Establishment of the Research System for Computational Science（Fiscal Year 2014）

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, RIST (Research Organization for Information Science and Technology) 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 K computer-compatible SCLS supercomputer system was provided to life science researchers of universities, academic institutes and private companies. It supports them to make active use of HPCI in life science field. The SCLS Evaluation Committee, whose members are M. Kanehisa (Chair of the committee, Kyoto University), N. Wada (Osaka University), A. Kidera (RIKEN), and Y. Eguchi (RIKEN), has proceeded with a public invitation of research themes, and has evaluated them. 25 research themes are adopted and, a total of 122 users, including 33 users of private companies, have utilized the system, as of 31 March, 2015.

• 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 FY2014, we provided technical support to develop pSpatiocyte software on K computer, which is designed to solve reaction-diffusion equations with a lattice-based Monte Carlo method.

• II-4. Holding User Workshops

In FY2014, hands-on workshops using SCLS supercomputer system were held with the aim of training of software programs, CafeMol, μ²lib, and GHOST-MP. The participants are mainly researchers of academia and industries. Because of the power of SCLS supercomputer system, the number of participants for each workshop is restricted to 10.
CafeMol (Participants:11)
μ²lib (Participants:10)
GHOST-MP (Participants:6)

 

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
From 17 October 2014 to 23 January 2015, CBRC held “Bioinformatics Research Seminars” once a week. Some of the seminars were held as public “HPCI Seminars”, and were also delivered by teleconference to the University of Tokyo’s Kashiwa, Hongo, and Shirokanedai campuses. A total of 413 students/researchers participated in the HPCI Seminars. E-learning materials of some lectures are produced and distributed to researchers and students.
(2) HPCI Workshops
HPCI Workshop “Big-data mining in life sciences – For improving health care service” was held for the public on Saturday, 4 October 2014. The number of participants is 121.
(3) HPCI Tutorials
Generally speaking, it is difficult for life-science researchers 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 for Beginners
There are 6 lectures, Fundamentals of Linux and Perl (67), Sequence analysis (40), ChIP-Seq data analysis (36), Fundamentals of R (41), Transcriptome data analysis using R (43), and Multivariate analysis/Gene network analysis (40). Data in parentheses are the numbers of participants. More than half of the participants are researchers, including medical doctors.
Participants provided feedback such as “This course was very helpful for me to understand bioinformatics, because there is no lecture on bioinformatics in my university.”
  2) Bioinformatics Practical Course for Drug Discovery
This course is set mainly for researchers of pharmaceutical companies. Participants provided feedback such as “I could get useful information and methods for drug discovery in my company.,” and “I could understand the underlying theory of tools which I usually use in my research.” Results showed that there is a great need for the tutorials. A total of 48 researchers/students participated in the course.
(4) HPCI E-Learning
There are currently six courses, such as bioinformatics and pharmaco-informatics, and 67 videos on offer, and anyone can repeatedly access all content for no cost simply by registering. The number of participants is 346. The rate of increase in graduate student’s participants is remarkable compared to last year.

• III-1-2. Implementation of Personnel Training and Education Programs (conducted by Osaka University Graduate School of Engineering Science)

(1) Lectures on Bio-simulation
An introductory course designed primarily for graduate students was held. The class was titled “Special Lectures in Bio-simulation (two credits)” and it covered the methodology of mathematical modelling of biophenomena and the computer simulation technologies. The number of credited students is 8.
(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) Introductory Lectures on Bio-simulation
An introductory course designed primarily for first-year undergraduate students was held. The class was titled “Fundamental Seminar on Introductory Bio-simulation (two credits)”. The number of credited students is 3.
(4) 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”

• III-2. Lectures for undergraduates, graduates, 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. Implementation of Lectures and Seminars at University

(1) Kobe University Faculty of Human Development
In this year, we provide a lecture for first-year undergraduate students at Kobe University Faculty of Human Development. The title is “What are Interdisciplinary Studies? ―Using Examples of the Integration of Biology with Physics, Chemistry　and Mathematics through the Mediation of the K Computer”. The number of participants is 314.
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.
(2) Remote Interactive Lectures
We co-held remote Interactive Lectures “Foundations of Computational Life Sciences”
collaborated with Education Center on Computational Science and Engineering, Kobe University.
Computational life sciences plays an important role in the development of a frontier science field, which has opened up a fruitful cooperation between life sciences and science/engineering, such as physics, chemistry and so on. To facilitate graduate students and researchers of academia and industry to understand the importance and usefulness, we begun the remote interactive lectures.
The number of registrants is 262, including 75 from 31 universities and 187 from 80 private companies.

• III-2-2. 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) Okinawa Prefectural High School Physics Teacher Workshop (7 Nov. 2014)
The report written by the organizer says participating teachers were impressed by the research of the brain simulation undertaken by using K computer.
2) Okayama Prefectural Tamashima High School Student Lecture (13 Dec. 2014)
During the lecture, 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 events shown below.
1) Seventh Annual Hyogo Science Fair (1 Feb. 2014, Kobe International Exhibition Hall) 　
SCLS also presented the Science Café 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.
2) Natural Science Division of the National High School Cultural Festival (28-31 July 2014, Tsukuba International Congress Center)
We provided the panel “Simulating the mechanism of life – Challenge to complexity of human body, and new medical care” to high school students. The number of participants is 525 from 163 high schools of 33 prefectures

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/seminars for researchers, which are shown below.
1) Okayama University Symposium (13 June 2014)
“Third K computer and the Life Sciences Symposium – Promoting Interdisciplinary Integration and Exchange in the Life Sciences”
2) Kyushu University Symposium (16 Sep. 2014)
“New Bioscience Field Development and K computer”
3) The 14th Annual Meeting of the Protein Science Society of Japan (26 June 2014)
“Supercomputing for drug discovery – Past, Present and Future -”
4) The 52nd Annual Meeting of the Biophysical Society of Japan (26 Sept. 2014)
“Supercomputing – the interface between computational science and information science -”

• 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 2014 Booth Exhibit (15-17 Oct. 2014)
2) RIKEN Open Day
Tsukuba campus (18 April 2014), Wako campus (19 April 2014), Harima campus (27 April 2014), Yokohama campus (6 Sept. 2014), Kobe campus (25 Oct. 2014)
3) Science Agora 2014 (7-9 Nov. 2014, National Museum of Emerging Science and Innovation)
4) Booth exhibition at Supercomputing Conference 2014 (16-21 Nov. 2014)
5) The 28th RIKEN Friends in Industry (17 Feb. 2015)
6) Kasumigaseki Study and Observation Day for Children (6-7 August 2014)

We also had a chance to exhibit the panel “Simulating the mechanism of life – Challenge to complexity of human body, and new medical care” at the publicity space of MEXT (Ministry of Education, Culture, Sports, Science and Technology) from 31 January to 22 April 2015.

• IV-3. Promoting public calls for proposals for the use of the SCLS supercomputer system

In order to actively support the broader use of HPCI among researchers and engineers in the life sciences, including 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. (see also II-1)

 

V. Disseminating Research Results

We are engaged in a number of activities to disseminate our research results of computational life sciences to researchers both in Japan and abroad.

• V-1. Publicity Activities

• V-1-1. Publicity content

(1) Pamphlets
To inform our research activities to researchers of academia and private companies, we made a pamphlet in which each SCLS researcher introduces his activity.
(2) Publishing Newsletters (in both Japanese and English versions)
We started to publish biannual newsletters at FY2011, succeeding to the publication “BioSupercomputing Newsletter” of Grand Challenge Application Project for Life Sciences which is the former project of our SCLS. This year, we made an effort to establish the connection between the newsletter and its Web version. The page of the Web version gets the highest access number, except the top page.
・BioSupercomputing Newsletter Vol.11 (Sep. 2014 Issue)
・BioSupercomputing Newsletter Vol.12 (March 2015 Issue)
(3) Website
To enhance and expand the website in line with the expansion of program activity, the design and structure of the website was renewed.
S-cruise Software in the website aims to promote the software developed with K computer by SCLS researchers.
All publications (research achievements) registered in the HPCI Publications Database have been added to the SCLS website. And almost all publications have linked to journal websites.
The number of current website page views increases three times as many as previous one by improved usability and accessibility;
-Work in conjunction with printed versions
-Add new pages and contents with attention to facilitate searching by using generic search keywords
-Put explanatory texts using generic terms to be easily identified, such as Newsletters and Movie Gallery
(4) Producing Visualization Content
Last year, we produced a visualization content of UT-Heart simulator and uploaded it to YouTube. It was introduced on the blogs of Scientific American. Partly because of the introduction, the content continues to get a high access number. This year, we produced a visualization content of “Molecular dynamic simulation in a cell”.

• V-1-2. Reporting and Press Releases for Media

SCLS is constantly engaged in disseminating research results among the general public by using media, such as TV, papers, magazines, and journals. We provided timely information to the press and also sent the media information that science journalists asked for and may be interested in around Japan and overseas. We have got some coverage of deliverables.
We continue to strengthen outreach activities to help media bring up the issue of our research in cooperation with AICS, RIST and other Strategic Fields.

• 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, two consortiums comprised of universities, pharmaceutical companies and vendors were established to accelerate new drug development. We support the consortiums for HPCI technology. Over 20 pharmaceutical companies are participating in the consortiums.

• 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.
The objective of this site is to contribute to increased industry competitiveness and the advancement of scientific technology and innovation. An environment that makes it easier for life science researchers and researchers and engineers in the medical and pharmaceutical industries (including health care facilities) to use the software can be created by providing user support and increasing user numbers in life science research and industry.

 

VI. Promoting Interdisciplinary Efforts

We promoted strategic alliances. Specifically speaking, promoted cooperation with other SPIRE fields, AICS, RIST, and the HPCI Consortium.

• VI-1. Collaboration with Industry

SCLS took part in the regular meetings on public outreach directors held by AIST, RIST, and the five SPIRE fields in 2014. The directors of all five fields of SPIRE and AICS gathered to promote inter-field collaboration, and to exchange and share information. Each field provided a report and shared information on future plans, thereby strengthening the cooperative framework.

• VI-2. Education and Outreach Activities

1) ISC14 (22 -26 June. 2014)
Held a joint exhibition with other SPIRE fields, AICS, and RIST
2) K Computer Symposium (23-24 Aug. 2014)
The five strategic programs delivered their speeches and held a joint exhibition.
3) Techno – Ocean 2014 (2-4 Oct. 2014)
Field 5 and SCLS delivered lectures at an organized session by AICS.
Title: Simulating the Human Body using the K computer, now and the future.
Participants: 164
4) Report Conference organized by RIST (31 October 2014)
The five strategic programs reported their research results and held a poster session.
5) SC14 (17-20 Nov. 2014)
Held a joint exhibition with other SPIRE fields, AICS, and RIST
6) MIRAI EXPO (28 Mar. – 5 Apr 2015)
SCLS exhibited posters with AICS at Hyogo Prefectural Government exhibition booth.
7) University Cooperative Lectures
Lecture on large-scale simulation at Kobe University, Graduate School of System Informatics. Lectures were taught by researchers from Kobe University Graduate School of System Informatics, AIST, and the SPIRE fields.