Vol.3 No.1 2010

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Research paper : A bioinformatics strategy to produce a cyclically developing project structure (M. Suwa et al.)−11−Synthesiology - English edition Vol.3 No.1 (2010) Discussions with Reviewers1 Emphasis points on how the research was carried out Comment (Motoyuki Akamatsu, Human Technology Research Institute, AIST) As a Synthesiology paper, it is expected that the content will be about “bioinformatics strategy” as mentioned in the title. “Strategic” means that the research was carried out by setting a goal and laying out the research scenario (process) beforehand. If the authors intentionally set up ways to conduct cyclical research, please describe them. If the authors did not intend to do so but things developed spontaneously, I think you should describe what were the conditions necessary for such cyclical development of the DB to occur. Also, I think the main point of this paper is the description of the cyclical development process of the DB, so I think the point will be easier to be understood if you include a diagram of this development process. Comment (Hideyuki Nakashima, Future University Hakodate) I think it better to stress the points on your research method for the sake of general readers (researchers of other fields). Answer (Makiko Suwa) The bioinformatics strategy described in the text was not necessarily conducted by setting up a research scenario beforehand and then following the road map. Rather, in retrospect, I feel the research developed extremely efficiently regardless of my intent, and therefore I focused on the driving forces that are unique to bioinformatics and that enabled such development. I think the overall flow of the development of the research project has a dynamic form where there is an upward spiral of the AuthorsMakiko SuwaPrinciple Research Scientist of Computational Biology Research Center, AIST. Completed studies at the Graduate School of Science and Engineering, Aoyama Gakuin University in 1986. Doctor (Science). Worked as technical official, associate researcher of education, Faculty of Technology, Tokyo University of Agriculture and Technology; senior investigator, Helix Research Institute Inc.: chief researcher, Electrotechnical Laboratory, Agency of Industrial Science and Technology; and research team leader and deputy director, Computational Biology Research Center, AIST. Assumed the current position in 2007. Specialties are bioinformatics and biophysics. In charge of the overall coordination for the Project described in this paper. Yukiteru OnoManager of 8th Business Group, Biolife Science System Enterprise Division, Information and Mathematical Science Laboratory, Inc. Completed the master’s course in biology at the Graduate School of Science, Nagoya University in 1994. Worked at JASTEC Co., Ltd. and assumed current position in 2001. Specialty is bioinformatics. For this paper, worked mainly on the web interface development for SEVENS and on the implementation of improvements resulting from the joint researches. interactions of the direction of individual research that progresses with multiple factors (core technology that matured over time, close collaboration with experimental researcher, environment that nurtures technological incubation, etc.) as driving forces, and the direction of the life science field that evolves extremely quickly. (This development process is shown in Fig. 5(a) and (b)). I think this form is the result of the characteristics of bioinformatics: it can set diverse directions depending on the situation since it is not strongly limited by research targets; and the individual researches are resolved in 1~2 years since the period required from basic research to application and realization is short. 2 Title Comment (Motoyuki Akamatsu) Please consider a title that represents the content from the synthesiological perspective. It must show that this is a paper that discusses research progress where the DB moved in an upward spiral through joint research. Answer (Makiko Suwa) The first title “Search and functional analysis of drug discovery target GPCR - Bioinformatics strategy” represented the content of the research, but as you indicated, it did not explain how the bioinformatics strategy is related to the entire Project when seen from a synthesiological perspective. Therefore, to clarify that point, I changed the title to “A bioinformatics strategy to produce a cyclically developing project structure - Comprehensive functional analysis of the drug design target genes.” 3 Type 2 Basic Research Comment (Motoyuki Akamatsu) At the end of paragraph 1 of section 3.2 “Gene identification and functional analysis pipeline,” it says that these combined researches can truly be called Type 2 Basic Research. If possible, can you explain what points you consider to be Type 2 Basic Research? Answer (Makiko Suwa) The description you indicate is the part about the development of gene identification and functional analysis pipeline. This can be called Type 2 Basic Research because the work is done from the perspective where the elemental programs that are established after accumulation of basic research are combined and systematized, and these are controlled and applied to the subject. I added this explanation. 4 Bioinformatics Comment (Hideyuki Nakashima) The explanation of “bioinformatics” on the first page emphasizes the aspect of information technology as a tool for biology. Certainly, that aspect is strong in this paper, but CBRC has emphasized that IT is not merely a tool I think it is better to add the points that the way of thinking and the approach of the information science are also important. Answer (Makiko Suwa) I agree that the description you indicate gives the impression that bioinformatics is “merely a tool”. It is because we intend to emphasize the advantages of bioinformatics technology, when looking at it from the perspective of reducing the difficulty in experimental research approach. Therefore, I modified the description so that it indicates first the general definition of bioinformatics and after, the above advantage as one part of the whole picture. Bioinformatics is a wide-ranging discipline with a collection of researchers of varying backgrounds. I feel that the understanding of the definition and the aspect one handles are diverse as they depend widely on the background of the

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