[ngi_aegis-all] VI-SEEM newsletter, issue#01, June 2016

Wed Jun 22 10:20:53 CEST 2016

http://vi-seem.us13.list-manage2.com/track/click?u=d1f2abf0a4402811d2eb843be&id=ded301dd98&e=437142ae9b

** newsletter
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** Issue #01
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June 2016

** Message from the project coordinator
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In the last decade, a number of coordinated and complementary e-Infrastructure initiatives were crucial for enabling high-quality research & ICT developments, by providing networking and computational resources, application support and training, in both South East Europe and Eastern Mediterranean (SEEM), and have supported the European vision of inclusive and smart growth, based on knowledge and innovation, enriching the European Research Area. These initiatives have helped to reduce the digital divide and brain drain in Europe, by ensuring access to regional e-Infrastructures to new member states, those on path to ascension, and those in the area identified by the European Neighbourhood Policy.
VI-SEEM builds on the existing e-Infrastructures and resources in the region to further facilitate synergies and enhance high-quality research via the provision of a single Virtual Research Environment (VRE). This VRE will significantly leverage and strengthen the research capacities and competitiveness of the regional scientific communities on the pan-European level.
“Joining the resources across the South East Europe and Eastern Mediterranean in a common platform targeting key research communities will ensure continuity, expand and diversify the available resources and services and further propel excellence across the region.”, says Dr. Ognjen Prnjat, Project coordinator.

** About VI-SEEM
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VI-SEEM is a three-year project that aims at creating a unique Virtual Research Environment in Southeast Europe and the Eastern Mediterranean, in order to facilitate regional interdisciplinary collaboration, with special focus on the scientific communities of Life Sciences, Climatology and Digital Cultural Heritage.
VI-SEEM unifies existing e-Infrastructures into an integrated platform to better utilize synergies, for an improved service provision that will leverage strengthen the research capacities of user communities, thus improving research productivity and competitiveness on the pan-European level.
The project kicked-off in October 2015 and the consortium consists of 16 partners: lead institutes from the SEEM region, specializing in provision of scientific computing and storage resources, and scientific user support.

VI-SEEM project receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 675121.

** VI-SEEM Scientific Communities
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Life Sciences

VI-SEEM will facilitate the laborious analysis and processing of big data arising from decoding the human genome in health and disease. The associated data analysis challenges include capture, curation, analysis, search, sharing, storage, transfer, and visualization. The Life Sciences community consists of 12 research institutes from 10 countries.
The project will facilitate the efficient collaboration of researchers by providing access to needed codes, data repositories, training material for data generation, processing and simulation setup. New knowledge will be produced and integrated into the existing e-Infrastructure. The Life Sciences community will lay the foundations for a larger infrastructure aiming to integrate all the laboratories that generate big data in the region in the future.

Climate

Local and regional climate modelling, weather forecasting and air quality simulations need a common working platform. The community will benefit from the combination of high-performance, grid and cloud computing together with the storage facilities and services, as it heavily relies on data from very scattered locations. VI-SEEM will create opportunities for users to engage in joint activities: with code repositories and training material for climate models, VRE will empower climate scientists from the 19 research groups in 13 countries. Services provided for and by this community contribute to the understanding of the societal challenge related to climate action.

Digital Cultural Heritage

The Cultural Heritage researchers pursue activities on a number of common themes and topics that will be impacted by the shared e-Infrastructure. Common data repositories and software, such as content management system MEDICI, algorithms for remote sensing image classification, idPromo for automatic object recognition etc, will advance the research capacity of the various groups to optimally utilize them.
Beyond the data needs, VI-SEEM will also facilitate the slow transition of the Cultural Heritage community towards computational more intensive activities, such as high detail rendering of 3D modelling, and simulations of environmental influence on historical buildings. Shared datasets, easy remote access and visualization enabled by the VI-SEEM platform will offer a novel approach to Cultural Heritage research that can foster innovation in methodologies and applications used. The Cultural Heritage Scientific Community of VI-SEEM consists of 11 research institutes from 7 countries.

** VI-SEEM delivers integrated e-Infrastructures
and resources to its Scientific Communities
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The user communities of the VI-SEEM Scientific disciplines have been provided with production infrastructure and services.
In total, 18.8 millions of CPU hours, 371.6 millions of GPU hours, 16.0 millions of Xeon Phi hours, 5.3 millions of IBM Cell hours, and 1.6 millions of Grid CPU hours per year, as well as 468 virtual machine cores and 10 petabyte of storage space are reserved and provided to the VI-SEEM scientific communities. This capacity has been achieved with the unification of modern and state-of-the-art networking, computing (HPC, Grid, Cloud), and storage technologies. The core of the resources consists of clusters with low-latency interconnection or supercomputers. Currently two of them, “Avitohol” from Bulgaria and “Leo” from Hungary, are listed in the November 2015 Top500 list of supercomputers (holding position no. 389 and no.402, respectively), while the Greek “ARIS” system is ranked among the top 500 supercomputers in the June 2015 list (at no. 468 spot) as measured by the LINPACK Benchmark (http://vi-seem.us13.list-manage1.com/track/click?u=d1f2abf0a4402811d2eb843be&id=fa1b200efe&e=437142ae9b).
Climate (http://vi-seem.us13.list-manage.com/track/click?u=d1f2abf0a4402811d2eb843be&id=f69c55d016&e=437142ae9b)
Life Sciences (http://vi-seem.us13.list-manage.com/track/click?u=d1f2abf0a4402811d2eb843be&id=7fb59afc6a&e=437142ae9b)
Digital Cultural Heritage (http://vi-seem.us13.list-manage1.com/track/click?u=d1f2abf0a4402811d2eb843be&id=7502e2b6bd&e=437142ae9b)
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Applications for supporting the regional Digital Cultural Heritage Scientific Community
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Digital Libraries, Online Visualization Tools, Data Management Systems and online access to repositories are part of the applications that have been selected for pilot integration and evaluation amongst the cultural heritage communities in Southeast Europe and the Eastern Mediterranean region.
The region is renowned for its ancient civilizations, and it constitutes an area of major socioeconomic and cultural developments during the medieval and early modern periods. The ongoing development of the VI-SEEM services will provide to the digital CH community support in the following applications:
Content/data management and shared access. The most popular type of application is that of a Digital Library, and communities requested support on semantic organization of data in order to make data available, discoverable, intelligible and searchable, as well as meta-data generation opportunities;
Visualization, especially for RTi data and 3D models via online integrated players. Two thrusts: a) the development of live (online) viewers for high resolution images, panoramic photographs, RTi files and 3D models; and, b) the integration of dynamic generation of 3d models from sequences of specialized image files (e.g., RTi); and,
Data processing, mainly regarding Image Classification/Analysis.

** VI-SEEM Climate applications: Regional Climate Modeling
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High resolution regional climate modelling is one of the strongest climate applications in VI-SEEM. Limiting the modelled area allows for much higher spatial resolution, which in turn enables a better representation of the local geography, but also allows for the deployment of more complex models. This helps to better understand and predict climate change, but also regional phenomena such as dust storms. One highly important topic of research is the fact that the Mediterranean is frequently affected by dust loads originating in North Africa and the Middle East. Accordingly, across many institutions, studying the impact of dust on weather and climate has a very high priority. The National Observatory of Athens (NOA) will address this topic by dynamic downscaling using WRF, coupled with its atmospheric chemistry component (WRF-CHEM). WRF-CHEM allows the simulation of the atmospheric state while calculating on-line dust emission mechanisms, and at the same time considering the
feedback of dust by direct and indirect effects on atmospheric (thermo-) dynamics. The WRF- CHEM model is already operational at NOA, presenting an exceptional skill in forecasting dust transfers over the Eastern Mediterranean region.

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Modeling and Molecular Dynamics (MD) study of proteins, membrane proteins and biological model membranes
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Proteins and biological model are responsible for signal transduction and are important drug targets. Therefore, in order to design more efficient drugs and drug delivery systems, a better understanding of the physicochemical interactions that govern biomembrane and protein interfaces is needed. Partners that will contribute are the Biomedical Research Foundation, Academy of Athens (BRFAA), Bioinformatics Group of the International Scientific-Educational Center of the National Academy of Sciences of the Republic of Armenia and the Drug Discovery Laboratory, Faculty of Medicine, Bar-Ilan University in Israel. Molecular physics department of the Yerevan State University and Armenian-Indian Center of Excellence in ICT will investigate amyloid proteins for Alzheimer’s disease.

Upcoming events
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This summer the first scientific results achieved using VI-SEEM infrastructure will be  presented at several scientific conferences:
* ** International conference on Applications of Mathematics in Technical and Natural Science (AMITANS 2016), 22–27 June 2016, Albena, Bulgaria (http://vi-seem.us13.list-manage.com/track/click?u=d1f2abf0a4402811d2eb843be&id=e755e80207&e=437142ae9b)
* ** 7th International Conference “Distributed Computing and Grid-technologies in Science and Education”, 4-9 July 2016, Dubna, Russia (http://vi-seem.us13.list-manage.com/track/click?u=d1f2abf0a4402811d2eb843be&id=a9b1ae8892&e=437142ae9b)
* ** ICT Innovations 2016, 5-7 September 2016, Ohrid, FYR Macedonia (http://vi-seem.us13.list-manage.com/track/click?u=d1f2abf0a4402811d2eb843be&id=2a5b6605e4&e=437142ae9b)
* ** SYNASC 2016 - 18th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, 24-27 September 2016, Timisoara, Romania (http://vi-seem.us13.list-manage.com/track/click?u=d1f2abf0a4402811d2eb843be&id=83220a0e87&e=437142ae9b)
* ** International Conference on Research Infrastructures 2016, 3-5 October 2016, Cape Town, South Africa (http://vi-seem.us13.list-manage1.com/track/click?u=d1f2abf0a4402811d2eb843be&id=397c09d59e&e=437142ae9b)
* Life Sciences VRE training, 20-21 October 2016, Belgrade, Serbia
* ** e-AGE 2016, 1-2 December 2016, Beirut, Lebanon (http://vi-seem.us13.list-manage.com/track/click?u=d1f2abf0a4402811d2eb843be&id=996502bca0&e=437142ae9b)

** (http://vi-seem.us13.list-manage.com/track/click?u=d1f2abf0a4402811d2eb843be&id=b818fb3ab8&e=437142ae9b)
** (vi-seem.eu)
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