ࡱ> 6859 "bjbj"0l4 4 4 4 @ $Cp p p p p p p p $ Bp p p p p  p p  p vp p  p   p d E٭c.4 0C[ [ GGF7 Tokyo 5th March 2003 Minutes from the Life Science Workshop Draft 1.0 Piotr Bala Session 1: Overview 9:00-10:30 Life Sciences Workshop has been opened by Peter Arzberger who gave overview of Workshop. He introduced Abbas Farazdel the chairmen of Life Sciences Research Group (LSRG) and workshop organizer. Abbas Farazdel presented history and achievements of the LSRG (presentation). Abbas presented and comment agenda of LSWS for GGF7. He encouraged participants to provide ideas for Open Session discussions. He presented call for papers for New Generation Computing. A special issue will be dedicated for LSWS papers. The deadline for submissions is May, 31st 2003. Papers will be reviewed. Comment from the participants: The LSRG survey do not capture research in the grids for life sciences. Abbas replied that this will be taken into account. Rick Stevens commented that GGF RG should go towards standards proposal for the community. This should be goal of this RG. Rick Stevens presentation: Biology and Grids (presentation). Rick presented current status of biology and its needs in terms of computing. The requirement for new way of thinking in biology, especially system biology. This also challenges RG to define standards and interfaces allowing application to use grids. Mark Ellisman via AccessGrid: Update on the Brain (presentation). Mark presented Biomedical Informatics Research Network build on top on NPACI infrastructure. The challenges in the image storage and image analysis has been presented. Abbas asked Mark which particular grid technology needs to be developed. Mark answered that we are challenging every bit of grid technology. Especially we need on-demand computing which is not well handled by the supercomputer centers. The security model is another important area. Qestion from the participants: Are there accounting issues important? Mark answered that the existing cost issues in HPC do not attract new communities. Peter Arzberger thanked all speakers and participants and summarized session. Session 2: BioGrid Initiatives 11:00-12:10 Session chaired by Larry Ang. Vincent Breton: Biomedical grid initiatives in Europe. (presentation). Vincent presented biomedical applications in the DataGrid project. He presented the European vision for crating HealthGrid a grid for health related research. John Broke asked how DataGrid broker fits to the other broker initiatives. Vincent replied that he sees role of GGF to establish standards for all development. Such standards will be adopted by DataGrid as well. Virinder Batra: North Carolina BioGRID: Challenges in Grid Deployment and Application Enablement (presentation). Virinder described infrastructure of the NCBioGRID, software used and main design criteria. Question from the participants: What are you using for webservices. Virinder answered that they use WebSphere. Than he was asked how NCBioGRID deals with complicated parameters. Virinder answered that this is problem which occurred and that they are working in this direction. Piotr Bala: EUROGRID and GRIP grid development for biomolecular biology. Piotr presented UNICORE architecture and its deployment in the EUROGRID project. Special attention was dedicated to the development of the application specific interfaces within UNICORE framework. Question from the participants was asked about resource broker model. Piotr answered that this is present in EUROGRID project and dedicated resource broker is being developed. The key person involved in this activity is John Broke from Manchester University present at this session and he can provide more details. John provided participants with more details on broker design and functionality. Larry Ang closed the session. Session 3: Portals and workflows 14:00-15:40 Session chaired by Akihiko Konyagaya Konyagaya Akihiko: OBIGrid (presentation) Akihiko presented development of tools for grid, especially for integration of databases. Rick Stevens asked question what is most important unsolved problem. Akihiko answered that the most important problem is how to use servers. Question from the participants: Have you been able to scale application to the grid level? Akihiko answered that they were started design to extend application to use more than on PC cluster however main work is based on the legacy code, some of them can run on the single cluster. Hideaki Sugawara: Web services and genome annotation (presentation) Heidaki presented DDBJ who is a partner of EMBL and GenBank in creation of gene repository. Mission of DDBJ is to integrate diverse database resources. The XML/SOAP technology is used to develop web access to the databases. Karpjoo Jeong: A Workflow and Grid Computing Systems for Molecular Simulation based Experiments. (presentation) Karpioo presented work based on legacy simulation packages. The typical job scenarios has been defined and adopted to the grid architecture. Abbas asked if they used parallel version of Charmm or Gaussian. Karpjoo: answered that they did not care on the parallelization of the application. Parallel task is treated as single application. Akihiko Konyogaya asked what about scalability of presented approach with the number of users? Karpjoo replied that current model is based on the pear-pear connections end the do not see any scalability problems there. Mark A. Miller: Encyclopedia of Life. (presentation) Mark presented The Encyclopedia of Life This is the computation intensive project to annotate genetic data. The biggest hump is establishing resource access. Question from the audience What are requirements for the tool? Mark answered that they were scripting everything together and typical scripting languages are used such as perl or python. Wilfred Li and Atif Shahab: iGAP Integrated Grid-enabled Genome Annotation Pipeline. (presentation) Wilfred and Atif presented iGAP which is a system based on the globus middleware. Question form the participants was asked if the globus MDS were inadequate? Atif replied that the main problem were that people do not publish services in MDS. Globus had such functionality, but people were not using it. After this talk session was closed. Session 4: Portals and workflows 16:00-17:30 Session chaired by Peter Arzberger Andrew C. Jones: Facilitating access to biological information with a global catalogue of life. (presentation) Andrew described Species 2000 vision to annotate living species. SPICE for Species 2000 allows to get information with the query based on the synonymous search. Question asked:What do you think of systems like Globus being used to implement such systems. Andrew answered that there was first implementation based on the Globus 2.0. They are interested rather in OGSA and in providing SPICE as grid service. Question was asked what do they mean by webservice and how it would be working. Andrew replied that the SPICE would execute set of commands. Authors did not think on providing database itself. Alex Gray: BiodiversityWorld: a GRID based problem solving environment for global diversity. (presentation). Alex presented problems of the Biodiversity a solution they took to provide user with access to the various data based on the access to the distributed databases of different kind and origin. Peter Arzberger: Pacific Rim Application and Grid Middleware Assembly and the National Biomedical Computation Resource (presentation) Peter presented global vision on the various activities SDSC is involved. He clearly stressed out that we really need to integrate knowledge and integrate people. Session was concluded by Abbas Farazdel. He pointed out Open Sessions which will take place next day and invited everyone to participate. Notes taken by Piotr Bala. \|CQ ? j"5\mH sH  H*mH sH  >*mH sH mH sH CD[\|}BC1f!  a T ( o   ? @ _ "_ ` K !"UH2PQxyyx@SfDEij, =! &dP=!!!m"n"o""""" &dP 1h. A!"#$% iB@B StandardowyCJ_HaJmHsHtH:@: NagBwek 1$@& >*mH sH BA@B Domy[lna czcionka akapitu0CD[\|}BC1f!a T(o?@_`K ! 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