AHeDD2008 / IPAB2008 Joint Symposium

Date:   October 16 (Thu) – 17 (Fri), 2008
Place:   Yebisu Garden Place, Tokyo, Japan
            (SGI Hall, Yebisu Garden Place Tower B1F, 4-20-3 Yebisu, Shibuya-ku)

*** The symposium has finished. Thank you very much for your participation. ***

Organizers:
Initiative for Parallel Bioinformatics (IPAB)  (President: Prof. Yutaka Akiyama)
AHeDD 2008 Organizing Committee

In cooperation with:
Global COE program “CompView” (Leader: Prof. Osamu Watanabe)
BMDRC, Seoul, Korea  (Director: Prof. Kyoung Tai No)
DDDC, Shanghai, China (Director: Prof. Hualiang Jiang) 
Japanese Society for Bioinformatics (JSBi)
Chem-Bio Informatics Society (CBI)
Japan Association for Medical Informatics (JAMI)
Japanese Society for Artificial Intelligence (JSAI)
SIGBIO/SIGMPS/SIGHPC, Information Processing Society of Japan (IPSJ)

Scope:
Accelerator Technology (GPGPU, FPGA, etc.) for bioinformatics and computational life sciences, Computational approaches for Drug Discovery (virtual screening, ADME, etc.), Clinical Informatics, and other topics related to bioinformatics and computational biology research.

Language:
Day 1: Japanese and English
Day2 : English
*Note: Most of presentations in Day1 will be given in Japanese, while Day2 presentations are all in English.

Greetings:

It is our great pleasure to hold the AHeDD2008/IPAB2008 joint symposium in Tokyo. The central theme of the symposium is “Novel Acceleration Technologies for Drug Discovery, Genome Analysis, and Clinical Informatics”.The two-day symposium will cover the new movement of hardware accelerator technology and general HPC technology, as well as their application to important scientific areas of drug discovery and bioinformatics. The symposium will be held as a unified event of AHeDD2008 and IPAB2008. We will have 2 special talks, 19 invited talks, 21 poster presentations, 7 exhibitions, and lunchon seminars.

AHeDD2008 is the 4th annual international symposium held by “Asia Hub for e-Drug Discovery” (AHeDD) project. AHeDD is an international research collaboration group founded in 2004, aiming at exchange of latest ideas and results on computational methods for drug discovery, and also construction of an Asian research community for sharing knowledge, training people, and incubating new business in e-drug discovery. AHeDD2008 succeeds previous AHeDD2005 (Jeju), AHeDD2006 (Seoul), and AHeDD2007 (Shanghai). For details, please visit the AHeDD Web page at http://www.e-drugdiscovery.org.

IPAB2008 is the 9th annual symposium held by “Initiative for Parallel Bioinformatics” (IPAB). IPAB was founded in 1999 and it became a formal non-profit organization in 2003. IPAB is a group of individual researchers and private companies aiming at contributing to the research and industrialization of bioinformatics and biomedical computing, by means of state-of-the-art information technologies, like as parallel computing and Grid technology. IPAB has decided to contribute to AHeDD activity, as a Japanese brunch of AHeDD.

On behalf of symposium organizers, I would like to express our sincere gratitude to all speakers, exhibitors, sponsors, and participants for joining this symposium. We wish this event may contribute to ignite and foster new international and interdisciplinary collaboration in this important research area.

AHeDD2008/IPAB2008 Program :

Day 1: Thu., October 16  “New Direction of IPAB”
Venue: SGI Hall (Yebisu Garden Place Tower B1F)

10:00-10:05  Opening Address
Prof. Yutaka Akiyama (President of IPAB / Tokyo Tech)

10:05-11:45  Session 1: Accelerator Technology
Coordinator: Prof. Fumikazu Konishi (Tokyo Tech)
(Senior Vice President, Head of Accelerator WG, IPAB)
10:05-10:35   Dr. Toshiyuki Sanuki  (DE, IBM Japan, Ltd.)
“Challenge for petascale computing”
10:35-11:05   Dr. Yosuke Tamura (CTO, Fixstars, Co.)
“Current state and applied case with software development for Cell/B.E.”
11:05-11:35   Dr. Masatsugu Hashimoto (CTO, SGI Japan, Ltd.)
"The Capability of GPU Computing"
11:35-11:45  Prof. Fumikazu Konishi (Tokyo Tech) 
“Introduction to accelerator WG activity in IPAB” 

11:45-13:00  Lunch Break
* Free Lunch-on Seminar, by NVIDIA JAPAN / ELSA Japan Inc.
* Commercial Exhibitions, and Poster Display

13:00-13:50  Special Talk
 Prof. Kenichi Hagihara (Osaka University) 
“Medical image processing using GPGPU”

13:50-15:20  Session 2: Clinical Informatics
Coordinator: Prof. Teruyoshi Hishiki (Toho University)
(Vice President, Head of Clinical Informatics WG, IPAB)
13:50-14:20   Prof. Teruyoshi Hishiki (Toho University) 
“IPAB’s new activity on Clinical Informatics”
14:20-14:50   Prof. Yutaka Suzuki (The University of Tokyo)
“Analysis of full-length cDNAs with next-generation DNA sequencers” 
14:50-15:20   Prof. Hiroshi Mizushima (Tokyo Medical and Dental University)
“Integrated database with comprehensive both clinical and molecular
information”

15:20-16:00  Cofee Break
*Commercial Exhibitions, and Poster Display

16:00-17:30  Session 3: e-Drug Discovery
Coordinator: Prof. Yutaka Akiyama (Tokyo Tech)
(President, Head of pharmaco-informatics WG, IPAB)
16:00-16:30   Prof. Kyoung Tai No (Yonsei University / BMDRC, Korea)
“Development of e-Organ and It's Application for Drug Repositioning”
16:30-17:00   Prof. Takatsugu Hirokawa (CBRC, AIST) 
“Protein structure-based virtual screening using concavity shape fingerprints”
17:00-17:30   Prof. Weiliang Zhu (DDDC, SIMM, China)
“Exploring Functional Conformations of Target Protein for Drug Discovery by Molecular Dynamics Simulations”

17:30   End of Day 1

18:00-20:00    Reception Party
at Beer Station Yebisu (3 min. on foot)
Food and All-you-can-drink Beer at Japanese most famous brewery
Participation Fee:  JPY2,000 (planned)

Day 2: Fri., October 17, “Asia Hub for e-Drug Discovery”
Venue: SGI Hall (Yebisu Garden Place Tower B1F)

10:30-10:45  Introduction to AHeDD activity
Prof. Kyoung Tai No (Yonsei University / BMDRC, Korea)
Prof. Weiliang Zhu (DDDC, SIMM, China)
Prof. Yutaka Akiyama (Tokyo Tech, Japan)

10:45-12:15  Session 4:  Frontiers of Drug Discovery Research
Chair: Prof. Kyong Tai No (Yonsei University / BMDRC, Korea)
10:45-11:15   Prof. Hong Gil Nam (POSTECH, Korea)
“Molecule-Level Imaging of Pax6 mRNA Distribution in Mouse Embryonic Neocortex by Molecular Interaction Force Microscopy”
11:15-11:45   Prof. Yun Tang (East China Univ. of Science and Technology, China)
“New potential inhibitor binding sites identified in HIV-1 integrase”
11:45-12:15   Dr. Tohru Natsume (BIRC, AIST, Japan)
“Systematic Analysis of Protein Interaction Networks”

12:15-13:30  Lunch Break
*Commercial Exhibitions, and Poster Display

13:30-14:20  Special Talk
Prof. Toshihisa Ishikawa (Tokyo Tech, Japan)
“Transporter mechanism-based drug molecular design: High-speed screening, QSAR analysis, and molecular orbital calculation”

14:20-15:20  Session 5:  Challenges for Important Targets
Chair: Prof. Weiliang Zhu (DDDC, SIMM, China)
14:20-14:50   Prof. Baik-Lin Seong (Yonsei University, Korea)
“Common Vaccine Platform for Seasonal and Pandemic Influenza”
14:50-15:20   Dr. Tomoko Niwa (Nippon Shinyaku Co., Ltd., Japan)
“Elucidation of Characteristic Structural Features of Protein Kinases: A Neural Network Approach”

15:20-16:10  Poster Presentation Time
Explanation by authors.  With Coffee service.

16:10-17:40  Session 6:  Novel Computing Techniques for Drug Design
Chair: Prof. Hiroshi Chuman (The University of Tokushima, Japan)
16:10-16:40   Prof. Jianfeng Pei (Peking University)
“De novo drug design - to be a more practical approach
16:40-17:10   Dr. Kunqian Yu (DDDC, SIMM, China)
"Drug discovery Grid of China”
17:10-17:40   Dr. Toshio Watanabe (RICS, AIST)
"Molecular Orbital Calculation for Large Molecule with Sakurai-Sugiura Method on Grid Computing Environment”

17:40   Closing Remark

*Special presentation of Computer demonstration and exhibition (E01-E08)
E01: Fixstars, Co.
E02: Information and Mathematical Science Laboratory Inc.
E03: Tokyo Institute of Technology Global COE program "CompView"
E04: Bestsystems, Inc.
E05: IBM Japan, Ltd.
E06: ClearSpeed Technology, Inc.
E07: NVIDIA JAPAN  /  ELSA Japan Inc.
E08: Science & Technology Systems, Inc.

*Poster Presentations (P01-P21)
P01: Shen J, Liu GX, Tang Y* (ECUST): “In silico prediction of blood-brain partitioning using a chemometric method called genetic algorithm based variable selection (GAVS).”
P02: Jing Chen, Jianfeng Pei, Dengguo Wei, Qingliang Li, Luhua Lai (Peking Univ.): “Improving virtual screening efficiency by receptor-based pharmacophore model”
P03: Kunqian Yu (DDDC, SIMM): “Drug discovery Grid of China”
P04: Kwang-Hwi Cho, Jeong-Hyun Kim (SoongSil Univ.): “SABA: Secondary structure Assignments program Based on Alpha Carbon”
P05: Ky-Youb Nam, Hanjo Kim (BMDRC): “In silico Integrated Drug Profiling System against Influenza Virus”
P06: Jong Young Joung (Yonsei Univ.): “Property-Weighted Vector driven Docking Algorithm Using Solvation Free Energy Density (SFED) model”
P07: Hwan You (Yonsei Univ.): "Prediction of Binding Free Energy of Protein-Protein complex using Statistical Mechanics Methods"
P08: Hyoungjun Son (Yonsei Univ.): “In silico prediction for phase II enzyme selectivity of UGT and SULT substrates”
P09: Hankil Son (Yonsei Univ.): "Classification of phase II metabolizing enzymes"
P10: Chang Joon Lee (Yonsei Univ.): "RP-Path : A Robust Method for Search Smallest Set of Smallest Rings (SSSR) with Path Included Distance (PID) Matrix"
P11: Young Mook Kang (Yonsei Univ.): "Prediction of Metabolism using MNA Descriptor and Artificial Neural Network"
P12: Su Yeon Kim (Yonsei Univ.): “Development of novel chemicals blocking export of glycogen synthase kinase 3 (GSK3) from nucleus to cytoplasm”
P13: Se Han Lee (Yonsei Univ.): “Solvation Free Energy Calculation Method with the SFED and GSFED Model”
P14: Hiroaki Umeda (RICS, AIST): "FMO-MO - molecular orbitals of the fragment molecular orbital method -"
P15: Hiroaki Umeda (RICS, AIST): "Grid-enabled large Fock matrix construction for FMO-MO method"
P16: Fumikazu Konishi, et.al  (Tokyo Tech): “The speed-up of  Crystallography & NMR System (CNS) with hardware SIMD accelerator”
P17: Fumikazu Konishi, et.al  (Tokyo Tech): “Development of an instant accelerator environment with Knoppix technology”
P18: Satoshi Matsuoka, Yutaka Akiyama, Akira Nukada, Toshio Endo, Yasuhiko Ogata, Fumikazu Konishi (Tokyo Tech): "HPC-GPGPU: Large-Scale Commodity Accelerated Clusters and its Application to Advanced Structural Proteomics"
P19: Naoya Maruyama, Akira Nukada, Satoshi Matsuoka (Tokyo Tech): “Preliminary Evaluation of Software-Based Memory Fault Tolerance in GPGPU"
P20: Kouta Toshimoto, et.al (Tokyo Tech): “In silico prediction of major drug clearance pathways by machine learning techniques”
P21: Yutaka Akiyama, et.al (Tokyo Tech): “A GPGPU-based ultra fast sequence comparison system for mapping short DNA fragments onto human/mouse full genome sequence”