Tomasz Bartyński

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.

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.

Invocation of operations from script-based Grid applications

In this paper we address the complexity of building and running modern scientific applications on various Grid systems with heterogeneous middleware. As a solution we have proposed the Grid Operation Invoker (GOI) which offers an object-oriented method invocation semantics for interacting with diverse computational services. GOI forms the core of the ViroLab virtual laboratory and it is used to invoke operations from within in-silico experiments described using a scripting notation. We describe the details of GOI (including architecture, technology adapters and asynchronous invocations) focusing on a mechanism which allows adding high-level support for batch job processing middleware, e.g. EGEE LCG/gLite. As an example, we present the NAMD molecular dynamics program, deployed on EGEE infrastructure. The main achievement is the creation of the Grid Object abstraction, which can be used to represent and access such diverse technologies as Web Services, distributed components and job processing systems. Such an application model, based on high-level scripting, is an interesting alternative to graphical workflow-based tools.

Universal grid client: grid operation invoker

In this paper we present a high-level approach to programming applications which use the Grid from the client side. This study is devoted to resolving the need for a language that would allow expressing the application logic in a precise way and combining it with the capability of remote access to powerful Grid resources and complex computational software. We introduce the concept of a universal Grid client - a Grid Operation Invoker (GOI). It provides a client-side interface to computational resources that use various middleware packages within a high-level scripting language. The system prototype is written in JRuby [1] which is a Java implementation of a popular object-oriented scripting language interpreter - Ruby [2]. We also present issues that have emerged in the course of work on GOI and which we have found challenging. Finally, we discuss Grid applications implemented in JRuby, proving that GOI can be used to solve highly complicated and computationally-intensive problems.

A Tool for Building Collaborative Applications by Invocation of Grid Operations

The motivation for this work is the need for providing tools which facilitate building scientific applications that are developed and executed on various Grid systems, implemented with different technologies. As a solution to this problem, we have developed the Grid Operation Invoker (GOI) which offers object-oriented method invocation semantics for interacting with computational services accessible with diverse middleware frameworks. GOI forms the core of the ViroLab virtual laboratory engine and it is used to invoke operations from within experiments described using a scripting notation. In this paper, after outlining the features of GOI, we describe how it is enhanced with a mechanism of so-called local gemswhich allows adding high-level support for middleware technologies based on the batch job-processing model, e.g. EGEE LCG/gLite. As a result, we demonstrate how a molecular dynamics program called NAMD, deployed on EGEE, was integrated with the ViroLab virtual laboratory.

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.

Cloud computing infrastructure for the VPH community

Abstract As virtualization technologies mature and become ever more widespread, cloud computing has emerged as a promising paradigm for e-science. In order to facilitate successful application of cloud computing in scientific research – particularly in a domain as security-minded as medical research – several technical challenges need to be addressed. This paper reports on the successful deployment and utilization of a cloud computing platform for the Virtual Physiological Human (VPH) research community, originating in the VPH-Share project and continuing beyond the end of this project. The platform tackles technical issues involved in porting existing desktop applications to the cloud environment and constitutes a uniform research space where application services can be developed, stored, accessed and shared using a variety of computational infrastructures. The paper also presents examples of application workflows which make use of the presented infrastructure – both internal and external to the VPH community.

Automatic proxy generation and load-balancing-based dynamic choice of services

The paper addresses the issues of invoking services from within workflows which are becoming an increasingly popular paradigm of distributed programming. The main idea of our research is to develop a facility which enables load balancing between the available services and their instances. The system consists of three main modules: a proxy generator for a specific service according to its interface type, a proxy that redirects requests to a concrete instance of the service and load-balancer (LB) to choose the least loaded virtual machine (VM) which hosts a single service instance. The proxy generator was implemented as a bean (in compliance to EJB standard) which generates proxy according to the WSDL service interface description using XSLT engine and then deploys it on a GlassFish application server using GlassFish API, the proxy is a BPEL module and load-balancer is a stateful Web Service.