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1

Genomic Virtual Laboratory

Cegielska B., Kaliszan D., Handschuh L., Figlerowicz M., Meyer N.

Computational Methods in Science and Technology

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2010

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Vol. 16, No. 1

39-49

EN

In contemporary science, virtual laboratories give a chance to improve research by facilitating access to high-throughput technologies and bioinformatics methods. The Genomic Virtual Laboratory (GVL) presented here was developed for automate analysis of data retrieved from a microarray experiment. The system was implemented for R Bioconductor-based analysis of results obtained in the study on human acute myeloid leukaemia (AML). The article extends the theoretical aspects of GVL presented earlier [8] and describes how the particular elements were integrated to establish the advanced system of two-colour microarray data analysis.

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Towards Deployment of the Remote Instrumentation e-Infrastructure (in the Frame of the DORII Project)

Cheptsov A., Keller R., Pugliese R., Prica M., Del Linz A., Plociennik M., Lawenda M., Meyer N.

Computational Methods in Science and Technology

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2009

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Vol. 15, nr 1

65-74

EN

While the majority of e-Infrastructures that are set up within the European Research Area by such projects as EGEE, DEISA etc. are basically focused on providing the high-performance computing support for scientific applications, a diverse set of the scientific communities coming from various fields (e.g. earthquake, environmental science, experimental science communities) develop and operate experimental equipment and remote instrumentation that have not been integrated yet or only partially integrated within the European Grid e-Infrastructure. The Deployment of Remote Instrumentation Infrastructure (DORII) project aims at setting up an advanced Grid-based e-Infrastructure specifically oriented to the support of remote instrumentation devices on Grid extending the level of scientific instruments' exploitation. The paper highlights the main application areas and usage scenarios, key tasks of the Remote Instrumentation Infrastructure’s deployment and presents the joint research architecture for DORII in terms of advanced middleware solutions addressing the main tasks of identified applications.

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Remote Oceanographic Instrumentation Integrated in a GRID Environment

Salon S., Poulain P.-M., Mauri E., Gerin R., Adami D., Davoli F.

Computational Methods in Science and Technology

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2009

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Vol. 15, nr 1

49-55

EN

The observations provided by oceanographic remote instruments are essential to the purposes of the operational oceanography that represents a constantly growing tool to monitor and predict the state of the marine resources. The management of a network of instruments deployed in the Mediterranean Sea is a complex task that may be greatly supported by the GRID technology. This paper presents the activity planned by the DORII EU-FP7 project concerning the floats and the glider. The aim of the project is to demonstrate the potentiality of the state-of-the-art eInfrastructure in the integration of the data driven control/interaction workflow that characterizes the instruments. We describe the communication between the elements of the workflow and the associated network topology.

4

New approach to Genomics Experiments Taking Advantage of Virtual Laboratory System

Handschuh L., Lawenda M., Stępniak P., Figlerowicz M., Stroiński M., Węglarz J.

Computational Methods in Science and Technology

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2009

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Vol. 15, nr 1

31-40

EN

Specialized software, on-line tools and computational resources are very common in contemporary science. One of the exemplary domain is genomics – a new branch of science that developed rapidly in the last decade. As the genome research is very complex, it must be supported by professional informatics. In a microarray field the following steps cannot be performed without computational work: design of probes, quantitative analysis of hybridization results, post-processing, and finally data storage and management. Here, the general aspects of virtual laboratory systems are presented together with perspectives of their implementation in genomics in order to automate and facilitate this area of research.

5

Integrating Instruments in the Grid for On-line and Off-line Processing in a Synchrotron Radiation Facility

Pugliese R., Prica M., Kourousias G., Del Linz A., Curri A.

Computational Methods in Science and Technology

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2009

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Vol. 15, nr 1

21-30

EN

Experimental stations in facilities like Synchrotrons and Free Electron Lasers produce very large data sets. With access to distributed computing paradigms and Grid infrastructures, the data are processed on-line. This requires considerable computing power and storage requirements. Moreover, the constant advances in sensors, detectors, and light source technologies yield frequent upgrades of the instrumentation and proportional increase of the computing requirements. Other than the computing needs, a key-point for successful experiments is the efficient collaboration between the involved scientists and their convenient access to the research facilities. A viable solution is developing suitable infrastructures that allow remote operation of the experimental facilities. We focus on the importance of the transparent integration of instruments in the traditional Grid. Such capability boosts further the concept of remote operation, on-line & off-line processing, and builds collaborative and distributed virtual research environments. Building on the foundations of previous European projects, the aim of DORII (Deployment of Remote Instrumentation Infrastructure) [1] is to develop and operate an infrastructure that addresses this issue and supports multiple activities of eScience. We will describe how we have applied the DORII infrastructure on remote operations and on-line & off-line processing in a synchrotron radiation facility.

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Enabling Technologies and Design Values for Building the Real World Web

McMullen D. F.

Computational Methods in Science and Technology

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2009

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Vol. 15, nr 1

83-93

EN

The notions of ubiquitous computing and networking, and the increasing availability of compact, low power sensing technologies naturally lead to the idea that we can expect to see large numbers of sensors embedded in the fabric of our everyday lives and that these could form a “Real World Web” of real-time data sources about our world. Implications for e-Research include sharing of real-time data from scientific instruments and aggregation of many types of information to answer complex questions as they arise. The World Wide Web was made possible through a combination of the increasing availability of the Internet, simple network protocols, and open content and delivery standards. The Real World Web can only grow and become self-sustaining if we pay attention to these same core design values of simplicity and openness. Recent developments in cloud computing and in Web 2.0 technologies and design stances provide enablers from which to build the Real World Web, but in addition, require a shift in thinking away from a classical Web services and layered standards model. This paper explores these issues and the role of the Real World Web as a paradigm for sharing instruments, sensors and other real-time data sources in e-Research collaborations.