my Grid aims to develop high-level middleware to support an e-scientist in conducting in silico e... more my Grid aims to develop high-level middleware to support an e-scientist in conducting in silico ex- periments in biology. An important part of this is to define a conceptual space - the myGrid informa- tion model - where both biological data and experimental processes are modelled, with emphasis on the latter. As such, it defines the basic concepts through which different aspects of the e-science process are represented and linked. The information model provides shared data abstractions that underpin important service interactions and so promote synergy between myGrid components. This paper describes how the information model captures the e-science process, including the collection of data, experiments, provenance and annotation.
Proceedings of the 2009 Summer Computer Simulation Conference, Jul 13, 2009
... of Computer Engineering Middle East Technical University 06530 Ankara, TURKEY [email protected]... more ... of Computer Engineering Middle East Technical University 06530 Ankara, TURKEY [email protected] ... SiMA builds upon a specialized and extended form of DEVS formalism, namely SiMA-DEVS, which: 1 – Formalizes the notion of “port types” leading to a strongly ...
The Grid is an emerging infrastructure that supports the discovery, access and use of distributed... more The Grid is an emerging infrastructure that supports the discovery, access and use of distributed computational resources. The emergence of a serviceoriented view of hardware and software resources on the grid raises the question as to how database management systems and technologies can best be deployed or adapted for use in such an environment. We argue that distributed query processing (DQP) can provide effective declarative support for service orchestration, and we describe an approach to service-based DQP (OGSA-DQP) on the Grid that supports queries over Grid Data Services (GDS)s provided by OGSA-DAI project, and over other services available on the Grid, thereby combining data access with analysis; uses the facilities of the OGSA to dynamically obtain the resources necessary for efficient evaluation of a distributed query; adapts techniques from parallel databases to provide implicit parallelism for complex data-intensive requests; and uses the emerging standard for GDSs to provide consistent access to database metadata and to interact with databases on the Grid. The service-based Distributed Query Processor is itself cast as a service referred to here as Grid Distributed Query Service (GDQS). In addition, OGSA-DQP employs another service for query evaluation referred to here as Grid Query Evaluation Service (GQES). As such, OGSA-DQP implements a service orchestration framework in two sense: both in terms of the way its internal architecture handles the construction and execution of distributed query plans and in terms of being able to query over data and analysis resources made available as services.
... Andrzej Najgebauer. Pages: 285 - 287. Development of a Small Tactical Simulation. Kresimir Co... more ... Andrzej Najgebauer. Pages: 285 - 287. Development of a Small Tactical Simulation. Kresimir Cosic, Imre Balogh, Drazen Penzar, Neven Sosteric, Sasa Bistrovic, Jadranka Jukic, Igor Korzinek, Ante Modric, Damir Poles, Ognjen Skunca. Pages: 288 - 292. ...
An approach to arrangement of component responsibilities in a component-based software system is ... more An approach to arrangement of component responsibilities in a component-based software system is proposed, in which black-box components constitute the major building blocks and perform the main part of computation while whitebox adapter components enhance their interoperability. We recommend a technique in which components contribute to the construction of the adapters in a structured way. A component supplies one or
Service-based approaches (such as Web Services and theOpen Grid Services Architecture) have gaine... more Service-based approaches (such as Web Services and theOpen Grid Services Architecture) have gained considerable attention recentlyfor supporting distributed application development in e-businessand e-science. The emergence of a service-oriented view of hardware andsoftware resources raises the question as to how database managementsystems and technologies can best be deployed or adapted for use insuch an environment. This paper explores one aspect of service-basedcomputing and data ...
Composition of DEVS models in heterogenous environments requires resolutions for manifold incompa... more Composition of DEVS models in heterogenous environments requires resolutions for manifold incompatibilities including data type and time resolution mismatch. This paper proposes a solution for implementing DEVS simulations in heterogenous environments with the help of connectors in the sense of component based software engineering. Our solution involves implementing connectors as atomic models to be used in mediation of data type and time resolution mismatches. Employing atomic models as connectors allows connector composition in the style of Reo and promotes higher level of reuse in simulation construction. In this paper we describe our solution formally and present a case study to demonstrate its application.
The Journal of Defense Modeling and Simulation: Applications, Methodology, Technology, 2012
In this paper we briefly present our views on composability of models and interoperation of simul... more In this paper we briefly present our views on composability of models and interoperation of simulations; we introduce our simulation software framework, namely Simulation Modelling Architecture (SiMA), and we present our contributions to the underlying formal model (i.e. discrete event system specification). We also present our simulation construction environment, which supports composability of simulation models through a simulation construction tool
OGSA-DQP is a distributed query processor exposed to users as an Open Grid Services Architecture ... more OGSA-DQP is a distributed query processor exposed to users as an Open Grid Services Architecture (OGSA)-compliant Grid service. This service supports the compilation and evaluation of queries that combine data obtained from multiple services on the Grid, including Grid Database Services (GDSs) and computational web services. Not only does OGSA-DQP support integrated access to multiple Grid services, it is itself implemented as a collection of interacting Grid services. OGSA-DQP illustrates how Grid service orchestrations can be used to perform complex, data-intensive parallel computations. The OGSA-DQP prototype is downloadable from www.ogsadai.org.uk/dqp/. This demonstration aims to illustrate the capabilities of OGSA-DQP prototype via a GUI Client over a collection of bioinformatics databases and analysis tools.
The data management problems in grid computing are often challenging in many aspects such as data... more The data management problems in grid computing are often challenging in many aspects such as data volumes, heterogeneity, structural complexity and semantic content. Thus, e-Scientists and scientific application developers stand to benefit from tools and environments that either hide, or help to manage, the inherent complexity involved in accessing and making concerted use of the diverse resources. This paper describes OGSA-DQP, a high level data integration tool for service-based grids, and illustrates how it can be used to support grid users, via an example scientific study in bioinformatics. The paper also discusses various options for employing OGSA-DQP to handle data integration tasks as service orchestrations involving both data and analysis services.
OGSA-DQP is an open source service-based Distributed Query Processor; as such, it supports the ev... more OGSA-DQP is an open source service-based Distributed Query Processor; as such, it supports the evaluation of queries over collections of potentially remote data access and analysis services. As it operates over several layers of service-oriented infrastructure, one particular need (both among the developer team and the relevant community) has been to investigate the impact of the infrastructure layers, understand performance issues, identify bottlenecks and improve the response times of queries where possible. This paper conveys experiences gained in doing so, by describing the experiments carried out and presenting the results obtained. <currentRow> <columnValue>YAL037W</columnValue> <columnValue>GO:0000004</columnValue> </currentRow>
CCGrid 2003. 3rd IEEE/ACM International Symposium on Cluster Computing and the Grid, 2003. Proceedings., 2003
MyGrid is an e-Science Grid project that aims to help biologists and bioinformaticians to perform... more MyGrid is an e-Science Grid project that aims to help biologists and bioinformaticians to perform workflow-based in silico experiments, and help them to automate the management of such workflows through personalisation, notification of change and publication of experiments. In this paper, we describe the architecture of myGrid and how it will be used by the scientist. We then show how myGrid can benefit from agents technologies. We have identified three key uses of agent technologies in myGrid: user agents, able to customize and personalise data, agent communication languages offering a generic and portable communication medium, and negotiation allowing multiple distributed entities to reach service level agreements.
e-Scientists stand to benefit from tools and environments that either hide, or help to manage, th... more e-Scientists stand to benefit from tools and environments that either hide, or help to manage, the inherent complexity involved in accessing and making concerted use of the diverse resources that might be used as part of an in silico experiment. This paper illustrates the benefits that derive from the provision of integrated access to contextual information that links the phases of a problem-solving activity, so that the steps of a solution do not happen in isolation, but rather as the components of a coherent whole. Experiences with myGrid workflow execution environment (Taverna) are presented, where an information model provides the conceptual basis for contextualisation. This information model describes key characteristics that are shared by many e-Science activities, and is used both to organise the scientist's personal data resources, and to support data sharing and capture within the myGrid environment.
In this paper we introduce a framework for parallel and distributed execution of simulations (Sim... more In this paper we introduce a framework for parallel and distributed execution of simulations (Sim-PETEK), a middleware for minimizing the total run time of batch runs and Monte Carlo trials. Sim-PETEK proposes a generic solution for applications in the simulation domain, which improves on our previous work done to parallelize simulation runs in a single node, multiple central processing unit (CPU) setting. Our new framework aims at managing a heterogeneous computational resource pool consisting of multiple CPU nodes distributed on a potentially geographically dispersed network, through a service-oriented middleware layer that is compliant to Web Services Resource Framework standard, thereby providing a scalable and flexible architecture for simulation software developers. What differentiates Sim-PETEK from a general-purpose, Grid-based job-distribution middleware is a number of simulation-specific aspects regarding the specification, distribution, monitoring, result collection and aggregation of simulation runs. These aspects are prevalent in the structure of the messages and in the protocol of interaction both among the constituent services of the framework and within the interfaces exposed to the external clients.
ABSTRACT This paper proposes a software engineering solution for implementing simulations via the... more ABSTRACT This paper proposes a software engineering solution for implementing simulations via the composition of models at different resolution levels with the help of formal methods. Our solution provides a systematic methodology that offers a well-defined sequence of stages to obtain executable converters for entity resolution mapping, given the types of entity attributes that are exchanged at model interfaces and the mapping specifications. Our methodology uses Event-B as the formal specification language and Discrete Event System Specification as the model composition framework; utilizes refinement relations between Event-B machines for the specification, verification and generation of the data conversion steps between models and employs a code generator that inputs the Event-B machine definitions to generate converter code that connects two model ports.
my Grid aims to develop high-level middleware to support an e-scientist in conducting in silico e... more my Grid aims to develop high-level middleware to support an e-scientist in conducting in silico ex- periments in biology. An important part of this is to define a conceptual space - the myGrid informa- tion model - where both biological data and experimental processes are modelled, with emphasis on the latter. As such, it defines the basic concepts through which different aspects of the e-science process are represented and linked. The information model provides shared data abstractions that underpin important service interactions and so promote synergy between myGrid components. This paper describes how the information model captures the e-science process, including the collection of data, experiments, provenance and annotation.
Proceedings of the 2009 Summer Computer Simulation Conference, Jul 13, 2009
... of Computer Engineering Middle East Technical University 06530 Ankara, TURKEY [email protected]... more ... of Computer Engineering Middle East Technical University 06530 Ankara, TURKEY [email protected] ... SiMA builds upon a specialized and extended form of DEVS formalism, namely SiMA-DEVS, which: 1 – Formalizes the notion of “port types” leading to a strongly ...
The Grid is an emerging infrastructure that supports the discovery, access and use of distributed... more The Grid is an emerging infrastructure that supports the discovery, access and use of distributed computational resources. The emergence of a serviceoriented view of hardware and software resources on the grid raises the question as to how database management systems and technologies can best be deployed or adapted for use in such an environment. We argue that distributed query processing (DQP) can provide effective declarative support for service orchestration, and we describe an approach to service-based DQP (OGSA-DQP) on the Grid that supports queries over Grid Data Services (GDS)s provided by OGSA-DAI project, and over other services available on the Grid, thereby combining data access with analysis; uses the facilities of the OGSA to dynamically obtain the resources necessary for efficient evaluation of a distributed query; adapts techniques from parallel databases to provide implicit parallelism for complex data-intensive requests; and uses the emerging standard for GDSs to provide consistent access to database metadata and to interact with databases on the Grid. The service-based Distributed Query Processor is itself cast as a service referred to here as Grid Distributed Query Service (GDQS). In addition, OGSA-DQP employs another service for query evaluation referred to here as Grid Query Evaluation Service (GQES). As such, OGSA-DQP implements a service orchestration framework in two sense: both in terms of the way its internal architecture handles the construction and execution of distributed query plans and in terms of being able to query over data and analysis resources made available as services.
... Andrzej Najgebauer. Pages: 285 - 287. Development of a Small Tactical Simulation. Kresimir Co... more ... Andrzej Najgebauer. Pages: 285 - 287. Development of a Small Tactical Simulation. Kresimir Cosic, Imre Balogh, Drazen Penzar, Neven Sosteric, Sasa Bistrovic, Jadranka Jukic, Igor Korzinek, Ante Modric, Damir Poles, Ognjen Skunca. Pages: 288 - 292. ...
An approach to arrangement of component responsibilities in a component-based software system is ... more An approach to arrangement of component responsibilities in a component-based software system is proposed, in which black-box components constitute the major building blocks and perform the main part of computation while whitebox adapter components enhance their interoperability. We recommend a technique in which components contribute to the construction of the adapters in a structured way. A component supplies one or
Service-based approaches (such as Web Services and theOpen Grid Services Architecture) have gaine... more Service-based approaches (such as Web Services and theOpen Grid Services Architecture) have gained considerable attention recentlyfor supporting distributed application development in e-businessand e-science. The emergence of a service-oriented view of hardware andsoftware resources raises the question as to how database managementsystems and technologies can best be deployed or adapted for use insuch an environment. This paper explores one aspect of service-basedcomputing and data ...
Composition of DEVS models in heterogenous environments requires resolutions for manifold incompa... more Composition of DEVS models in heterogenous environments requires resolutions for manifold incompatibilities including data type and time resolution mismatch. This paper proposes a solution for implementing DEVS simulations in heterogenous environments with the help of connectors in the sense of component based software engineering. Our solution involves implementing connectors as atomic models to be used in mediation of data type and time resolution mismatches. Employing atomic models as connectors allows connector composition in the style of Reo and promotes higher level of reuse in simulation construction. In this paper we describe our solution formally and present a case study to demonstrate its application.
The Journal of Defense Modeling and Simulation: Applications, Methodology, Technology, 2012
In this paper we briefly present our views on composability of models and interoperation of simul... more In this paper we briefly present our views on composability of models and interoperation of simulations; we introduce our simulation software framework, namely Simulation Modelling Architecture (SiMA), and we present our contributions to the underlying formal model (i.e. discrete event system specification). We also present our simulation construction environment, which supports composability of simulation models through a simulation construction tool
OGSA-DQP is a distributed query processor exposed to users as an Open Grid Services Architecture ... more OGSA-DQP is a distributed query processor exposed to users as an Open Grid Services Architecture (OGSA)-compliant Grid service. This service supports the compilation and evaluation of queries that combine data obtained from multiple services on the Grid, including Grid Database Services (GDSs) and computational web services. Not only does OGSA-DQP support integrated access to multiple Grid services, it is itself implemented as a collection of interacting Grid services. OGSA-DQP illustrates how Grid service orchestrations can be used to perform complex, data-intensive parallel computations. The OGSA-DQP prototype is downloadable from www.ogsadai.org.uk/dqp/. This demonstration aims to illustrate the capabilities of OGSA-DQP prototype via a GUI Client over a collection of bioinformatics databases and analysis tools.
The data management problems in grid computing are often challenging in many aspects such as data... more The data management problems in grid computing are often challenging in many aspects such as data volumes, heterogeneity, structural complexity and semantic content. Thus, e-Scientists and scientific application developers stand to benefit from tools and environments that either hide, or help to manage, the inherent complexity involved in accessing and making concerted use of the diverse resources. This paper describes OGSA-DQP, a high level data integration tool for service-based grids, and illustrates how it can be used to support grid users, via an example scientific study in bioinformatics. The paper also discusses various options for employing OGSA-DQP to handle data integration tasks as service orchestrations involving both data and analysis services.
OGSA-DQP is an open source service-based Distributed Query Processor; as such, it supports the ev... more OGSA-DQP is an open source service-based Distributed Query Processor; as such, it supports the evaluation of queries over collections of potentially remote data access and analysis services. As it operates over several layers of service-oriented infrastructure, one particular need (both among the developer team and the relevant community) has been to investigate the impact of the infrastructure layers, understand performance issues, identify bottlenecks and improve the response times of queries where possible. This paper conveys experiences gained in doing so, by describing the experiments carried out and presenting the results obtained. <currentRow> <columnValue>YAL037W</columnValue> <columnValue>GO:0000004</columnValue> </currentRow>
CCGrid 2003. 3rd IEEE/ACM International Symposium on Cluster Computing and the Grid, 2003. Proceedings., 2003
MyGrid is an e-Science Grid project that aims to help biologists and bioinformaticians to perform... more MyGrid is an e-Science Grid project that aims to help biologists and bioinformaticians to perform workflow-based in silico experiments, and help them to automate the management of such workflows through personalisation, notification of change and publication of experiments. In this paper, we describe the architecture of myGrid and how it will be used by the scientist. We then show how myGrid can benefit from agents technologies. We have identified three key uses of agent technologies in myGrid: user agents, able to customize and personalise data, agent communication languages offering a generic and portable communication medium, and negotiation allowing multiple distributed entities to reach service level agreements.
e-Scientists stand to benefit from tools and environments that either hide, or help to manage, th... more e-Scientists stand to benefit from tools and environments that either hide, or help to manage, the inherent complexity involved in accessing and making concerted use of the diverse resources that might be used as part of an in silico experiment. This paper illustrates the benefits that derive from the provision of integrated access to contextual information that links the phases of a problem-solving activity, so that the steps of a solution do not happen in isolation, but rather as the components of a coherent whole. Experiences with myGrid workflow execution environment (Taverna) are presented, where an information model provides the conceptual basis for contextualisation. This information model describes key characteristics that are shared by many e-Science activities, and is used both to organise the scientist's personal data resources, and to support data sharing and capture within the myGrid environment.
In this paper we introduce a framework for parallel and distributed execution of simulations (Sim... more In this paper we introduce a framework for parallel and distributed execution of simulations (Sim-PETEK), a middleware for minimizing the total run time of batch runs and Monte Carlo trials. Sim-PETEK proposes a generic solution for applications in the simulation domain, which improves on our previous work done to parallelize simulation runs in a single node, multiple central processing unit (CPU) setting. Our new framework aims at managing a heterogeneous computational resource pool consisting of multiple CPU nodes distributed on a potentially geographically dispersed network, through a service-oriented middleware layer that is compliant to Web Services Resource Framework standard, thereby providing a scalable and flexible architecture for simulation software developers. What differentiates Sim-PETEK from a general-purpose, Grid-based job-distribution middleware is a number of simulation-specific aspects regarding the specification, distribution, monitoring, result collection and aggregation of simulation runs. These aspects are prevalent in the structure of the messages and in the protocol of interaction both among the constituent services of the framework and within the interfaces exposed to the external clients.
ABSTRACT This paper proposes a software engineering solution for implementing simulations via the... more ABSTRACT This paper proposes a software engineering solution for implementing simulations via the composition of models at different resolution levels with the help of formal methods. Our solution provides a systematic methodology that offers a well-defined sequence of stages to obtain executable converters for entity resolution mapping, given the types of entity attributes that are exchanged at model interfaces and the mapping specifications. Our methodology uses Event-B as the formal specification language and Discrete Event System Specification as the model composition framework; utilizes refinement relations between Event-B machines for the specification, verification and generation of the data conversion steps between models and employs a code generator that inputs the Event-B machine definitions to generate converter code that connects two model ports.
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