Marek Kasztelnik

The Collage Authoring Environment

Abstract The Collage Authoring Environment is a software infrastructure which enables domain scientists to collaboratively develop and publish their work in the form of executable papers. It corresponds to the recent developments in both e-Science and computational technologies which call for a novel publishing paradigm. As part of this paradigm, static content (such as traditional scientific publications) should be supplemented with elements of interactivity, enabling reviewers and readers to reexamine the reported results by executing parts of the software on which such results are based as well as access primary scientific data. Taking into account the presented rationale we propose an environment which enables authors to seamlessly embed chunks of executable code (called assets) into scientific publications and allow repeated execution of such assets on underlying computing and data storage resources, as required by scientists who wish to build upon the presented results. The Collage Authoring Environment can be deployed on arbitrary resources, including those belonging to high performance computing centers, scientific e-Infrastructures and resources contributed by the scientists themselves. The environment provides access to static content, primary datasets (where exposed by authors) and executable assets. Execution features are provided by a dedicated engine (called the Collage Server) and embedded into an interactive view delivered to readers, resembling a traditional research publication but interactive and collaborative in its scope. Along with a textual description of the Collage environment the authors also present a prototype implementation, which supports the features described in this paper. The functionality of this prototype is discussed along with theoretical assumptions underpinning the proposed system.

The UrbanFlood common information space for early warning systems

Early Warning Systems (EWS) can play a crucial role in mitigating the effects of natural disasters. Modern EWSs leverage wireless sensors for real-time monitoring of natural phenomena and computing-intensive scientific applications for scenario-based prediction and analysis of sensor data. This paper presents the UrbanFlood Common Information Space (CIS), a framework facilitating the creation, deployment and reliable operation of early warning systems. CIS proposes a reference architecture for EWS and provides services to address problems common to all EWSs as complex software systems: integration of legacy scientific applications, workflow orchestration, allocation of computational resources and robust operation. We demonstrate a flood early warning system created using the CIS technology and discuss the benefits of our approach which include shorter EWS development time, exposing EWS as a set of reusable services, platform independence and extensibility.

Exploratory programming in the virtual laboratory

GridSpace 2 is a novel virtual laboratory framework enabling researchers to conduct virtual experiments on Grid-based resources and other HPC infrastructures. GridSpace 2 facilitates exploratory development of experiments by means of scripts which can be written in a number of popular languages, including Ruby, Python and Perl. The framework supplies a repository of gems enabling scripts to interface low-level resources such as PBS queues, EGEE computing elements, scientific applications and other types of Grid resources. Moreover, GridSpace 2 provides a Web 2.0-based Experiment Workbench supporting development and execution of virtual experiments by groups of collaborating scientists. We present an overview of the most important features of the Experiment Workbench, which is the main user interface of the Virtual laboratory, and discuss a sample experiment from the computational chemistry domain.

Managing entire lifecycles of e-science applications in the gridspace2 virtual laboratory --- from motivation through idea to operable web-accessible environment built on top of PL-Grid e-infrastructure

The GridSpace2 environment, developed in the scope of the PL-Grid Polish National Grid Initiative, constitutes a comprehensive platform which supports e-science applications throughout their entire lifecycle. Application development may involve multiple phases, including writing, prototyping, testing and composing the application. Once the application attains maturity it becomes operable and capable of being executed, although it may still be subject to further development --- including actions such as sharing with collaborating researchers or making results publicly available with the use of dedicated publishing interfaces. This paper describes each of these phases in detail, showing how the GridSpace2 platform can assist the developers and publishers of computational experiments.

Virtual Laboratory for Development and Execution of Biomedical Collaborative Applications

The ViroLab Virtual Laboratory is a collaborative platform for scientists representing multiple fields of expertise while working together on common scientific goals. This environment makes it possible to combine efforts of computer scientists, virology and epidemiology experts and experienced physicians to support future advances in HIV-related research and treatment. The paper explains the challenges involved in building a modern, inter-organizational platform to support science and gives an overview of solutions to these challenges. Examples of real-world problems applied in the presented environment are also described to prove the feasibility of the solution.

High-Level Scripting Approach for Building Component-Based Applications on the Grid

In this paper, we describe a top-down approach to solution of the problem of component composition on the Grid. The proposed method is based on the use of a dynamic scripting language. It enables designing a simple API to define component composition in an elegant and concise way. GScript [17] provides constructs to create component instances (deployment), connect their ports (composition) and invoke the component methods with the minimum amount of code. As GScript is based on Ruby [26], it also provides the full flexibility of a programming language, with a rich set of control constructs of component applications (workflows). GScript hides all the details of the underlying Grid infrastructure, so the programmer may focus on the application logic, while the process of resource selection and component deployment is performed automatically. We describe the architecture of the runtime library needed to support the high-level features, and propose a set of development tools, based on the Eclipse platform. We report on a prototype which demonstrates the applicability of the approach to construct applications from both MOCCA (CCA) and ProActive (GCM) components.

Evaluation of Cloud Providers for VPH Applications

Infrastructure as a Service (IaaS) clouds are considered interesting sources of computing and storage resources for scientific applications. However, given the large number of cloud vendors and their diverse offerings, it is not trivial for research projects to select an appropriate service provider. In this paper, we present the results of evaluation of public cloud providers, taking into account the requirements of the biomedical applications within the VPH-Share project. We performed a broad analysis of nearly 50 cloud providers and analyzed the performance and cost of 26 virtual machine instance types offered by the top three providers who meet our criteria: Amazon EC2, Rack Space and Soft Layer. We hope our results will be helpful for other research projects that are considering clouds as a potential source of computing and storage resources.

Holistic approach to management of IT infrastructure for environmental monitoring and decision support systems with urgent computing capabilities

Abstract Modern environmental monitoring and decision support systems are based on complex IT infrastructures comprising multiple hardware and software subsystems that need to provide a variety of Quality of Service (QoS) guarantees required for urgent computing services, essential in emergency situations. Such IT infrastructures need to be managed in order to maintain the quality of service, which–especially when operating in the urgent mode–involves optimization of multiple, often conflicting, objectives and making trade-offs between them. Existing approaches do not solve this issue optimally because they focus on delivering quality of service within individual subsystems in isolation. We propose a holistic approach to system management which takes into account knowledge about the system as a whole—in particular the interplay of conflicting objectives and configuration options across all subsystems. We argue that such an approach produces a better configuration of the involved subsystems, improving the resolution of trade-offs between cost, energy and performance objectives, leading to their better overall fulfillment in comparison with the non-holistic approach in which individual subsystems are managed in isolation. We validate our approach using a prototype implementation of the holistic optimization algorithm—the Holistic Computing Controller, and applying it to a smart levee monitoring and flood decision support system.

ViroLab Security and Virtual Organization Infrastructure

This paper introduces security requirements and solutions present in the ViroLab Virtual Laboratory. Our approach is to use a federated Single Sign-On mechanism based on the Shibboleth framework that enables multiple partners to authenticate against their local identity systems and use resources provided by all other partners. Since the basic Shibboleth capabilities do not meet our specific requirements related to supporting non-web-based services, we created a set of custom tools that allow us to develop a homogeneous, Shibboleth-based security solution for both Web and non-web-based software components. This paper describes these tools in detail, together with other services of the virtual laboratory which have been integrated with the security infrastructure. A decentralized, attribute-based approach facilitating the creation and management of virtual organizations is the key achievement of our work.

Scripting language extensions offered by the gridspace experiment platform

Many existing problem solving environments provide scientists with convenient methods for building scientific applications over distributed computational and storage resources. In many cases a basic set of features of such environments is sufficient to conduct a complete experiment flow. However, complex cases often require extensions supporting an external piece of software or a communication standard not integrated beforehand. Most environments deal with such cases by providing an extension facility and letting third parties add required features. The GridSpace environment also includes several mechanisms for extending its own functionality and here we describe how this can be accomplished. We focus on extensions already implemented such as local job submission and scripting language repositories, as well as on a GUI extension point which can be used to add custom graphical user interfaces to GridSpace experiments independently of their release process.