH would take it upon itself to “manage” the Systems Biology revolution, at least within the United States. At a time of deep confusion within the biological and biomedical research community about what Systems Biology is, and whether it was going to have any lasting impact, the NIGMS had the vision to support Centers that would lead by example, lighting the way for researchers everywhere. Even more remarkably, the NIGMS had the foresight to insist that Centers devote themselves not just to the task of producing exemplary Systems Biology research, but also in lighting the way in education, community outreach, and institutional transformation. The NIGMS also demanded that Center leadership, along with a subset of each Center’s membership, get together annually to share their accomplishments in science, education, and outreach. Out of these meetings grew a sense of common purpose and community that led to the establishment of a common web portal (at www.systemscenters.org) and a broad commitment to sharing resources and expertise for the benefit of the wider scientific community. Ultimately, the activities of the National Centers for Systems Biology galvanized a large group of scientific professionals into working together to make the Systems Biology revolution accessible to everyone. One of the ways in which the Centers work together is that, if a task of importance to all of us needs to be done, one of the Center directors will always step forward to do it. In this case—on the occasion of the first Centers reaching their final (10th) “sunset” year—my Center volunteered to organize the publication of this booklet, commemorating all of the National Centers for Systems Biology that have been designated to date. It has been a pleasure and an honor to bring together the stories and accomplishments of each current Center, and to see the common threads of excitement, innovation, and hope that run through all of them. I hope you enjoy reading this. Arthur D. Lander Director, Center for Complex Biological Systems University of California, Irvine 1 © 2013 This book was printed by OC Printworks, Irvine California. The typeface is Adobe Caslon Pro. The contents of these pages were assembled from summaries and photos generously provided by each of the 15 current National Centers for Systems Biology, as well as from information obtained from NIH program staff. The individual Centers retain copyright to their own pages. All other materials, with the exception of the cover art, are available for re-use under a Creative Commons 3.0 Unported License. The cover art was created by Yawei “Jenn” Ge, who just received her bachelor’s degree in Applied Mathematics and Biology from Brown University, and perhaps someday will become a Systems Biologist. The editorial team consisted of Arthur Lander, Felix Grün and Karen Martin, from the Center for Complex Biological Systems (UC Irvine), and Bodo Stern, from the Center for Modular Biology (Harvard). 2 Contents Foreword ........................................................................................................................................................... 1 Table of Contents .............................................................................................................................................. 3 How it All Began ............................................................................................................................................... 4 Current National Centers for Systems Biology Center for Cell Decision Processes (MIT).............................................................................................. 6 Center for Modular Biology (Harvard) ................................................................................................. 10 Center for Quantitative Biology (Princeton)......................................................................................... 14 Center of Genome Dynamics (The Jackson Laboratory) ....................................................................... 18 Center for Systems Biology (Institute for Systems Biology) ................................................................... 22 Duke Center for Systems Biology (Duke) ............................................................................................. 26 Systems Biology Center New York (Mt. Sinai) .....................................................................................30 Center for Complex Biological Systems (UC Irvine) ............................................................................. 34 Chicago Center for Systems Biology (University of Chicago and Northwestern) .................................... 38 New Mexico Center for Spatiotemporal Modeling (University of New Mexico).................................... 42 San Diego Center for Systems Biology (UC San Diego) ........................................................................ 46 Center for Systems and Synthetic Biology (UC San Francisco) ............................................................. 50 Virtual Physiological Rat Project (Medical College of Wisconsin) ........................................................ 54 Center for RNA Systems Biology (UC Berkeley and UC San Francisco) ............................................... 57 Microbial Ecology and Theory of Animals Center for Systems Biology (University of Oregon) .............. 59 Emeritus Centers ............................................................................................................................................ 63 The Program in Numbers ................................................................................................................................ 64 Acknowledgements .......................................................................................................................................... 66 3 How It All Began By the late 1990s, biomedical researchers were producing a wealth of detailed information on the molecular components of biological systems, particularly of cellular systems. Rapid development of genomics, imaging, and molecular tagging technologies, and high-throughput approaches made it abundantly clear that the acquisition of new data would only accelerate. However, attempts to obtain quantitative understanding on how these myriad of components interact dynamically to produce life processes had only begun, and would be critical to any application to biomedical research. James Anderson, Program Director NCSB 1997-2012 In response, the National Institute of General Medical Sciences (NIGMS) convened a workshop of “Complex Biological Processes” research at a level diverse researchers in 1997 (www.nigms.nih.gov/ more amenable to individual research labs. However, news/reports/complexbio.htm) to collect input on by early 2000, follow-up analysis of the response to approaches for the study of complex biological these initiatives indicated that a much more sizeable processes. It was apparent that this study would program would be required to promote require the expertise of diverse quantitative interdisciplinary collaboration and interdisciplinary scientists, engineers and mathematicians. Based on training with strong commitment and support from the recommendations of this workshop, in 1998 the the institutions. NIGMS Advisory Council approved several funding initiatives to provide supplements to existing awards In 2000, the NIGMS Advisory Council approved a (PA-98-024), to promote the development of new P50 Center program in complex biological systems research projects (R01 and P01, PA-98-077) with research. The first Request for Applications (RFA- the adoption of quantitative approaches to complex GM-01-001) was issued in 2001 with the title biological systems, and to develop courses that would “Centers of Excellence in Complex Biomedical provide training for quantitative biology. Systems Research”. The NIGMS awarded two P50 Centers under this program in 2002, two Centers in The programs were intended to advertise NIGMS 2003 and one Center in 2004. interest in stimulating what at that time was termed In 2004, NIGMS changed the name of the program to National Centers for Systems Biology (RFA-GM- 05-010, most recent http://grants.nih.gov/grants/ guide/pa-files/PAR-12-187.html), a reflection of the general acceptance of the concept of systems biology and the true mission of the program. The overarching goal is to establish national leaders
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