Establishment of the Research System for Computational Science（Fiscal Year 2011）
High Performance Computing Development Group（Makoto Taiji, RIKEN）
Management of computational resources
➣ Management of computational resources
We organized a management committee for the efficient use of computational resource offered by K computer. The committee consists of Program Director, Deputy Program Director, Group Leader and Group Director in Field 1. In order to manage application software development efficiently, we assigned the computational resources to application software in consideration of their progress. Then we prioritized them with the advice of the Working Group of Field 1 of theStrategic Programs for Innovative Research, MEXT.
➣ Purchase and installation of computing facilities
We introduced computing environments to prepare for using K computer efficiently.
- Storage System for Theme 4(Large-scale analysis of life data)
- PC Cluster for software developments
- K computer compatible system
Establishment of High Performance Computing Development Group and User Support
➣ Human Resource Management
Four staff members were assigned for supporting a super massively parallel computer
One staff member was assigned for supporting database
➣ Assignment of account for the K computer
MP-CAFEE and GHOST-MP have been assigned to period I, Ⅱand Ⅲ.
GENESIS, SCUBA, EX-Throm, BENIG have been assigned to period Ⅳ.
➣ Bridge between Strategic Programs for Innovative Research and AICS
We announced AICS’s information to users.
AICS was made to accept a demand of users.
The meeting for exchanging views about the promotion of the use of K computer was held on September.
We participated in RIKEN AICS HPC Summer School.
Strategic Programs for Innovative Research Workshop was held with AICS and the other four fields.
Planning and Coordination Group（Satoru Tomita, RIKEN）
Human Resource Development and Education
Our mission is to foster the skills necessary to support research and development in high-performance computing and to raise awareness of career opportunities in computational life sciences among young people. To accomplish these goals, we have organized specialized training programs in collaboration with Advanced Industrial Science and Technology (AIST), Computational Biology Research Center (CBRC) and Osaka University, and mounted educational outreach programs for high school students, and undergraduate and graduate students.
➣ Advanced Industrial Science and Technology (AIST), Computational Biology Research Center (CBRC), HPCI Educational Program
- HPCI Seminar Series (12 sessions: 2011 October 7 – 2012 January 13)
The mission of the CBRC HPCI Educational Program is to promote maximal utilization of computers in life science research and education, and to provide information on computing in biology. A twelve-session seminar series was presented by CBRC researchers and offered as a University of Tokyo credit-earning course, entitled Special Lectures on Computational Biology (2011 Winter Semester: Department of Computational Biology, Graduate School of Frontier Sciences). Total participants numbered 401, including 159 graduate students. The curriculum consisted of introductory general lectures followed by extensive discussions of the state-of-the-art in computational biology research and development.
- e-Learning Material Preparation
The CBRC HPCI Educational Program prepared e-learning materials in the form of videotapes of the HPCI Seminar Series, which are intended for development of sustainable personnel and education systems. The video materials are scheduled for release via the CBRC HPCI Educational Program website in early fiscal year 2012
- HPCI Workshop
An HPCI workshop focused on use of the Next-Generation Sequencer was held at the AIST Tokyo waterfront annex on January 26 2012. Invited speakers included Professor Ken Kurokawa (Department of Biological Information, Tokyo Institute of Technology), Dr. Masayuki Machida (Bioproduction Research Institute, AIST, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology), Professor. Hiroyuki Sasaki (Division of Epigenomics, Department of Molecular Genetics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University), and Dr. Carsten Daub(RIKEN). Total participants numbered 125.
- HPCI Tutorial
An HPCI Tutorial focused on use of the Next-Generation Sequencer was held March 8-9 2012 at the AIST Tokyo waterfront annex. The tutorial was aimed primarily at experimentalists. The goal of the two-day program was dissemination of computational tools for analyzing sequence data. In all, 33 participants received hands-on training using PCs. Cutting-edge research examples motivated introduction of new analysis techniques, and free web-based tools and software were distributed to participants.
➣ Osaka University, Graduate School of Engineering Science, Education Program for Predictive Medicine and Drug Discovery on High Performance Computational Infrastructure
- Biosimulation Series (12 sessions: 2011 December 10 – 2012 January 28)
The Biosimulation Series consisted of twelve lectures on mathematical modeling approaches to biological phenomena and four hands-on training sessions on computational simulation techniques for undergraduate students. The series was held as Osaka University, Graduate School of Engineering Science as a for credit course and was also made available as part of the extension curriculum. In all, 11 students participated (9 undergraduates earned university credits, and 2 participants completed the extension curriculum).
- Bioinformatics Series (6 sessions: 2012 January 21 and 28)
An introductory Bioinformatics Series was offered through the Graduate School of Engineering Science at Osaka University for graduate students. Although this series was not approved for course credit by Osaka University, total participants numbered 7, including 5 graduate students and two other individuals.
- Collaboration Seminar with Industry and Academia: K computer for Drug Discovery and Medical Care
Industry-academe collaboration seminars were held in Osaka on October 19 2011 (63 participants) and in Tokyo on January 25 2012 (102 participants). At both venues, current K computer users presented their research activities, and industrial researchers wishing to access the K computer proposed research activities and application software requirements. The strong showing in Tokyo, stemmed in part from advance publicity in the print media (newspaper and medical journal).
- HPCI Educational Program Symposium
- The 8th “Supercomputing and Medical care, Bio”
The 8th “Supercomputing and Medical care, Bio” meeting was held at Icho Kaikan, Osaka University on July 6 2011 to introduce supercomputer applications software for use by medical care researchers and biologists. In addition to formal presentations, discussion sessions focused on the contributions and expectations for bioinformatics in medical care and biotechnology. Total participants numbered 109.
- Education Program for Predictive Medicine and Drug Discovery, plenary session and symposium, focused on utilization of K computer was held on January 8 2012 as a Satellite of 24th Bioengineering Conference, Osaka University. Total participants numbered 200.
➣ RIKEN, Strategic Programs for Innovative Research Field1 Planning and Coordination Group
The Planning and Coordination Group presented lectures to high school students explaining the importance of high-performance computational infrastructure and informatics research for the life sciences. The Planning and Coordination Group also presented sessions on computational life sciences in collaboration with the Graduate School of Pharmaceutical Science, Tokyo University of Science, the Graduate School of Biomedical Science, Tokyo Medical and Dental University, and the University of Fukui. Total participants at all three venues numbered 97, 10 and 63, respectively.
- Educational outreach for high school students
- Much of research in the life sciences today utilizes tools coming from physics, chemistry, and mathematics. The Planning and Coordination Group made presentations to high school students highlighting the importance of such interdisciplinary approaches and presented work on simulations of biological systems using the K computer. Feedback from the participants showed that the students gained a much broader view of the potential impact of supercomputing in biology.
- The Planning and Coordination Group surveyed high school student attendees at the 2011 Supercomputing Contest, which is a programming contest using supercomputer for high school students (Osaka University, August 22-26 2011). The results of this survey will guide future outreach efforts.
- The Planning and Coordination Group also organized exhibition booths at the “Science Fair in Hyogo” in Kobe on February 5 2012 and at the Koshien Olympics of Science” in Nishinomiya city on March 25 2012. At both, we introduced our outreach activities for high school students. Learning tools for the students included a DNA base sequence puzzle game and aspartame dipeptide bond molecular modeling game.
Establishment of Human Networks
High Performance Computing Infrastructure Systems (HPCI systems) encompass the K computer and computational facilities at nine universities. In September 2012, these systems will be made available on a peer-reviewed basis to researchers in academia and industry. The Planning and Coordination Group held symposia to foster better understanding of the HPCI, and to promote utilization of HPCI systems by life science research communities.
The Planning and Coordination Group also introduced its activities and research projects via exhibition booths and workshops at select scientific meetings and symposia.Major activities were as follows:
- Supercomputer “K” and computational life sciences in Kyusyu (Symposium)
Collaborating Institution: Graduate School of Systems Life sciences, Kyusyu University.
The symposium focused on future utilities of K computer in life science for researchers in Kyusyu and Okinawa on October 6 2011. Formal presentations were augmented with lively panel discussion.
- “Supercomputational Life science in Japan”, PDB 40 Symposium (Poster Presentation), Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
The impact of the K computer on life sciences research was presented at the PDB 40 symposium, which celebrated the 40th Anniversary of Protein Data Bank (October 28-30 2011).
- Booth exhibition at SC11 (Supercomputing 2011) meeting, Washington State Convention and Trade Center, Seattle, WA, USA.
Outreach activities and research programs were presented at SC11 November 12-18 2011.
Dissemination of Research Outcomes
The Planning and Coordination Group disseminated its activities and research programs for the Strategic Programs for Innovative Research Field1 via re-designed websites, newsletters (semi-annual) collaborating with RIKEN Computational Science Research Program, brochures (annual), and logos.
From left to Right: BioSupercomputing Newsletter Vol.5, Vol.6, Brochure top pages and logos.
RIKEN opens its facilities and introduces its research activities to the general public on an annual basis. The Strategic Programs for Innovative Research Field1 joined in the RIKEN AICS Open House on November 5 2011. Demonstrations included origami figures representing double stranded DNA and an icosahedral virus.
Participants: ~2,000 members of the general public.
The Planning and Coordination Group held a seminar open to the general public in collaboration with the 2011 Annual Conference of Japanese Society for Bioinformatics, Chem-Bio Informatics Society Annual Meeting 2011 and Kobe city at the Kobe Convention Center on November 9 2011. Sessions aimed at the lay audience were presented by computational life science researchers to explain how supercomputers are used in medical care and for discovery of pharmaceuticals.
- Workshops by Five Strategic Programs for Innovative Research
The Planning and Coordination Group organized workshops for researchers on June 22 and October 3 2011 to exchange technical information and share issues beyond professional discipline to promote effective use the K computer. Dr. Kousuke Matsunaga (RIKEN) and Dr. Kouichi Takahashi (RIKEN) presented on June 22 and Professor Yutaka Akiyama (Tokyo Institute of Technology) on October 3. In addition, Dr. Yuji Sugita joined the meeting as a discussion panelist in October 3. Participants were 68 and 77, respectively.
- Collaborative meetings with AICS, Five Strategic Programs for Innovative Research and Next-Generation Integrated Simulation Nanoscience and Living matter projects
AICS, which manages and operates the K computer, Five Strategic Programs for Innovative Research, and Next-Generation Integrated Simulation Nanoscience and Living matter projects, which develop research using the K computer, conduct collaborative meetings every couple of months to promote closer cooperation. At these meetings, progress and management situations of the K computer were reported by AICS and issues arising during use of K computer were discussed by various participants.
- Collaboration with Next-Generation Integrated Simulation Living matter project
As there are significant commonalities in researches topics between the Next-Generation Integrated Simulation Living matter project and the Strategic Programs for Innovative Research Field1, we are actively promoting collaborative relationships to advance research in computational life science. Efforts are being reported in a new semi-annual BioSupercomputing Newsletter. Dr. Ryutaro Himeno, Vice-Program Director of the Next-Generation Integrated Simulation Living matter project, serves as an observer at the monthly steering committee meetings of the Strategic Programs for Innovative Research Field 1.
- Participation in a working group for public dissemination of information on computational science
Following the nuclear accident at Fukushima of March 11 2011, a working group focused on information dissemination in computational science to the public was established under aegis of the AICS and Five Strategic Programs for Innovative Research collaboration. This working group has examined some of the challenges regarding information dissemination and the role of science in Japanese society. In addition, the working group has addressed ways of transmitting information from academia concerning future natural and manmade disasters. In March 2012, the working group released a midterm report.
- Participation in network meeting for AICS and Five Strategic Programs for Innovative Research
A network meeting for AICS and Five Strategic Programs for Innovative Research to promote information sharing and enhance institutional and programmatic collaboration was held at the University of Tokyo, Hongo Campus on September 29 2011. This group will hold periodic meetings at various sites within Japan to promote development of K computer research and development programs.
- Industry/Academic collaboration to promote a medical industrial city in Kobe
The Planning and Coordination Group joined cooperation meetings with representatives from industry, local universities, the science museum, and Kobe city government on November 29 2011 and February 29 2012. These meetings were intended to build an organized coordination effort aimed at developing a medical industrial city in Kobe. Participants numbered 23 and 14, respectively.