Wednesday, November 19, 2008

Grid Computing in Ateneo de Manila University: An Overview

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{ Note: Draft Version 1.0, 16 November 2008 }

Grid Computing Projects in Ateneo de Manila University: An Overview

(Paper presented during a talk on Grid Computing on October 10, 2008 in GSI, Darmstadt, Germany.)


by

Rafael P. Saldaña, Ph.D.

Coordinator

Ateneo Grid and High Performance Computing Group

School of Science and Engineering

Ateneo de Manila University

E-mail: rsaldana@ateneo.edu


1.0 Introduction



To date, Ateneo de Manila University through the Ateneo Grid and High Performance Computing Group of the School of Science and Enginering of ADMU is part/has been part of several national and international grid computing related projects, namely:


1.1 Medical Grid Project
1.2 Onco-Media Project
1.3 Philippine e-Science Grid Project
1.4 PANDA Grid Project
1.5 EUAsiaGrid Project


2.0 The Medical Grid Project


The Medical Grid Project (MGP) was started in 2004 to answer the computational and storage demands of modern medicine. It is an international collaboration involving researchers from Japan, the Philippines, and Taiwan to study and demonstrate the idea of using grid technology for medical applications.

In recent years, imaging technologies such as computed tomography (CT) and magnetic resonance imaging (MRI) have played significant roles in medicine. Obtaining sophisticated high resolution images of human bodies, non-invasive investigation of the different functions of the human brain, and excellent detection of diseases are but a few significant applications that are made possible by the development of these technologies.


In particular, the technique known as functional MRI (fMRI) has led to numerous new findings in perception, cognition, motor control, language, memory and emotion. These findings in turn deepened our understanding of the mechanisms of the human brain which would contribute to many fields, including neurology, neurosurgery, diagnostic radiology, cognitive psychology, human engineering and information science. These new imaging technologies are still evolving. For instance, functional MRI demands the processing of huge data sets. For it to attain widespread clinical use, it is indispensable to achieve prompt or immediate reporting of analysis results. This requires considerable computing resources which are not readily available in many medical imaging facilities. In this project, we are attempting to establish a system for managing these computational demands using computational grids.


The Medical Grid Project plans to provide 1) cost-effectiveness in the dissemination and maintenance of high performance analysis system, 2) robustness in the analysis by integrating different methodologies, and 3) prompt reporting capability based on real-time processing.


The project would promote the research and development of medical technologies by providing on-demand access to high performance analysis systems. Since biological data are usually complex, no single method would be ideal for extracting all the information in the data. Integration of different methodologies would be pursued in maximizing the extracted information from complex signals. The benefit of Medical Grid is obvious, and could be easily expanded into modalities other than fMRI.


Following are the Participating Sites in the Medical Grid Project:


  • Grid Technology Research Center, AIST, Tsukuba, Japan
  • Department of Gerontechnology, National Center for Geriatrics and Gerontology, Aichi, Japan
  • Sato Laboratory, Osaka University, Osaka, Japan
  • Department of Psychology, National Taiwan University, Taiwan
  • School of Science and Engineering, Ateneo de Manila University, Philippines
  • Center for Optoelectronic Biomedicine and Department of Medical Imaging, National Taiwan University, College of Medicine and Hospital, Taiwan


3.0 The Onco-Media Project

3.1 Summary

ONCO-MEDIA is an acronym for ONtology and COntext Related MEdical Image Distributed Medical Access. Below is a short summary of the ONCO-MEDIA Project:


Content-based visual information retrieval (CBVIR) or Content-Based Image Retrieval (CBIR) has been one on the most vivid research areas in the field of computer vision over the last years. In the medical field, images, and especially digital images, are produced in ever-increasing quantities and used for diagnostics and therapy. The availability of large and steadily growing amounts of visual medical data and the development of the Internet underline the need to create thematic access methods that offer more than simple text-based queries or requests based on matching exact database fields.

Many CBIR programs and tools have been developed to formulate and execute queries based on the medical image visual content and to help browsing. Still, no general breakthrough has been achieved with respect to large varied databases with documents of differing sorts (modalities) and with varying characteristics (anatomy, pathology). Answers to many questions with respect to semantic descriptors, semantic gap, medical image and report fusion indexing or context-sensitive navigation and query are still unanswered.

On the other hand, computation and data grids have also encountered a large success among the scientific computing community in the past few years. The medical imaging community is increasingly aware of the potential benefit of these technologies in facing today medical image analysis and retrieval challenges.

In this context, the aim of ONCO-MEDIA project is to deploy a medical image semantic content-based application on a large scale grid test bed, by taking into account the context of the user and of the navigation / query and by matching semantic visual concepts extracted from the medical image with those (textual) extracted from the associated medical reports.

3.2 Goals:

3.2.1. Develop a novel grid-distributed, contextual and semantic based, intelligent information access framework for medical images and associated medical reports focusing on:
a. Robust visual indexing and retrieval algorithms for medical images; b. Robust fusion indexing intelligent techniques for medical images and associated medical reports; c. Developing a grid-distributed medical image retrieval application that links the medical concepts of the images and text documents based on medical ontology using intelligent methods; d. Methods for context-sensitive navigation and query;

3.2.2. Explore new medical image diagnosis assistance, teaching and research access applications using semantic, visual and context-sensitive medical information with the grid computing facilities;

3.2.3. Crystallize a network of research excellence in the field of distributed medical images access among Asian, French and French Switzerland partners, leveraging on their complementary scientific values and experience.


3.3 Partner Institutions

3.3.1 IPAL – CNRS, I2R A*STAR, NUS, UJF Singapore


3.3.2 National Center for Geriatrics and Gerontology, FBIL, Japan

3.3.3 University of Nice - Sophia Antipolis


3.3.4 National Taiwan University


3.3.5 University of Paris 6, France


3.3.6 Ateneo de Manila University, Philippines

3.3.7 CREATIS - CNRS, Inserm, INSA Lyon, France

3.3.8 LIRIS - CNRS, Univ. Lyon 2, France

3.3.9 UNIGE, Univ. Hospitals of Geneva, Switzerland

3.3.10 University of Franche-Comté, Besançon, France

3.3.11 Institute of Automation, Chinese Academy of Sciences, Beijing, China


3.4 Principal Investigators and Co-Principal Investigators:

Principal Investigator:

Daniel RACOCEANU, A/Prof. Dr. -habil, Ing.
IPAL - Image Perception, Access & Language—IPAL
French National Research Center - UMI CNRS 2955NUS, I2R A*STAR, UJF
Singapore

Co-Principal Investigators:

Hugues BENOIT-CATTIN, Prof.CREATIS -UMR CNRS 5515, Inserm U630
Research and Applications Center in
Image and Signal Processing – Medical ImageLyon, France

Heng-Shuen CHEN, A/Prof, MD, PhD.
NTU - National Taiwan University
Taipei, Taiwan

Patrick BREZILLON, PhD, Dr. Habil.
LIP6 - UMR CNRS 7606
Laboratory of Computer Sciences, Paris 6
Pierre & Marie Curie University (Paris 6)
Paris, France

Toshiharu NAKAI, ScD
FBIL - Functional Brain Imaging Lab
NCGG - National Institute of Geriatrics and Gerontology
Aichi, Japan

Henning MULLER, PhD
UNIGE - University Hospitals of Geneva
Medical Informatics Service
Geneva, Switzerland


Rafael P. SALDANA, Ph.D., A/Prof
School of Science and Engineering
Ateneo de Manila University,
Manila, Philippines

Johan MONTAGNAT, Ph.D.
I3S - UMR CNRS 6070
Computer Science, Signals and Systems Laboratory in Sophia Antipolis, Nice, Sophia Antipolis, France

Serge MIGUET, Prof.
LIRIS - UMR CNRS 5205
Lyon Research Center for Images and Intelligent Information Systems, Lyon,France

Tianzi JIANG, PhD
CASIA, Institute of Automation
Chinese Academy of Sciences
Beijing, China

Noureddine ZERHOUNI, Prof.
FEMTO-ST Institute - UMR CNRS 6174 - UFC / ENSMM / UTBM
Automatic Control and Micro-Mechatronic Systems Department
University of Franche-Comté, Besançon, France


4.0 The Philipppine e-Science Grid Project

The Department of Science and Technology (DOST) has provided funding, under its Grants-in-Aid (GIA) Program, to implement the Philippine e-Science Grid (PSiGrid) Program. The three-year program (2008-2011), which aims to establish a grid infrastructure in the Philippines to improve research collaboration among educational and research institutions, both locally and abroad, covers three (3) projects, namely:

(1) Boosting Grid Computing Using Reconfigurable Hardware Technology (Grid Infrastructure);

(2) Developing a Federated Geospatial Information System (FedGIS) for Hazard Mapping and Assessment; and

(3) Boosting Social and Technological Capabilities for Bioinformatics Research (PBS).

The Program will be implemented by the Advanced Science and Technology Institute (ASTI), an attached institute of the DOST focusing on R&D in ICT and Microelectronics.

Website: http://www.psigrid.gov.ph/index.php?option=com_frontpage&Itemid=1

The School of Science and Engineering of Ateneo de Manila University is part of the Philippine e-Science Grid Project.

5.0 The PANDA Grid Project

The PANDA Grid project started in 2003 is based on AliEn gridware developed by ALICE at CERN. In 2006, the gridware has been upgraded to AliEn2.

PANDA refers to Proton Antiproton Annihilations at GSI, Darmstadt, Germany.

The PANDA experiment at the accelerator HESR (FAIR / GSI) addresses several fundamental questions in the physics of strong interaction. Antiproton beams stored in the HESR will hit an internal target in fixed target experiments. These interactions will generate a lot of mesons and baryons consisting of the heavier strange and charm quarks and will copiously produce gluons. Antiproton-proton annihilations are a unique possibility to firmly establish the QCD-predicted gluonic excitations (hybrids, glueballs) in the charmonium range, since alternative methods have severe limitations. The study of glueballs is a key to the understanding of long-distance QCD. The necessary precision and high statistics can be generated with sufficient luminosity by a hydrogen cluster-jet target

Following major experimental topics of PANDA will benefit from the extremely high statistics and will therefore be high-precision tests of the strong interaction:


Charmonium spectroscopy: precision measurement of mass, width and decay branches of all charmonium states in order to extract information on the quark-confining potential.
Establishment of the QCD-predicted gluonic excitations (charmed hybrids, glueballs) in the charmonium mass range (3-5 GeV/c2).


Search for modifications of meson properties in the nuclear medium in the charm sector and their possible relationship to partial restoration of chiral symmetry.

Though its MEDGRID cluster, the School of Science and Engineering of Ateneo de Manila University is now taking part in building up and experimenting with the future computing infrastructure for PANDA.

PANDA grid is a framework, which is built around Open Source components. Its main task is to combine the computing resources of the participating institutes in a structured manner and to provide a common environment to perform highly demanding computing tasks for the PANDA project.

The grid was initially developed by the ALICE collaboration as environment for simulation, reconstruction and analysis of detectors and particle events.

Ateneo de Manila University is an active partner in this consortium and maintains a node of the PANDA grid. Semi-annual workshops are effected to keep the node administrators up-to-date with new developments and to perform coordinated updates of the systems. The next meeting will be organized by Ateneo de Manila University's Grid and High Performance Computing Group in 2009.

Sources:

PANDA Letter of Intent (2004).
PANDA Technical Progress report (2005).
http://www.gsi.de/portrait/index_e.html

PANDA International Collaboration:

Uppsala Univ., Schweden - LNF-INFN, Italy - GSI, Germany - KVI Kroningen, Netherlands - Univ. Brescia, Italy - Univ. Catania, Italy - Univ. Torino, Italy - TU Dresden, Germany - Univ. Frankfurt, Germany - TSL Uppsala, Schweden - Univ. Erlangen, Germany - Univ. Münster, Germany, FZ Jülich, Germany - LANL Los Alamos, USA - Politechnico Torino - Italy, Univ. Cracow, Polen - Univ. Silesia, Polen - Ruhr-Univ. Bochum - Germany, Univ. Genova, Italy - Univ. Trieste, Italien, Univ. Tübingen, Germany - TU München, Germany - Univ. Mainz, Germany - Univ. Gießen, Germany - Univ. Bonn, Germany - Univ. Glasgow, Great Britain - Univ. Pavia, Italy - JINR Dubna, Russia - Northwestern Univ. Evanston, USA - BINR Dubna, Russia - SINS Warsaw, Polen.

http://tau.ep1.rub.de/HyperNews/get/PndGrid/17.html

PANDA GRID Development Adding Sites:

How member institutions should contribute considering the PANDA projected acquisition rate (~250 TB/year) and the immediate need of large scale simulations of the PANDA detector, no single institution (not even GSI) will have the computing resourcesto process this amount of data in a timely manner.

Therefore it isnecessary to put together our resources in a coordinated way.

The GRID is designed exactly for this purpose. The PANDA GRID can be developed only with the contribution of the PANDA member institutions. Glasgow University provides the infrastructure as well as local resources. However, a GRID project implies pooling collaboration's resources in a coherent, structured manner.Pooling resources means that each institution contributes their localresources and gets access to remote resources contributed by others.

Local resources mean:

* CE: computing elements, that is computers (desktops for example)or/and computing farms. No special hardware configurations arerequired at this time but the machine(s) should run a flavor of linux.

* SE: storage elements, i.e. some hard drive space so that jobinput/output files can be stored locally. The hard drive space shouldbe of the order of 5 GB per site. The physical space can be locatedon an pre-existing filesystem.

* FTD: file transfer deamons running that copy files back and forthbetween the server and the local hard drive when necessary. Firewallsshould be configured to allow these transfers.A setup containing these three elements is what we call here aSite. Each Site would in principle correspond to a PANDA memberinstitution. A new Site to the AliEn-PANDA Grid can be added by a person who canperform administration tasks at the respective site location.

Theadministration of a GRID Site can be done by one person and would require an estimated time of 5 hours/month. Heads of institutions should allocate the manpower to do this. The initial Site installation would require less than one hour and is explained in the "Admin HowTo" on the left hand side menu on the GRID portal: http://panda.physics.gla.ac.uk/ .

Once the head of theinstitution delegates an administrator for GRID integration, the respective administrator should read the documentation mentioned above and then contact Dr. Dan Protopopescu as soon as possible. It is important to start testing the GRID now.

For more information visit http://panda.physics.gla.ac.uk/t/request.html or contact Dr. Dan PROTOPOPESCU Department of Physics & Astronomy, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK Tel: +44 141 330-8634 FAX: +44 141 330-5889.

List of PANDA Grid Member Sites:

Websites:

http://mlr2.gla.ac.uk:7001/stats?page=siteMLstatus

http://raffysaldana.blogspot.com/2008/11/panda-grid-member-sites.html

1. Ateneo de Manila University (Philippines)

2. Bucharest (Romania)

3. Dubna (Russia)

4. Frascati (Italy)5. Frascati-2G (Italy)

6. GSI (Germany)

7. GridServer (United Kingdom)

8. Juelich (Germany)9. Juelich_2 (Germany)

10. KVI (Netherlands)11. KVI_PBS (Netherlands)

12. NPE (United Kingdom)13. PGDB (United Kingdom)

14. Pavia (Italy)

15. SMI (Austria)

16. ScotGrid-2G (United Kingdom)

17. Torino (United Kingdom)

18. Torino-2G (Italy)

19. Vienna (Austria)


6.0 The EUAsiaGrid Project

Project Website: http://www.euasiagrid.org/

The EUAsiaGrid Project is an international consortium project funded by the European Commission under its FP7 Program.

6.1 Objectives

The following are the objectives of the EUAsiaGrid Project:

  • Promote awareness in the Asian countries of the EGEE infrastructures, middleware and services by means of specific dissemination activities, such as workshops’, training events, conferences and hands-on demonstrations;
  • Capture local e-Science user requirements in terms of resources needed, Grid services, application software, and training needs, building on results of the EGI_DS projects.
  • Build a EuroAsian Grid community by identifying and aggregating new and existing user communities into a virtual Grid-based research space.
    Assist regional integration with the wider Grid infrastructure in collaboration with the EGEE III Asian Federation and the EUChinaGrid and EU-IndiaGrid projects, thus significantly contributing to the creation of a human network in the area of Grids, e-Science and e-Infrastructures between Europe and Asia.
  • Promote common e-Science application in Asia and Europe, by supporting the early user communities already engaged in Grid applications (Life science, Particle Physics), and engaging new ones by coordinating common actions of dissemination and training;
  • Provide specific training materials and events targeted to the needs of users in the Asian countries as established in part in Objective 2, and in part building on the experience gained from the EUChinaGrid and EU-IndiaGrid projects.
  • Foster international cooperation by working in synergy with members of the EGEE II Asian Federation, and the EU-IndiaGrid and EUChinaGrid projects.

6.2 Project Partners

Following is a list of project partners and a brief introduction about each partner:


6.2.1 INFN Italy
Istituto Nazionale di Fisica Nucleare is the Italian National Institute of Nuclear and Particle Physics. Founded in 1952, INFN is a governmental research organization, which promotes, co-ordinates and funds nuclear, particle and high-energy physics research. INFN staff research personnel amounts to more than 1500 peoples with an equivalent number of associates from University and other Scientific National Institutes.

6.2.2 CESNET Czech Republic
CESNET z.s.p.o. is a public non-profit organization established in 1996 by all the universities and the Academy of Science of the Czech Republic to do research and development of advanced network technologies and applications, including the development and operation of the national Grid infrastructure, related training and research activities. The infrastructure built and operated by CESNET is open to all the research institutions in the Czech Republic, both from academia and industry.


6.2.3 NCeSS UK National Centre for e-Social Science is funded by the UK’s Economic and Social Research Council (ESRC) to investigate and promote the use of e-Science technologies to benefit social science research. NCeSS also researches the development and use of e-Science technologies and advises on the future strategic direction of e-Social Science. The overall budget for the 2008-2011 NCeSS research programme is £10 million of which ESRC funds £8 million.

6.2.4 HealthGrid France

The HealthGrid association was founded to bring the necessary long term continuity between the projects addressing the deployment of Grid technology for healthcare, and is already identified at a world. This international dimension has been strengthened by the edition of the HealthGrid White Paper in 2004 with contributions from more than 40 experts from Europe, Asia and North America as well as by the setup of the HealthGrid.US Alliance early in 2007.

6.2.5 AdMU Philippines (Ateneo de Manila University)

School of Science and Engineering Ateneo de Malina University is one of the oldest and most established universities in the Philippines. It has an excellent reputation in the sciences, humanities, social sciences and management education. In 2000 the School of Science and Engineering built one of the first Beowulf clusters in the Philippines. In 2003 the School entered into a joint research collaboration with Japanese institutions on medical applications of grid computing.

6.2.6 ANU Australia

Australia National University has a reputation as a centre of excellence in both teaching and research and was progressively built by a range of academic leaders. ANU is able to propose focusing on the possible social benefits available though the use of a common grid infrastructure and EGEE enabled applications to expand some of the activities of the APAN Medical working group to use the facilities provided by the existing grid infrastructure.

6.2.7 ASGC Taiwan

Academia Sinica Grid Computing Centre is one of leading high performance computing and communication centres in Taiwan, which provides advanced services for Grid Computing. Under the support of National Science Council, ASGC has provided the Grid-related technology and infrastructure support for the LHC experiments (ATLAS and CMS) in Taiwan since 2002. In 2005 ASGC has formally become one of the 11 WLCG Tier-1 centres (the only Tier-1 in Asia) providing services, coordination and support to HEP scientists worldwide.

6.2.8 ASTI Philippines
Advanced Science and Technology Institute is a research and development agency under the Department of Science and Technology of the Government of the Republic of the Philippines. ASTI was created in 1987 and is mandated to conduct scientific research and development in the advanced fields of Information and Communications Technology and Microelectronics

6.2.9 HAII Thailand
Hydro and Agro Informatics Institute was founded on 16th January 2004 as a part of National Science and Technology Development Agency (NSTDA), the Ministry of Science and Technology, Thailand. HAII is an informatics institute on water resources and agriculture in Thailand with the applications of advanced science and technology responding to His Majesty the King’s initiative

6.2.10 IDA Singapore
Infocomm Development Authority is a Singapore where computer resources connected via a high-speed network are shared in a secure, reliable, and efficient manner by authenticated users. Such resources will be shared for a variety of application domains and sectors, in an effort to improve the economic and technological competitiveness and quality of life in Singapore.

6.2.11 IOIT-HCM Vietnam
Institute of Information Technology ) is a research institute on Computer Science, being under the Vietnamese Academy of Science and Technology (VAST). The IOIT-HCM was founded based on Department of Applied Mathematics Department established in 1981. The main functions of IOIT-HCM is researching and deploying the new technology to apply the Information Technology into the domain of Economy, Social, Science and Technology.

6.2.12 ITB Indonesia

Institut Teknologi Banding was founded on March 2, 1959. The present ITB main campus is the site of earlier engineering schools in Indonesia. Although these institutions of higher learning had their own individual characteristics and missions, they left influence on developments leading to the establishment of ITB. Currently, the Inherent has connected more than 80 universities in Indonesia and by the end of 2007, the network will be connected up to 120 universities in Indonesia. ITB became one of the members of Asia Pacific Advanced Network.

6.2.13 NECTEC Thailand

National Electronics and computer Technology Center is a statutory government organization under the National Science and Technology Development Agency (NSTDA), Ministry of Science and Technology. Its main responsibilities are to undertake, support and promote the development of electronics and computer technologies through research and development activities. NECTEC also provides linkage between research communities and industries through the established industrial clusters.

6.2.14 UPM Malaysia

University Putra Malaysia is a public university and one of the four research universities in Malaysia in recognition of its high quality research and education by the Ministry of Higher Education, Malaysia. UPM academic and research entities comprised of 16 faculties and 11 institutes with research, post-graduate training and under-graduate programmes in the various fields including basic sciences and engineering, agriculture, medicine, biotechnology, computer science and ICT and economics and policy studies.

6.2.15 MIMOS Malaysia

MIMOS Berhad is Malaysia’s leading applied research organization in information & communication technologies aimed at growing globally competitive indigenous industries. MIMOS pursues exploratory and industry-driven applied research through multi-stakeholder smart partnerships with universities, research institutes, Government and industries with a focus on frontier technologies. MIMOS’ applied research areas, based on real-world trends, are Cyberspace Security, Encryption Systems, Grid Computing, Communication Technologies, Micro Energy, Micro Systems (MEMS/NEMS),

6.3 Work Packages


Work Package 1 : Project administrative and technical management

WP1 is devoted to the financial and administrative and technical management of the project. This activity will involve mainly the Project Manager, the Project Office and the Collaboration Board.

TASK1.1 Administrative management

TASK1.2 Technical management

Work Package 2: Requirement capture and coordination policy definition

In the first phase this WP aims to collect information from the scientific communities of the Asian countries about their computing, storage, application support and training requirements, in order to understand which scientific domains and applications could profit more from the use of the EGEE Grid middleware.

TASK 2.1 Survey of requirements

TASK 2.2 Forum development

TASK 2.3 Technical roadmap planning workshops

TASK 2.4 Development of a technical roadmap

TASK 2.5 Review of wider context

Work Package 3: Support of scientific applications

The applications selected at the time of submission of EUAsiaGrid proposal belong to the following fields: high energy physics, computational chemistry, mitigation of natural disasters, bioinformatics and biomedics and social science applications.

TASK3.1 EGEE applications support (M1-M24)

TASK3.2 Collection of specification and requirements of the regional applications (M1-M8)

TASK3.3 Promoting new applications (M8-M24)

Work Package 4: Dissemination

This WP will spread the word about the benefits of using the EGEE infrastructure and services to both existing and new user communities. For most communities the first contact with EUAsiaGrid and EGEE will be through the dissemination activities. Therefore the outcome of the overall project will depend much on the dynamism and perseverance of the dissemination team and also on the quality and effectiveness of the actions to be taken.

TASK 4.1 Production of dissemination materials

TASK 4.2 Websites

TASK 4.3 Events organization

Work Package 5: Training

Training is of strategic importance to introduce state of the art grid technologies and services to an international community of users covering a broad range of scientific areas. Training events will provide the required knowledge to interested users, enabling them to explore the use of these new technologies in their scientific applications. They will also contribute to further disseminating the project outputs and to advertise the benefits of grid technologies because trainees can also act themselves as further dissemination vectors within their communities.

TASK 5.1 Production of training materials

TASK 5.2 Training event scheduling and organization



7.0 Acknowledgment

Dr. Fabian Dayrit, Dr. Luis Sarmenta, Dr. Pablo Manalastas, Dr. Nathaniel Libatique, Dr. Gregorio Tangonan, Dr. John Paul Vergara, Dr. Reginald Marcelo, Dr. Ma. Mercedes Rodrigo, Mr. Allan Espinosa, Mr. Rod Michael Coronel

Office of the President, Ateneo de Manila University

Office of the Vice-President for Loyola Schools, Ateneo de Manila University

School of Science and Engineering, Ateneo de Manila University

CHED COE Mathematics Fund (Commission on Higher Education Center of Excellence Program)

Deparment of Mathematics, Ateneo de Manila University

Department of Information Systems, Communications and Computer Science (DISCS), Ateneo de Manila University

Electronics, Communications and Computer Engineering Department, Ateneo de Manila University

ICT-Asia Program of the French Government

Embassy of France in the Philippines

European Commission FP7 ICT Program

German Ministry of Education

Department of Science and Education (DOST)

Medical Grid Project

Onco-Media Project

Philppine e-Science Grid Project

PAND Grid Project

EUAsiaGrid Project

GSI Darmstadt and Dr. Kilian Schwarz


8.0 Selected References (Partial List):

Medical Grid Project

Ontology for fMRI as a Biomedical Informatics MethodToshiharu Nakai, Epifanio Bagarinao, Yoshio Tanaka, Kayako Matsuo, and Daniel RacoceanuMagn Reson Med Sci 7 (2008) 141-155


Enabling the Sharing of Functional MRI Datasets with BAXSQL [poster, pdf (203kb)]Bagarinao E, Tanaka Y, Matsuo K, Nakai T, 14th Annual Meeting of Organization for Human Brain Mapping, NeuroImage 41, S1-142, 2008BAX: A Toolbox for the Dynamic Analysis of Functional MRI DatasetsBagarinao E, Matsuo K, Nakai T, and Tanaka YNeuroinformatics 6, 109-115, 2008

Medical Grid: Using Grid Technology for Brain StudiesBagarinao E, Nakai T, and Tanaka YPhilippine Information Technology Journal 1, 3-7, 2008

Enabling On-Demand Real-Time Functional MRI Analysis Using Grid TechnologyE. Bagarinao, K. Matsuo, Y. Tanaka, L.F.G. Sarmenta, and T. NakaiMethods of Information in Medicine 44, 665-673, 2005

The Application of Grid Computing to Real-Time Functional MRI AnalysisE. Bagarinao, L. Sarmenta, Y. Tanaka, K. Matsuo, and T. NakaiLecture Notes in Computer Science (Springer-Verlag) 3358, 290-302, 2004

The Medical Grid Project: Bridging the Computational Gap in Functional MRI AnalysisE. Bagarinao, L. Sarmenta, Y. Tanaka, K. Matsuo and T. NakaiProceedings of the 32nd Conference of the Japan Society of Magnetic Resonance in Medicine, Otsu City, Shiga Prefecture, Japan, September 16 - 18, 2004

Real-Time Functional MRI Analysis Using Grid Computing [poster, pdf (445kb)]

E. Bagarinao, L. Sarmenta, Y. Tanaka, K. Matsuo, and T. Nakai7th International Conference on High Performance Computing and Grid in Asia Pacific Region, Omiya Sonic City, Tokyo Area, Japan, July 20 – 22, 2004


Real-time fMRI on Grid. Epifanio Bagarinao.Philippine-Japan Symposium on the Medical Applications of Grid Technology, Metro Manila, Philippines, Feb. 16, 2004


Grid Computing and XML Web Services.Luis F.G. Sarmenta. Philippine-Japan Symposium on the Medical Applications of Grid Technology, Metro Manila, Philippines, Feb. 16, 2004


The Application of Grid Computing to Real-Time Functional MRI AnalysisE. Bagarinao, L. Sarmenta, Y. Tanaka, K. Matsuo, and T. NakaiLecture Notes in Computer Science (Springer-Verlag) 3358, 290-302, 2004


The Medical Grid Project: Bridging the Computational Gap in Functional MRI AnalysisE. Bagarinao, L. Sarmenta, Y. Tanaka, K. Matsuo and T. NakaiProceedings of the 32nd Conference of the Japan Society of Magnetic Resonance in Medicine, Otsu City, Shiga Prefecture, Japan, September 16 - 18, 2004

Enabling On-Demand Real-Time Functional MRI Analysis Using Grid TechnologyE. Bagarinao, K. Matsuo, Y. Tanaka, L.F.G. Sarmenta, and T. NakaiMethods of Information in Medicine 44, 665-673, 2005

Real-time fMRI on GridEpifanio BagarinaoPhilippine-Japan Symposium on the Medical Applications of Grid Technology, Metro Manila, Philippines, Feb. 16, 2004

Onco-Media Project:

SFBI’06 - First Singaporean-French Biomedical Imaging Workshop,12-13 October 2006, Biopolis, Singapore
Co-organizers Hugues Benoit Cattin (CREATIS) and Daniel Racoceanu (IPAL).
Strong implications of the Singaporean Bioimaging Consortium (SBIC) - Biopolis, into the organization of the workshop.
6 publications in SFBI’07 Proceedings, involving ONCO-MEDIA partners [schedule & papers]

• AIRS 2006 – Asian Information Retrieval Symposium, 18 Oct. 2006,Singapore
Organizer – Daniel Racoceanu (IPAL) [schedule, abstract]
3 publications issued in Lecture Notes for Computer Science (LNCS)· Bo Qiu, Daniel Racoceanu, Chang Sheng Xu, Qi Tian, Stripe: Image Feature Based on a New Grid Method and Its Application in ImageCLEF, Lecture Notes in Computer Science, Springer Berlin/Heidelberg, H.T. Ng et al. (Eds.): Asian Information Retrieval Symposium, Singapore 16-18 Oct. 2006, Volume 4182/2006, ISSN 0302-9743, ISBN 978-3-540-45780-0, pp. 489-496. [pdf]

· Henning Muller, Joris Heuberger, Adrien Depeursinge, Antoine Geissbuhler, Automated Object Extraction for Medical Image Retrieval Using the Insight Toolkit (ITK), Lecture Notes in Computer Science, Springer Berlin/Heidelberg, H.T. Ng et al. (Eds.): Asian Information Retrieval Symposium, Singapore 16-18 Oct. 2006, Volume 4182/2006, ISSN 0302-9743, ISBN 978-3-540-45780-0, pp. 476–488. [pdf]

· Daniel Racoceanu, Caroline Lacoste, Roxana Teodorescu and Nicolas Vuillemenot, A Semantic Fusion Approach Between Medical Images and Reports Using UMLS, Lecture Notes in Computer Science, Springer Berlin/Heidelberg, H.T. Ng et al. (Eds.): Asian Information Retrieval Symposium, Singapore 16-18 Oct. 2006, Volume 4182/2006, ISSN 0302-9743, ISBN 978-3-540-45780-0, pp. 460–475. [pdf]
2 invited talks – partners from ONCO-MEDIA

• HealthGrid 2007 Conference, 24-27 April 2007, Geneva, Switzerland
Co-organizer – Henning Muller (Geneva University Hospital)
ONCO-MEDIA common publication - poster session : · ONCO-MEDIA consortium, The ONCO-MEDIA project challenges, HealthGrid 2007 Conference, Poster Session, 24-27 April 2007, Geneva, Switzerland [pdf]


• IEEE Healthcom 2007 Conference, June 19-22, 2007, Taipei, Taiwan
Co-organizer – Heng-Shuen Chen (National Taiwan University)
Prof. Toshiharu Nakai (NCGG, Japan) – invited speaker:

· Toshiharu Nakai, IEEE Healthcom 2007 (Keynote Lecture), International Convention Center, National Taiwan University Hospital, Taipei, Taiwan, June 22, 2007
A/Prof Wee-Kheng Leow (NUS/IPAL) – scientific committee

• AIST 2007 (National Institute of Advanced Industrial Science and Technology from Japan) - ONCO-MEDIA Workshop, 18-19 July 2007,Tsukuba, Japan
8 oral presentations [schedule & presentations]


• JAMIIT 2007 (Japanese Society of Medical Imaging Technology) Annual Meeting, 20th of July 2007, Tsukuba, Japan
4 oral presentations in ONCO-MEDIA—JAMIIT special session, 2 oral presentation in JAMIIT regular session
Publication of the 6 papers in JAMIIT proceedings [proceedings]

• Special Journal Issue in Medical Imaging Technology (MIT) [cover]
Special Issue of November 2007 - Ontology and Context Related Medical Image Distributed Intelligent Access - 6 journal publications:

· Patrick Brezillon, Daniel Racoceanu, A Context Model for Content Based Medical Image Retrieval, Medical Imaging Technology, Vol.25, No.5, November 2007, pp.327-332. [pdf]

· Mei-Ju Su, Heng-Shuen Chen, Chung-Yi Yang, Sao-Jie Chen, Robert Chen, Wen-Jeng Lee, Po-Hsun Chen, Ping-Kung Yip, Hon-Mon Liu, Fei-Pei Lai, Daniel Racoceanu, Diagnostic Decision Support by Intelligent Medical Image Retrieval with Electrical Medical Record Enhance Dementia Treatment, Medical Imaging Technology, Vol.25, No.5, November 2007, pp.350-355. [pdf]

· Johan Montagnat,Tristan Glatard, Diane Lingrand, Texture-based Medical Image Indexing and Retrieval on Grids, Medical Imaging Technology, Vol.25, No.5, November 2007, pp.333-338. [pdf]

· Yoshio Tanaka,Status and Future Direction of Grid Computing, Medical Imaging Technology, Vol.25, No.5, November 2007, pp.339-343. [pdf]

· Epifanio Bagarinao, Yoshio Tanaka, Toshiharu Nakai, Building Grid-Based Applications for the Management and Analysis of Neuroimaging Data Sets for the Medical Grid, Medical Imaging Technology, Vol.25, No.5, November 2007, pp.344-349. [pdf]

· Asmâa Hidki, Adrien Depeursinge, Henning Muller, The MedGIFT project: Global perspectives of a medical doctor, Medical Imaging Technology, Vol.25, No.5, November 2007, pp.356-361. [pdf]


· Roxana Teodorescu, Daniel Racoceanu, Wee-Kheng Leow and Vladimir Cretu, Prospective Study for Semantic Inter-Media Fusion in Content-Based medical Image Retrieval, original paper, Medical Imaging Technology, Vol.26, No.1, January 2008, pp.1-11. [pdf]


• MIST 2007 (International Medical Informatics Symposium in Taiwan) – ONCO-MEDIA workshop, Hualien-Taipei, Wan-Fang Hospital, Taipei, Taiwan, 19th of November 2007
6 presentations :

· Toshiharu Nakai, Kayako Matsuo, Epifanio Bagarinao, Data Management for Neuroimaging in Medical GRID, ONCO-MEDIA - MIST 2007 workshop, Hualien-Taipei, Wan-Fang Hospital, Taipei, Taiwan, November 15-19, 2007. [slides]

· Rafael Saldaña, A Web-Based Query and Retrieval System of Federated DICOM Image Archives, ONCO-MEDIA - MIST 2007 workshop,Hualien-Taipei, Wan-Fang Hospital, Taipei, Taiwan, November 15-19, 2007. [slides]

· Mei-Ju Su, Heng-Shuen Chen, Hon-Mon Liu, Ping-Keung Yip, Wen-Yih I. Tseng, Diagnostic Decision Support by Intelligent Medical Image Retrieval with Electronic Medical Record for Dementia Treatment Enhancement, ONCO-MEDIA - MIST 2007 workshop, Hualien-Taipei, Wan-Fang Hospital, Taipei, Taiwan, November 15-19, 2007. [slides]

· Patrick Brezillon, Daniel Racoceanu, Contextual Approach in Image Processing. Application to cerebral MRI, ICT ONCO-MEDIA - MIST 2007 workshop, Hualien-Taipei, Wan-Fang Hospital, Taipei, Taiwan, November 15-19, 2007. [slides]

· Daniel Racoceanu, Jean-Romain Dalle, Bo Qiu, Ling-Ling Chan, Wee-Kheng Leow, Joo-Hwee Lim and Judy Tan Sock Pheng, Knowledge Based Approach for Stroke Diagnosis , ONCO-MEDIA – MIST’2007 workshop, International Medical Informatics Symposium in Taiwan, Hualien-Taipei, Wan-Fang Hospital, Taipei, Taiwan, November 15-19, 2007.

· Wee-Kheng Leow, MMedWeb (Multimedia Medical Conceptual Web for Intelligent Information Access) SERC-A*STAR project, ONCO-MEDIA – MIST’2007 workshop, International Medical Informatics Symposium in Taiwan, Hualien-Taipei, Wan-Fang Hospital, Taipei, Taiwan, November 15-19, 2007.


• 5th ICT ASIA Seminar, Taipei, Taiwan, 19-22 November 2007
2 presentations of ONCO-MEDIA partners

· Heng-Shuen Chen, From Rural Telemedicine to National Health Informatics Project -Taiwan Experience, 5th ICT-Asia Regional Seminar, Taipei, Taiwan, Nov 19-21, 2007. [slides]

· Rafael Saldaña, Medical Image Analysis and Information Retrieval with Grid Computing Applications, 5th ICT-Asia Regional Seminar, Taipei, Taiwan, Nov 19-21, 2007. [slides]

• BMEI2008, International Conference on BioMedical Engineering and Informatics, 27 - 30 May 2008, Sanya, Hainan, China

· Adina Eunice Tutac, Daniel Racoceanu, Thomas Putti, Wei Xiong, Wee-Kheng Leow, Vladimir Cretu, Knowledge-Guided Semantic Indexing of Breast Cancer Histopathology Images, BioMedical Engineering and Informatics : New Development and the Future, Proceedings of the First International Conference on BioMedical Engineering and Informatics, Editors : Yonghong Peng and Yufeng Zhang, Published by IEEE Computer Society, 27 - 30 May 2008, Sanya, Hainan, China, pp. 107-112. [pdf]


• ICT4Health, First International Symposium on ICT For Health, February 29th-1st March 2008, Ateneo de Manila University, Manila, Philippines (program)

· D. Racoceanu, Medical Image/Case Based Reasoning using Medical Knowledge to improve Diagnosis Assistance. Showcases: Early Diagnosis of Brain stroke from brain CT, Ultrasound Guided Biopsy for Breast Cancer Diagnosis, First International Symposium on ICT for Health (ICT4Health 2008), Keynote Lecture, February 29th-1st March 2008, Ateneo de Manila University, Manila, Philippines.

· Jiang Liu, Joo Hwee Lim, Daniel Racoceanu, Wong Wing Kee Damon, Huiqi Li, Leaking detection for Medical image segmentation, First International Symposium on ICT For Health (ICT4Health 2008), February 29th-1st March 2008, Ateneo de Manila University, Manila, Philippines.

· Sorina Camarasu, Hugues Benoit-Cattin, Johan Montagnat, Daniel Racoceanu, Content-Based Medical Image Indexing and Retrieval on Grids, First International Symposium on ICT For Health (ICT4Health 2008), February 29th-1st March 2008, Ateneo de Manila University, Manila, Philippines.

· Patrick Brezillion, Medical Context , First International Symposium on ICT For Health (ICT4Health 2008), February 29th-1st March 2008, Ateneo de Manila University, Manila, Philippines.

· Andrei Coronel and Rafael Saldaña, Towards a Philippine Cancer Grid, First International Symposium on ICT For Health (ICT4Health 2008), February 29th-1st March 2008, Ateneo de Manila University, Manila, Philippines.

· Jean-Romain Dalle, Daniel Racoceanu, Wee-Kheng Leow, and Thomas Putti, Contribution to Automated Breast Cancer Grading on Hispatological Images

· Dianne Lingrand, Johan Montagnat and Tristan Glatard, Estimation of Latency on Production Grid Over Several Weeks

· Epifanio Bagarinao, Toshiharu Nakai, and Yoshio Tanaka, Medical Grid: Using Grid Technology for Brain Studies

· Xin Zhou, Mikko Pitkanen, Adrien Depeursinge, and Henning Muller, A Medical Image Retrieval Application Using Grid Technologies To Speed Up Feature Extraction

• ISGC 2008—International Symposium on Grid Computing, Academia Sinica, Taipei, Taiwan, 7-11 April 2008.

· Rafael P. SALDAÑA, Grid Computing for Health and the Environment: Experiences and Perspectives in the Philippines, Invited speaker, International Symposium on Grid Computing , Academia Sinica, Taipei, Taiwan, 7-11 April 2008.

• PITJ - Philipines Information Technology Journal
ONCO-MEDIA special issue

· Sorina Camarasu, Hugues Benoit-Cattin, Johan Montagnat, Daniel Racoceanu, Grids for Content-based Medical Image Indexing and Retrieval (in reviewing process)

· Jiang Liu, Joo Hwee Lim, Daniel Racoceanu, Wong Wing Kee Damon, Huiqi Li, Leaking detection for Medical image segmentation (in reviewing process)


· Epifano Bagarinao, Toshiharu Nakai, Yoshio Tanaka, Medical Grid Technologies for Brain Studies, Philipines Information Technology Journal, vol. 1, no. 1, February 2008.

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1 comment:

arron said...

With the local government pumping in a lot of money into Singapore's medical industry, I feel that singapore hospitals are very good now. Top notch service with speedy service time.