Marko Krznaric

GRIDCC: real-time workflow system

The Grid is a concept which allows the sharing of resources between distributed communities, allowing each to progress towards potentially different goals. As adoption of the Grid increases so are the activities that people wish to conduct through it. The GRIDCC project is a European Union funded project addressing the issues of integrating instruments into the Grid. This increases the requirement of workflows and Quality of Service upon these workflows as many of these instruments have real-time requirements. In thispaper we present the workflow management service within the GRIDCC project which is tasked with optimising the workflows and ensuring that they meet the pre-defined QoS requirements specified upon them.

Integrating Research on Thyroid Cancer after Chernobyl — the Chernobyl Tissue Bank

The only unequivocal radiological effect of the Chernobyl accident on human health is the increase in thyroid cancer in those exposed in childhood or early adolescence. In response to the scientific interest in studying the molecular biology of thyroid cancer after Chernobyl, the Chernobyl Tissue Bank was established. The project is supported by the governments of Ukraine and Russia, and financially supported (in total around US

Adding instruments and workflow support to existing grid architectures

3 million) by the European Commission, the National Cancer Institute of the USA and the Sasakawa Memorial Health Foundation of Japan. The project began collecting a variety of biological samples from patients on 1 October 1988, and has supplied material to 21 research projects in Japan, the USA and Europe. The establishment of the Chernobyl Tissue Bank has facilitated co-operation between these research projects and the combination of clinical and research data provides a paradigm for cancer research in the molecular biological age.

Enabling QoS for Service-Oriented Workflow on GRID

Many Grid architectures have been developed in recent years. These range from the large community Grids such as LHG and EGEE to single site deployments such as Condor. However, these Grid architectures have tended to focus on the single or batch submission of executable jobs. Application scientists are now seeking to manage and use physical instrumentation on the Grid, integrating these with the computational tasks they already perform. This will require the functionality of current Grid systems to be extended to allow the submission of entire workflows. Thus allowing the scientists to perform increasingly larger parts of their experiments within the Grid environment. We propose here a set of high level services which may be used on-top of these existing Grid architectures such that the benefits of these architectures may be exploited along with the new functionality of workflows.

Numerical Integration with Exact Real Arithmetic

As the main computing paradigm for resource- intensive scientific applications, Grid[1] enables resource sharing and dynamic allocation of computational resources. It promotes access to distributed data, operational flexibility and collaboration, and allows service providers to be distributed both conceptually and physically to meeting different requirements. Large- scale grids are normally composed of huge numbers of components from different sites, which increases the requirements of workflows and quality of service (QoS) upon these workflows as many of these components have real-time requirements. In this paper, we describe our web services based QoS-aware workflow management system(WfMS) from GridCC project[7] and show how this WfMS can aid to ensure workflows meet the pre-defined QoS requirements and optimise them accordingly.

The Chernobyl Tissue Bank - A Repository for Biomaterial and Data Used in Integrative and Systems Biology Modeling the Human Response to Radiation

We show that the classical techniques in numerical integration (namely the Darboux sums method, the compound trapezoidal and Simpsons rules and the Gauss-Legendre formulae) can be implemented in an exact real arithmetic framework in which the numerical value of an integral of an elementary function is obtained up to any desired accuracy without any round-off errors. Any exact framework which provides a library of algorithms for computing elementary functions with an arbitrary accuracy is suitable for such an implementation; we have used an exact real arithmetic framework based on linear fractional transformations and have thereby implemented these numerical integration techniques. We also show that Eulers and Runge-Kutta methods for solving the initial value problem of an ordinary differential equation can be implemented using an exact framework which will guarantee the convergence of the approximation to the actual solution of the differential equation as the step size in the partition of the interval in question tends to zero.

Enabling Scientists Through Workflowand Quality of Service

The only unequivocal radiological effect of the Chernobyl accident on human health is the increase in thyroid cancer in those exposed in childhood or early adolescence. In response to the scientific interest in studying the molecular biology of thyroid cancer post Chernobyl, the Chernobyl Tissue Bank (CTB: www.chernobyltissuebank.com) was established in 1998. Thus far it is has collected biological samples from 3,861 individuals, and provided 27 research projects with 11,254 samples. The CTB was designed from its outset as a resource to promote the integration of research and clinical data to facilitate a systems biology approach to radiation related thyroid cancer. The project has therefore developed as a multidisciplinary collaboration between clinicians, dosimetrists, molecular biologists and bioinformaticians and serves as a paradigm for tissue banking in the omics era.

Running a Production Grid Site at the London e-Science Centre

There is a strong desire within scientific communities to Grid-enable their experiments. This is fueled by the advantages of having remote (collaborative) access to instruments, computational resources and storage. In order to make the scientists experience as rewarding as possible two technologies need to be adopted into the Grid paradigm: those of workflow, to allow the whole scientific process to be automated, and Quality of Service (QoS) to ensure that this automation meets the scientists’ needs and expectations. In this chapter we present an end-to-end workflow pipeline which takes a user’s design and automates the processes of workflow design, resource selections and reservation through to enacting the workflow on the Grid, thus removing much of the complexity inherent within this process.

Computing a Required Absolute Precision from a Stream of Linear Fractional Transformations

This paper describes how the London e-Science Centre cluster MARS, a production 400+ Opteron CPU cluster, was integrated into the production Large Hadron Collider Compute Grid. It describes the practical issues that we encountered when deploying and maintaining this system, and details the techniques that were applied to resolve them. Finally, we provide a set of recommendations based on our experiences for grid software development in general that we believe would make the technology more accessible.

EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management

A real number can be represented as a sequence of nested, closed intervals whose lengthes tend to zero. In the LFT approach to Exact Real Arithmetic the sequence of intervals is generated by a sequence of one-dimensional linear fractional transformations (1-LFTs) applied to a base interval, [9,13,11,4,12,7].