e-Science initiatives in Venezuela
📝 Abstract
Within the context of the nascent e-Science infrastructure in Venezuela, we describe several web-based scientific applications developed at the Centro Nacional de Calculo Cientifico Universidad de Los Andes (CeCalCULA), Merida, and at the Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas. The different strategies that have been followed for implementing quantum chemistry and atomic physics applications are presented. We also briefly discuss a damage portal based on dynamic, nonlinear, finite elements of lumped damage mechanics and a biomedical portal developed within the framework of the \textit{E-Infrastructure shared between Europe and Latin America} (EELA) initiative for searching common sequences and inferring their functions in parasitic diseases such as leishmaniasis, chagas and malaria.
💡 Analysis
Within the context of the nascent e-Science infrastructure in Venezuela, we describe several web-based scientific applications developed at the Centro Nacional de Calculo Cientifico Universidad de Los Andes (CeCalCULA), Merida, and at the Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas. The different strategies that have been followed for implementing quantum chemistry and atomic physics applications are presented. We also briefly discuss a damage portal based on dynamic, nonlinear, finite elements of lumped damage mechanics and a biomedical portal developed within the framework of the \textit{E-Infrastructure shared between Europe and Latin America} (EELA) initiative for searching common sequences and inferring their functions in parasitic diseases such as leishmaniasis, chagas and malaria.
📄 Content
The term “e-Science” was introduced by John Taylor in 2000 envisioning the new trends that were starting to occur in global collaborations in key areas of science. It defines a set of computational (hardware & middleware) and data services that enable service oriented science [10,11,7]. These infrastructures and facilities have made it possible to develop computational “collaboratories” [13], defined as places where scientists work together to solve complex interdisciplinary problems despite geographic and organizational boundaries. Such collaboratories provide uniform access to computational resources, services and/or applications. They also expand the resources available to researchers, foment multidisciplinary collaborations and problem solving, increase the efficiency of research and accelerate the dissemination of knowledge.
The IT hardware infrastructure to support these multidisciplinary and distributed collaborations include high-speed networks, supercomputers, workstation clusters and new expensive shared experimental/simulations facilities such as sensors, satellites, high-performance-computer simulations and high-throughput devices, among others. The software environments allow a user to authenticate, submit a job, monitor running jobs, manage input/output data through distributed file systems and visualize results. The new computing environments and tools should support all these requirements, and must be presented to the scientific communities in terms of the applications themselves rather than in the form of complex computing protocols. The grid must be viewed as a seamless extension of the user computer facilities regarding both job execution/monitoring and data access/management. The recent move of the grid community to a service-oriented architecture and the proposal for an Open-Grid-Services Architecture (OGSA) based on commercially supported web-services technology is therefore of great significance [8].
In this paper we mainly concentrate on the portal functionalities and the different strategies we have been followed for implementing web-based scientific applications that are required to make e-Science a reality in our region. We briefly describe some of the web-based scientific applications developed at the Centro Nacional de Cálculo Científico Universidad de Los Andes (CeCalCULA1 ) and at the Instituto Venezolano de Investigaciones Científicas (IVIC2 ). CeCalCULA was established in 1997 as a joint effort between the Universidad de Los Andes, the Fondo Nacional para la Ciencia y la Tecnología and the Corporación Parque Tecnológico de Mérida for the transfer of computer-intensive technology in science and engineering projects. In the last decade this national center has also provided the local scientific research community with consulting services, computing power and IT training. It is considered a main asset of the National Academic Network of Research Centers and National Universities3 and has contributed to generate a favorable atmosphere for innovation which has been reviewed in recent studies of multilateral organizations4 . The Computational Physics and Computational Chemistry Laboratories of IVIC have been heavy users of high performance computing (HPC) and software and database developers since the beginning of the 90s, and therefore there is much current interest in the possibilities of the new e-Infrastructure.
The structure of the paper is as follows. In Section 2 the national and regional leadership of CeCalCULA in organizing hands-on workshops on IT, HPC and networking is summarized. In Section 3 we discuss strategies for adapting and upgrading legacy scientific applications to a web-based grid environment. The Damage Portal an e-Engineering application of lumped damage mechanics based on dynamic, nonlinear finite elements is presented in Section 4, followed in Section 5 by the Blast2EELA Biomedical Portal implemented within the E-Infrastructure shared between Europe and Latin America (EELA) initiative. Conclusions and future projects are outlined in Section 6.
In the past ten years CeCalCULA has organized a string of national and regional (Caribbean Basin and Andean countries) workshops and schools aimed at high-level researchers and professionals. The Workshop on New Techniques and Tools for Computational Sciences 5 held in December 1996 was the first workshop on scientific computing in Venezuela. It attracted more than a hundred HPC users in several disciplines, initiating an important and irreversible trend in the country as it became the cornerstone in the identity of a young academic and research community that used the computer as a fundamental scientific tool. Additionally it served as the launchpad for CeCalCULA as a national HPC center. This first successful meeting was followed up two years later by the First Latin-American Workshop on Parallelism and High Performance Computing 6 which convened the Caribbean and Andean regions. The Second Latin-American Work
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