EUCLIS AT U.P.:  SCIENCE  WITH  S.M.I.L.E.S.

MANILA, OCTOBER 11
 (STAR) STAR SCIENCE By Eduardo R. Mendoza, Ph.D. - (First of two parts) On Jan. 22 this year, two Filipinas addressed an international scientific meeting at Frauenchiemsee (near Munich, Germany) to launch a novel information system called EUCLIS (EUCLOCK Information System). Just last month, IET Systems Biology, the pioneer journal dedicated to this new field (from the UK Institution of Engineering and Technology), published the paper “EUCLIS — An Information System for Circadian Systems Biology” and selected it as its “featured paper” (1). Of the five authors, two are the above-mentioned recent MS graduates and another two are current MS students in Computer Science at UP Diliman. EUCLIS, a software system envisioned to evolve to a lasting information infrastructure for the worldwide chronobiology community, is designed and developed entirely at UP Diliman. It demonstrates that Filipino researchers and students already successfully engage in leading-edge work in the emerging field of computational systems biology.

What is novel about EUCLOCK and its information system EUCLIS? EUCLOCK, a research network of over 30 of the leading chronobiology laboratories in Europe, was launched in January 2006 with a funding of over 16 million euros for five years. Chronobiology studies circadian clocks, which enable organisms to anticipate daily environmental changes by adjusting behavior, physiology and gene regulation. The impact of such processes on health and quality of life in regulating sleep and well-being was described in a previous Star Science essay (2). The simulation of shift work for mice to investigate its long-term effects on health and a systematic study of the “light at night” theory (that exposure to light during sleep increases cancer risk) are two examples of highly relevant EUCLOCK research. EUCLIS (accessible at http://www.bioinfo.mpg.de/euclis) supports this research by enabling geographically distributed teams to securely store and share experimental data and other important chronobiology information such as annotated lists of relevant genes in different organisms and a library of over 14,000 chronobiology references. EUCLIS Version 1.5 — to be released end of this month at the 16th European Chronobiology Summer School in Hungary — will go beyond enabling direct scientific collaboration and support community building through Clock Family Trees (an interactive documentation of the scientific genealogy of chronobiologists) and Clock Museum (an electronic collection of memorable chronobiology events).

EUCLIS is one of the current projects of the SMILES initiative at UP Diliman. SMILES (Statistics, Mathematics and Informatics in the Life and Environmental Sciences) was launched in March 2003 (then called “Mathematical and Computational Biology Initiative”) to enable interdisciplinary research in accelerating mathematical and computational approaches to understanding biological systems. Collaboration in SMILES is done consistently through Joint Experimenter-Modeler projects (JEMs). Though challenging — especially in the initial period as very differently trained specialists struggle to understand one another’s concepts and research philosophies — JEMs enable incrementally integrating, increasingly quantitative experimentation and predictive modeling. In the EUCLIS project, the UP students work very closely with the team of Prof. Till Roenneberg at the Center for Chronobiology at the Ludwig-Maximilians-University in Munich (Germany) and other EUCLOCK researchers. In another SMILES project, MS students at UPD Computer Science worked closely with scientists at the International Rice Research Institute in Los Baños to develop components of the new information system for the Generation Challenge Program-2 (GCP2).

Mid-term focus on three specific areas is a further SMILES strategy in building sustainable research and education in Computational Systems Biology. Both EUCLIS and the GCP2 project are part of WINKS (Web-based INtegrated Knowledge-oriented Systems) and represent the more data integration-oriented research efforts in the field. The other two focus areas are DIMPLES (Digital IMage Processing in the Life and Environmental Sciences) and MOLES (Modeling NetwOrks in the Life and Environmental Sciences).

Image processing has emerged as one of the key techniques for studying biological processes in living cells (in vivo bioimaging). Fluorescent substances are attached to the cellular components of interest and careful analysis of the intensity changes allows the quantification of component amounts and location over time. These “time series” of data form the basis of quantitative models, which allow the researchers to simulate and eventually predict new system characteristics to be verified by further experimentation. DIMPLES projects include a completed two-year project of developing a Graphical Protocol Editor (an easy-to-use interface for planning and executing bioimaging experiments) for the innovative integrated microscopy system iMIC (Till Photonics, Germany) (3) and a current project for analyzing single cell gene expression in the context of synthetic gene delivery systems (LMU Physics). The planned Bioimaging Core Facility within the National Science Complex will enable collaboration with local experimental groups in this area in the future.

The second part of this essay will report on Filipino progress in modeling biological networks — the key area of Computational Systems Biology.

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(1) Riza Theresa B. Batista, David B. Ramirez, Roselyn D. Santos, Maria Celeste I. del Rosario, Eduardo R. Mendoza: EUCLIS – An Information System for Circadian Systems Biology, IET Systems Biology, Vol. 1 No. 5, September 2007

(2) Cherry Mae G. Ignacio. Biological Clocks, Star Science, 12/07/2006

(3) Philip Zuñiga, Alva Balbuena, Eduardo Mendoza: A Graphical Protocol Editor for an Integrated Microscopy System, Proceedings of the 5th ASEAN Microscopy Conference, Nov 24-25, 2005, Manila

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Eduardo Mendoza, Ph.D., is a senior research scientist at the Physics Department and Center for NanoScience of Ludwig-Maximilians-University (LMU) in Munich, Germany. He is an adjunct professor at the Department of Computer Science and Mathematics Department of UP Diliman. A member of PAASE, he can be reached at mendoza@lmu.de.


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