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Issue #02
November 2016

Message from the co-ordinator


End of the first project year is marked by the consolidation of a range of generic and discipline-specific e-Infrastructure services available through the VI-SEEM Virtual Research Environment. You are invited to browse and get to know our catalogue at https://services.vi-seem.eu and the related Virtual Research Environment at https://vre.vi-seem.eu/.

Year 1 marks also the opening up of this environment to the research communities in the fields of Climate, Digital Cultural Heritage and Life Sciences. First call for VRE access is now open to the communities from Southeast Europe and the Eastern Mediterranean with the deadline of 14th November.

VI-SEEM service catalogue


The necessity for solid but flexible IT service management is one of the keystones for the service-oriented design. The specifics of the federated environment, such as the one found in VI-SEEM, impose requirements for service management tools that cannot be met using common off-the-shelf solutions. Hence, special care must be taken for the design and the implementation of easy to use, custom solution that is tailor made for scientific communities. VI-SEEM project has developed IT service catalogue and portfolio management that allows various ways of accessing and editing the information about the services offered by the project. For each service, relevant details are presented to the users, enabling them to discover and request access to the needed services.

VI-SEEM service catalogue lists 10 services, grouped in 5 categories: 
  • Compute: includes HPC, Grid and Cloud computing resources of the VI-SEEM infrastructure, available through the VRE to the user communities.
  • Data Storage including: VI-SEEM Archival service provides safe data archiving, automatic replication according to predefined policies with high availability and performance, accessible through the VI-SEEM iRODS federation. VI-SEEM Simple storage allows users to keep and sync research data on various devices, as well as to share this data thus making it a useful tool in collaborative environment.  VI-SEEM Repository represents the main storage service that allows users to deposit and share data, including regional datasets,  publications and their associated data as well as software or references to software and workflows.
  • Application specific: encompasses several services, ranging from discipline specific application environments, optimised and tailored for the needs of the VI-SEEM communities, workflow and code repositories designed to support the three target VI-SEEM communities, discipline specific dataset collections as well as two application level services. Clowder is a research data management system designed to support any data format and multiple research domains, with three major extension points: preprocessing, processing and previewing. Live Access Server is highly configurable server designed to provide flexible access to geo-referenced scientific data, usable by multiple user communities.
  • Authentication and authorization infrastructure enables unified access to all VI-SEEM services.
  • Service provisioning: contains the IT service management platform itself, as a tool for maintaining the service catalogue.
During the lifetime of the project, many new services will be added to this central service catalogue for the VI-SEEM project, enabling the users from the scientific communities to have a one-stop-shop for all the services available through the VI-SEEM Virtual Research Environment.

VI-SEEM opens its 1st call for proposals for project access to services and supporting infrastructures


VI-SEEM opens its first Call for Proposals for projects accessing the VI-SEEM services and the supporting e-Infrastructure. The call is addressed to scientists and researchers that work in academic and research institutions in the region of Southeastern Europe and the Eastern Mediterranean, in particular Albania, Armenia, Azerbaijan, Bosnia and Herzegovina, Bulgaria, Cyprus, Egypt, FYR of Macedonia, Georgia, Greece, Hungary, Israel, Jordan, Lebanon, Moldova, Montenegro, Romania, Serbia and Turkey. The project proposals should address open research topics in specific fields of Life Sciences, Climate research, and Digital Cultural Heritage.

VI-SEEM offers a broad set of generic as well as application-specific services in the region of South-eastern Europe and the Eastern Mediterranean, with special focus on the scientific communities of Life Sciences, Climatology and Digital Cultural Heritage. Services are in the areas of: Compute resource (HPC, Grid and Cloud); Storage and Data services; Datasets; Software and Scientific Workflows; Application-specific services.

Access to underlying computational resources will be awarded for a maximum period of 12 months, while access to underlying storage resources may be provided for up to 2 years, beginning January 2017.

The list of services and resources offered by the VI-SEEM VRE can be found at: https://services.vi-seem.eu and in the VI-SEEM VRE at: https://vre.vi-seem.eu

These services create a unique Virtual Research Environment (VRE), thus improving research productivity and competitiveness on the pan-European level. Via this call VI-SEEM opens possibilities for regional scientists from the selected scientific fields to have access to the advanced resources and services that the VRE offers.

VI-SEEM Login: seamless, secure access to the VI-SEEM VRE services


VI-SEEM Login enables individual researchers to seamlessly and securely access VI-SEEM services using federated authentication mechanisms. Through VI-SEEM Login, users are able to authenticate using the credentials provided by the Identity Provider (IdP) of their Home Organisation in eduGAIN, which has become the primary mechanism to interfederate for global research and education collaboration, bringing together more than 2000 Universities and Institutes around the world. Complementary to eduGAIN, VI-SEEM Login enables users that do not have an account on one of the federated IdPs, to still be able to access VI-SEEM services using social identity providers or other selected external identity providers. To achieve this, VI-SEEM Login has built-in support for SAML, OpenID Connect and OAuth2 providers and already enables user logins through Google, LinkedIn and Facebook.

VI-SEEM Login simplifies administrative processes for both community managers and service providers by serving as a central hub between federated Identity Providers and Service Providers. The main advantage of this approach is that it allows for all entities to establish and maintain technical and trust relation only to a single entity, the VI-SEEM Login service, which acts as a Service Provider towards the Identity Providers and as an Identity Provider towards the Service Providers. Common technical services, such as Identity Provider discovery and user account management are provided centrally by VI-SEEM Login, and do not have to be implemented by each individual service. VI-SEEM Login is also responsible for aggregating user attributes originating from various authoritative sources (IdPs and attribute authorities) and delivering them to the connected service providers in a harmonised and transparent way. Service Providers can then use the received attributes for controlling access to their resources.

What’s next: all the user communities of the VI-SEEM scientific disciplines are expected to be on board the VI-SEEM Login platform by the end of the year. Furthermore, the new OpenID Connect interface will be introduced, aiming for a faster and easier integration experience for new services.

https://services.vi-seem.eu/ui/catalogue/services/#VI-SEEM_Login 
http://wiki.vi-seem.eu/index.php/Access_to_resources

Digital Cultural Heritage
Life Sciences
Climate

Climate Scientific Community paper: accelerated chemical kinetics in the EMAC chemistry-climate model                              


The global climate model ECHAM/MESSy Atmospheric Chemistry (EMAC) is used to study climate change and air quality scenarios. The EMAC model is constituted by a nonlocal dynamical part with low scalability, and local physical/chemical processes with high scalability. The EMAC chemistry-climate model does not benefit from the support of accelerators which are nowadays installed in many HPC systems. We study strategies to offload the calculation of the atmospheric chemistry to accelerator technologies (GPU and Intel MIC), as in typical model configurations this is the most computational resource-demanding subtask. The proposed solutions extend the Kinetic Pre Processor (KPP) general purpose open-source software tool used in atmospheric chemistry. The changes proposed are expected to contribute to the eventual adoption of accelerated architectures in presently available implementations of Earth system models, towards exploiting the potential of a fully Exascale-capable platform.

This research paper has been supported by VI-SEEM and the detailed results can be found at: 
http://bit.ly/2ehSHUd
Climate Scientific Community paper: WRF-ARW Model for the Prediction of High Temperatures in South and South East Regions of Armenia


The ultimate goal of the study is to develop an early warning system for the south and southeast regions of Armenia (11 in total) by defining specific thresholds for issuing alerts for adverse and severe weather phenomena. High temperature, wind and precipitation weather elements are discussed in the article, based on the experiments performed during the summer periods of 2011 and 2014. The system has been implemented based on the mesoscale Weather Research and Forecasting (WRF) model, which is adapted to the territory of Armenia and used for operational weather forecasting.
The verification methodology is to analyze the model results against observations received from four ground hydrometeorological stations located in the south and southeast regions of Armenia. The correlation coefficients, standard deviations of the differences and biases are calculated for the air temperature and wind speed and for precipitation amount and yes/no contingency tables are constructed.

The full paper, supported by VI-SEEM,  is available at:
 http://bit.ly/2fORAwH

Life Sciences Community: Computer-aided drug designs




The use of computers in biology has enabled a better understanding of mechanistic aspects in health and disease, and has accelerated the development of novel therapeutics. The ultimate goal of the Life Science (LS) community is to be able to define regional characteristics of the populations in South East Europe & Eastern Mediterranean (SEEM) in order to describe their needs in targeted therapies. This is undertaken by the analysis of datasets through integration of data within the VI-SEEM Virtual Research Environment.

One of the focal points of the LS community is computer-aided drug design (CADD) that aims to utilize data from the SEEM region in order to assist the effort for developing personalized therapies in SEEM. Computer-aided drug design of small molecule candidate drugs has recently manifested major successes and it's becoming an essential tool in assisting fast and cost-efficient lead generation in both academia and industry. By using computational methods and the 3D structural information of the protein target, it is now feasible to investigate the detailed underlying molecular and atomic interactions involved in ligand:protein interactions, thus interpreting experimental results in detail. To achieve this aim, the LS community in the SEEM region is in need of a variety of infrastructures, including networking, computing, data infrastructures as well as workflows, variety of codes and application-level services. In this respect the aim is for the VI-SEEM VRE to create and provide the necessary services over a unified infrastructure in order to facilitate research for understanding of disease mechanisms and computer-aided drug design for the SEE and EM populations.

VI-SEEM project participants are heavily involved with CADD activities and will ensure the proper function of the VRE within the CADD framework. Project participants and related institutes within VI-SEEM assist in data collection and analysis, run and optimize computational codes and use the research results to understand the molecular basis of diseases associated with SEE and EM areas with projections to develop personalized therapies. The VRE partners combine their research interests in order to achieve the common goal in an interdisciplinary approach. Such an undertaking requires the use of computational resources for data production, data analyses, storage, and visualization. Partners that contribute in this area are the Biomedical Research Foundation, Academy of Athens (BRFAA), Department of Molecular Design and Biochemical Pharmacology (MDBP), Institute of Molecular Biology “Roumen Tsanev”, Bulgarian Academy of Sciences, the Department of Structure and Function of Chromatin (SFC), Institute of Molecular Biology “Roumen Tsanev”. Bulgarian Academy of Sciences, the Drug Discovery Laboratory, Faculty of Medicine, Bar-Ilan University in Israel, the Faculty of sciences and mathematics, University of Montenegro and the Faculty of Pharmacy, Ss. Cyril and Methodius University of Skopje.

News from the partners: SESAME scientists gain faster access to VI-SEEM Virtual Research Environment


Inter-disciplinary scientific collaboration in the VI-SEEM community has been further enhanced with SESAME (Synchrotron-Light for Experimental Science and Applications in the Middle East) gaining enhanced access to the VI-SEEM data sets and services via its recently established advanced connectivity to GÉANT.

SESAME will provide a vital resource for a wide variety of physics applications, both in the SEEM region and further afield: developing new materials, probing the structure of DNA, penetrating the secrets of chemical compounds, designing pharmaceuticals, performing disease infrared imaging, assessing archaeological artefacts, measuring soil pollution and much else besides.

Once the facility will reach full working capacity, it will produce thousands of gigabytes every day, which will be transferred to HPC centers in and outside the region for analysis, including partners in the Virtual Research Environment of VI-SEEM.

Upcoming events


VI-SEEM worskhops and dissemination events

  • VI-SEEM dissemination event, December 2016, Nicosia , Cyprus
  • VI-SEEM dissemination event, 3-4 December 2016, Amman, Jordan
  • VI-SEEM dissemination event, 22 December 2016, Novi Sad, Serbia
  • Regional training workshop for the Digital Cultural Heritage Scientific community, February 2017, Alexandria, Egypt
Related conferences organized or co-organized by the VI-SEEM partners:

About VI-SEEM


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.

Copyright © 2016 VI-SEEM GRNET S.A., All rights reserved.


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