Establishment of the Research System for Computational Science（Fiscal Year 2013）
We improve the software and execution environments necessary for researchers to make effective use of the HPCI (High Performance Computing Infrastructure) environment. The operational execution is pushed forward in continued, close collaboration with research & development members. In addition, cooperation continues with the other strategic fields and AICS (RIKEN Advanced Institute for Computational Science).
At the same time, education and public outreach activities are undertaken for enhancement of understanding of computational life sciences.
I. Efficient management of computational resources
A steering committee was established within SCLS* to consider strategic planning for the effective allocation of K computer resources and other strategies.
Information on technologies and operations regarding K computer is provided to researchers through AICS and RIST (Research Organization for Information Science and Technology). We support R&D members for increasing the performance of their application software.
SCLS* Strategic Programs for Innovative Research Field 1 “Supercomputational Life Science”
II. Supporting Research Utilizing K computer and HPCI
II-1. Consolidation and operation for efficient HPCI Utilization
The SCLS supercomputer system (K computer-compatible supercomputer system) was consolidated and began operations in March 2013 to provide broader support for life science researchers and engineers to make active use of HPCI. A total of 167 users have utilized the system.
II-2. K computer User Support
SCLS’s K computer users are provided with the information they need to utilize the K computer at briefings held on a regular basis by AICS and RIST. The users can also make contact with AICS/RIST to request for technical supports at any time.
II-3. Providing Support on high performance computing
In FY 2013, we provided technical support to programs, pSpatiocyte, MARBLE, GHOST-MP, and mu2lib. In addition, as a necessary tool in large-scale data analysis, the R (language for statistical computing) has also been installed on the K computer.
II-4. Holding User Workshops
In FY 2013, hands-on workshops using SCLS computer were held with the aim of training and dissemination of software developed by SCLS member. The participants are mainly researchers of academia and industries.
III. Personnel Development/Training
In order to cultivate personnel able to utilize HPCI, and to construct a cutting-edge computing research educational hub, personnel training activities are undertaken at universities, research institutions, high schools, and other bodies. The following personnel development programs are being promoted in collaboration with Osaka University, the Computational Biology Research Center (CBRC) at the National Institute for Advanced Industrial Science and Technology, and other institutions.
III-1. Training and education for researchers and students
III-1-1. Implement personnel training and education programs (conducted by CBRC)
(1) HPCI Seminars
CBRC generally holds “Bioinformatics Research Seminars” once a week. Some of the seminars are held as public “HPCI Seminars”, and are also delivered by teleconference to the University of Tokyo’s Kashiwa, Hongo, and Shirokanedai campuses.
(2) HPCI Workshops
HPCI Workshop “Next-generation drug discovery made possible by HPC – Harnessing Big Data” was held for the public on Thursday, September 11.
(3) HPCI Tutorials
One of the characteristics of HPCI Tutorials is that they offer practical learning with a PC for each participant. It is difficult to learn how to use a computer through self-study, so the tutorials are particularly effective in training beginners including wet-lab researchers. We delivered two courses this year.
1) Bioinformatics Practical Course
2) Pharmaco-informatics Practical Course
Participants provided feedback such as “I have been using this without knowing what it meant up until now, but the explanations finally helped me understand the point of analysis.” Results showed that there is a great need for the tutorials.
(4) HPCI E-Learning
E-Learning courses are effective self-study tools that allow participants to study from home or the office when they have spare time, and also allow them to choose the subjects they are interested in. One other advantage is that they allow learners to listen to difficult sections as often as necessary in order to gain an understanding of the content. There are currently six courses, such as bioinfomatics and pharmaco-informatics, and 59 videos on offer, and anyone can repeatedly access all content for no cost simply by registering.
III-1-2. Implementation of Personnel Training and Education Programs (conducted by Osaka University Graduate School of Engineering Science)
(1) Lectures on Biosimulation
An introductory course designed primarily for graduate students was held. The class was titled “Special Lectures in Biosimulation (two credits)” and it covered the methodology of mathematical modelling of biophenomena and the computer simulation technologies.
(2) Lectures on Bioinformatics
An introductory course designed primarily for graduate students was held. The class, titled, “Bioinformatics (one credit)” covered the application of information technologies in the life sciences and medical fields, and included data analysis as used in the life sciences, and parallel computing technologies utilized in the medical fields.
(3) Industry-Academia Seminars
We organize two seminars every year, which are held at Tokyo and Osaka, Japan. The title is “Industry-Academia Seminar on the use of K computer in Drug Discovery and Medicine”
(4) Organized Session “Drug Discovery through supercomputing with the K Computer”
The session was held at the 2013 Annual Convention for the Japanese Society for Bioinformatics.
III-2. Lectures for undergraduates, graduates, and high school students and teachers
In order to cultivate the young people who will contribute to computational life sciences in the future, classes are held at educational institutions, such as Super Science High Schools and universities.
III-2-1. Development of Computational Life Science E-Learning Materials
In order to promote the utilization of HPCI and application software, lectures held through the program were recorded and developed as e-learning materials to be posted on the website.
III-2-2. Implementation of Lectures and Seminars at University
In this year, we provide a lecture to Kobe University Faculty of Human Development. The title is “Using computer as an intermediary for the integration of biology, physics, chemistry and mathematics”.
Through the discipline known as computational life science, the concept that “all knowledge is connected” surprised many of the students, and it seemed to be taken as a completely fresh idea.
III-2-3. High School Student Education and Outreach
(1) Holding Classes for High School Students and Teachers
We delivered lectures using nucleic acid sequencing puzzles and peptide modelling material to students and teachers of high schools.
1) Okayama Prefectural High School Biology Teacher Workshop (Aug. 29)
In feedback received through questionnaire, many of the participating teachers expressed their desire to use the practical labs on sequencing puzzles and molecular modelling as material in their own classes.
2) Hyogo Prefectural Nishiwaki High School Student Lecture (Oct. 18)
3) Okayama Prefectural Tamashima High School Student Lecture (Dec. 13)
4) Hyogo Prefectural Kakogawa Higashi High School Student Lecture (Dec. 20)
During the three lectures, students worked hard the nucleic acid sequencing puzzle and learned about structure using the amino acid molecular model.
(2) Presentations at Science Events for High School Students
We provided a panel exhibition for high school students at the event shown below.
1) Joint Meeting of “Science of Japan Science Teaching” and “Japan Society of Physics and Chemistry Education” (Aug. 8-9, Kwansei Gakuin University)
2) Sixth Annual Hyogo Science Fair (Feb. 2, 2014, Kobe International Exhibition Hall)
3) Third Annual Kagaku-no-Koshien National Gathering (Mar. 23, 2014, Hyogo Prefectural Gymnasium)
SCLS also presented the Science Café at “Sixth Annual Hyogo Science Fair” for students considering a career in science to freely discuss any worries or concerns they had with seniors who are undergraduate/graduate students in the scientific fields.
IV. Building Human Networks
To expand the support of SCLS research and development and promote the use of the HPCI, we encourage stronger collaboration with the public and researchers of academia, medical institutes and industries.
IV-1. Holding Symposia in Collaboration with Academic Societies and Hub Universities around the Country
We held several symposia/workshops for researchers, which are shown below.
1) Okayama University Symposium (July 19, 2013)
“Second K computer and the Life Sciences Symposium – Promoting Interdisciplinary Integration and Exchange in the Life Sciences”
2) Hokkaido Univ.-RIKEN Joint Symposium (Aug. 1, 2013)
“Paving the Way to the Future with Bio-predictive Simulation – The Challenge of Using High Performance Computers in Medicine”
3) Kyushu University Symposium (Sep. 19, 2013)
“New Bioscience Field Development and K computer”
4) SCLS and SPIRE Field 2 Joint Symposium in Nagoya (Dec. 17, 2013)
“Calculating Biomacromolecular Complexes – What Happens During Interaction?”
5) The 51st Annual Meeting of the Biophysical Society of Japan (Oct. 28-30, 2013)
“The Future of Life Science and Computational Science”
6) The 36th Annual Meeting of the Molecular Biology Society of Japan (Dec. 4, 2013)
“Leveraging Supercomputers for Hierarchical and Systems Understanding of Life towards Strategic Intervention against Diseases”
IV-2. Poster Presentations and Displays at Symposia and Other Gatherings
We provided a panel exhibition for the public and researchers, which are shown below.
1) Bio Japan 2013 Booth Exhibit (Oct. 9-11, 2013)
2) RIKEN Open Day (Sep. 28, 2013)
3) Science Agora 2013 (Nov. 9-10, 2013, National Museum of Emerging Science and Innovation)
4) Booth and Short Lecture at SC13 (Nov. 17-22, 2013)
5) The 27th Annual RIKEN-Industry Exchange Conference (Feb. 13, 2014)
IV-3. Promoting public calls for proposals for the use of the SCLS supercomputer
In order to actively support the broader use of HPCI among researchers and engineers in the life sciences, including in medical treatment and drug discovery, SCLS is streamlining SCLS supercomputer system and has implemented a public call for proposals for its use. In addition, lectures and seminars are held to aid in the promotion of the use of the SCLS supercomputer system.
V. Disseminating Research Results
We are engaged in a number of activities designed to help with the release and understanding of information regarding computational life science.
V-1. Publicity Activities
V-1-1. Publicity content
Animated content was created from content for pamphlets aimed at the public titled “For Better Health” (8 pages, A5).
(2) Publishing Newsletters (in both Japanese and English versions)
The newsletter continued to be published in 2012.
・BioSupercomputing Newsletter Vol.9 (Sep. 2013 Issue)
・BioSupercomputing Newsletter Vol.10 (Feb. 2014 Issue)
To enhance and expand the website in line with the expansion of program activity, the design and structure of the website underwent renewal. (SCLS website)
S-cruise Software in the website aims to promote the software developed with K computer by SCLS researchers.
(4) Producing Research Introduction Content
SCLS sets up exhibits at high schools, science museums, and science events around the country. To cultivate the next generation of young people who will enter the fields of computational life science, panel displays aimed at high school students with an interest in math and science were produced to introduce them to SCLS research.
(5) Producing Heart Simulator Visualization Content
A video was produced to help viewers visualize a heart simulator, UT-Heart, in order to pass on information on research results to the general public and to demonstrate applications of simulators to health-care professionals.
V-1-2. Reporting and Press Releases for Media
As a part of the strategy to publicize research results among the general public, SCLS co-hosted a briefing for media outlets in cooperation with SPIRE Field 2 and AICS(Sep. 9, 2013).
V-1-3. Holding K computer Tours and Lectures
To promote greater understanding of the computational life sciences, SCLS and AICS cooperated in conducting a tour of the K computer facility and in holding a lecture to provide an outline of the SPIRE and its research themes.
V-2. Collaboration with Industry
To disseminate research results and promote utilization of K computer, an organization comprised of universities, pharmaceutical companies and vendors was established to accelerate new drug development. We support the organization for HPCI technology.
V-3. Software Dissemination
We established the portal site “S-cruise Software”. This download portal was added to the SCLS website to disseminate software developed through SCLS.
VI. Promoting Interdisciplinary Efforts
We promoted strategic alliances. Specifically speaking, promoted cooperation with other SPIRE fields, AICS, and the HPCI Consortium.