1. Cooperative experiments in VL-e: from scientific workflows to knowledge sharing Z.Zhao (1) V. Guevara( 1) A. Wibisono(1) A. Belloum(1) M. Bubak(1,2) B. Hertzberger(1) (1) Informatics Institute, University of Amsterdam, The Netherlands (2) Institute of Computer Science AGH, Krakow, Poland Bioinformatics use case Complex Scientific experiments Complex scientific experiments involve distributed scientific data and resources, and are often shared among scientists from different domains. Cooperative experiments involve not only coordination of resources and computing processes, but also the sharing and transfer of knowledge among scientists. Support for Cooperative experiments has become, an important requirement for the e- Science middleware. Semantic technologies enhance the storage and query of Grid resources and the high level searching and matching between different resources. Discussion We can clearly see the importance for supporting cooperative experiments in e-Science; the tools developed in the VL-e project are towards this direction. Compared to the web 2 based cooperative environments, such as myExperiment, VL-e tools have clear focus on the runtime issues of the workflow, which makes the VL-e tools complementary with these web 2 environments. Currently, there are close discussion going between VL-e and the MyExperiment society, such as proposing WSVLAM workflows as new workflow types which are shared between scientists, and making workflow bus as generic execution interface for different workflows shared over MyExperiment environment. The Virtual resource Browser (VBrowser) offers scientists an environment in which they can: interactively access resources to manipulate data (upload, download, search, annotate, and view), start applications and monitor resources access data files stored in different security domains, file systems, and protocols, including the Storage Resource Broker (SRB), Grid-FTP, SSH, and web services. The Framework for Interactive Parameter Sweep (FRIPS) aims to support: interactive execution of applications monitoring of the experiment execution, viewing intermediate results, changing parameter ranges and setting new policies. The WS-VLAM is a workflow system to coordinate the execution of distributed Grid-enabled software components. Developed following the OGSA/WSRF standard Provides a client-side applications allowing scientists to design and monitor the execution of the workflows. Provides server-side applications, including a workflow engine that schedules and executes the workflow on the Grid. (4) Publication and sharing After the successful execution of the application workflow, the workflow components are: semantically annotated stored in a shared repository The workflow components are available to all scientists in the VL-e project and other worldwide via a web application (HAMMER) allowing to: query and download description of the workflow components to the user space so they can create new version of the application workflow. (4) Publication and sharing After the successful execution of the application workflow, the workflow components are: semantically annotated stored in a shared repository The workflow components are available to all scientists in the VL-e project and other worldwide via a web application (HAMMER) allowing to: query and download description of the workflow components to the user space so they can create new version of the application workflow. (1) Problem investigation To perform /in silico /experimentation with genomics data, biologists need tools to process and compare datasets and explore the obtained results interactively. The traditional program used to identify RIDGEs in transcriptome maps: take hours to run in a typical desktop computer, lacks the versatility needed for interactive and explorative analysis (2) Experiment Prototyping A modular and generalized version of the original program is first developed and executed across grid-enabled resources. Workflow templates are created and ready to use. (1) Problem investigation To perform /in silico /experimentation with genomics data, biologists need tools to process and compare datasets and explore the obtained results interactively. The traditional program used to identify RIDGEs in transcriptome maps: take hours to run in a typical desktop computer, lacks the versatility needed for interactive and explorative analysis (2) Experiment Prototyping A modular and generalized version of the original program is first developed and executed across grid-enabled resources. Workflow templates are created and ready to use. (3) Experiment execution Scientist use the workflow template to perform the experiment on grid-enabled resources, details of this complex infrastructure is hidden through the use of: the resource browser is used to browser distributed storage resources to select the appropriate data sets. an intuitive workflow composer is used to parameterize and extend variants of the workflows.. (3) Experiment execution Scientist use the workflow template to perform the experiment on grid-enabled resources, details of this complex infrastructure is hidden through the use of: the resource browser is used to browser distributed storage resources to select the appropriate data sets. an intuitive workflow composer is used to parameterize and extend variants of the workflows.. VL-e Approach The mission of the Dutch Virtual Laboratory for e-Science project is to provide generic functionalities that support a wide class of specific e-Science application environments. A set of tools are being developed for: modeling and managing workflow templates browsing resources composing and executing workflows on Grid-enabled resources supporting workflow interoperability. Key phases in the lifecycle of a scientific experiment The development of a scientific experiment has different activities performed at different periods of time. These activities can be grouped in a general lifecycle with four phases: problem investigation experiment prototyping experiment execution results publication The VLE-WFBus provides interface to wrap and integrate legacy scientific workflows. Provides tools to recognize different workflow descriptions, Describe the meta information according to a predefined schema. Launch workflows, and monitor its execution. Contacts: zhiming Zhao, e-mail: z.zhao@uva.nl Problem investigation: Look for relevant problems Browse available tools Define the goal Decompose into steps Experiment Prototyping Design experiment workflows Develop necessary components Experiment execution Execute experiment processes Control the execution Collect and analysis data Results Publication Annotate data Publish data Shared repositories Key tools for supporting the lifecycle of a scientific experiment This work was carried out in the context of the Virtual Laboratory for e-Science project. This project is supported by a BSIK grant from the Dutch Ministry of Education, Culture and Science (OC&W) and is part of the ICT innovation program of the Ministry of Economic Affairs (EZ). Project Leader : L.O. Hertzberger Phone: 020 525 7464 Fax: 020 525 74 90 e-mail: bob@science.uva.nl Related Links: http://www..vl-e.nl http://www.science.uva.nl /~gvlam/wsvlam http://www.science.uva.nl /~gvlam/wsvlam DNA micro-array experiment Micro-beam experiment Experimentation Environment Data Model Common aspects of an experiment Process and data flow in an experiment Annotations on an experiment Process Flow Template Grid accessible infra: apparatus, systems, network Information gathering ExperimentationInterpretation Access to devices Access to data Access to information In each of the phases of the lifecycle, support for cooperative interactions is required and we describe this support from three dimensions: information sharing communication coordination.