Virtual Laboratory for Collaborative Applications

Virtual Laboratory for Collaborative Applications

Marian Bubak (University of Amsterdam, The Netherlands and ACC CYFRONET AGH, Poland), Maciej Malawski (Institute of Computer Science AGH, Poland), Tomasz Gubala (ACC CYFRONET AGH, Poland), Marek Kasztelnik (ACC CYFRONET AGH, Poland), Piotr Nowakowski (ACC CYFRONET AGH, Poland) and Daniel Harezlak (ACC CYFRONET AGH, Poland)
DOI: 10.4018/978-1-60566-374-6.ch027
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Abstract

Advanced research in life sciences calls for new information technology solutions to support complex, collaborative computer simulations and result analysis. This chapter presents the ViroLab virtual laboratory, which is an integrated system of dedicated tools and services, providing a common space for planning, building, improving and performing in-silico experiments by different groups of users. Within the virtual laboratory collaborative applications are built as experiment plans, using a notation based on the Ruby scripting language. During experiment execution, provenance data is created and stored. The virtual laboratory enables access to distributed, heterogeneous data resources, computational resources in Grid systems, clusters and standalone computers. The process of application development as well as the architecture and functionality of the virtual laboratory are demonstrated using a real-life example from the HIV treatment domain.
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Background

In this section we begin with definitions of the most important terms we are going to use, which explain how we understand the virtual laboratory and related concepts. Subsequently, we analyze the state of the art and discuss other solutions, which influence the approach we are following in our research.

Key Terms in this Chapter

MOCCA: is a CCA-compliant component framework based on H2O resource sharing platform, which enables building and running scientific applications on the Grid.

Experiment Planning Environment: (EPE) is an Eclipse-based interface used by developers to create experiment plans.

Ruby: is a modern, interpreted, dynamically typed, object-oriented, scripting programming language.

Virtual Laboratory: is a set of integrated components that, used together, form a distributed and collaborative space for e-science (see.http://virolab.cyfronet.pl).

Experiment plan: is a recipe that describes the process of experiment execution in the environment of the virtual laboratory.

Experiment: is a process that combines data with a set of activities that act on that data in order to yield experiment results.

Grid Object Instance: is the specific instance of a service, component etc., which implements the functionality of a given Grid Object.

Grid Object: is the abstraction of a Grid computational resource, accessible in the Grid Space environment as a simple object of the host language.

Experiment Management Interface: (EMI) is a Web-based user interface used for browsing and executing experiments as well as managing their results.

Grid Object Implementation: is an abstract description of a Grid Object, taking into account the specific middleware technology in which this Grid Object is implemented (e.g. Web Service or MOCCA component).

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