1st Call for proposals for projects accessing VI-SEEM services

Introduction

 

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. Such services are in the areas of Compute resource provisioning (HPC, Grid and Cloud), Storage and Data services provisioning, Dataset provisioning, Software and Scientific Workflow provisioning as well as Application Specific service provisioning. These services create a unique Virtual Research Environment (VRE), thus improving research productivity and competitiveness on the pan-European level.

VI-SEEM is opening the 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 South Eastern Europe and the Eastern Mediterranean. More specifically these are (in alphabetical order): 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.

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 it offers.

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

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.

 

Scope and criteria of access

 

The first call enables researchers from selected countries and research fields to obtain access to the advanced services of the VI-SEEM Virtual Research Environment.

 

Eligible projects are only the ones that address one of the following scientific and/or social challenges:

In the field of Life Sciences

  • LS Area A: Modeling and Molecular Dynamics (MD) study of important drug targets
  • LS Area B: Computer-aided drug design
  • LS Area C: Analysis of Next Generation DNA sequencing data
  • LS Area D: Synchrotron data analysis
  • LS Area E: Image processing for biological applications

In the field of Climate Research

  • CR Area A: Regional climate modelling to better understand and predict climate change and impacts, and phenomena such as dust storms
  • CR Area B: Air quality modelling, including atmospheric chemistry and air pollution transport
  • CR Area C: Weather forecast and extreme weather prediction, model development, application

In the field of Digital Cultural Heritage

  • Area A: Online services and access to repositories in order to enable studies of the cultural heritage assets in the region (e.g., searchable digital libraries; with support of meta-data and OCR for Latin characters).
  • Area B: Online visualization tools and data management systems to drive breakthrough contributions to art historical problems (e.g., interactive visualization viewer of RTI files and 3D models with digital libraries integration).
  • Area C: Unsupervised feature learning in photogrammetric techniques, data processing for image classification; semantic referencing; and geo-referencing.

 

Project proposals must be of high scientific and social value.

 

The criteria for the evaluation of projects for accessing the available resources will be:

  • Scientific excellence
  • Scientific and/or social impact of the proposed research
  • The need for usage of the selected services and resources
  • The ability to provide project results (mainly data sets but also services and software) as services for other future VRE users
  • Maturity and experience of the principal investigator and his/her team in the research field as well as in using the selected resources and services
  • Feasibility of the project based on the technical evaluation and the availability of resources
  • Potential for the collaboration among scientists in more than one eligible country for this call

 

A limited number of applications will be selected based on the project proposal demand and the availability of resources.

 

VI-SEEM aims at a balanced provision of resources to the whole spectrum of scientific fields between the three target communities that this call addresses, as well as to as many as possible countries in the South-eastern Europe and Easter Mediterranean region.

 

Eligibility

 

Eligible applicants (as Principal Investigators) are scientists affiliated with academic or research institutions in the following countries: (in alphabetical order): Albania, Armenia, Azerbaijan, Bosnia and Herzegovina, Bulgaria, Cyprus, Egypt, Former Yugoslav Republic of Macedonia, Georgia, Greece, Hungary, Israel, Jordan, Lebanon, Moldova, Montenegro, Romania Serbia and Turkey.

Collaborators in proposals might reside in any country provided that no specific geographical restrictions apply for access by the corresponding centres that offer resources in the various resource-providing countries.

Industrial partners may participate only as collaborators in proposal that is led by academic or research institutions in the eligible countries, and only if the aims and objectives of the project is open research with results to be published in research journals or conferences.

For more information on the resources provided to the VRE please refer to section: Available Services and Resources.

 

As specified in Section 2 the research should address one of the predefined scientific areas in Life Sciences (LS Areas A, B, C, D, E), Climate Research (CR Areas A, B, C) and Digital Cultural Heritage (DCH Areas A, B, C).

 

Applicants should commit to using the resources that will be allocated to them, as well as to providing reports of their work based on the proposed time schedule (see below). Further to that, scientists should acknowledge the use of the VI-SEEM VRE services in all publications presenting results obtained from using the allocated resources.

 

Available Services and Resources

 

The infrastructure of the VI-SEEM VRE consists of resources of various types – HPC resources – clusters and supercomputers with different hardware architectures, Grid sites, Clouds with possibility to launch virtual machines (VMs) for services and distributed computing, and storage resources with possibility for short and long term storage.

 

Computational and Storage Services Available

 

HPC Resources: The HPC resources of the project consist of clusters with low-latency interconnection or supercomputers. Most of the systems are based on CPUs with x86_64 instruction set, some of them equipped with accelerators (GPUs and Intel Xeon Phi coprocessors), but also there are BlueGene/P systems, as well as one based on the Cell processor (PS3 cluster IMAN1-Booster/King). HPC resources are offered by the following countries: Albania, Armenia, Bulgaria, Cyprus, Egypt, FYR of Macedonia, Greece, Hungary, Jordan, Romania and Serbia. In total 19 million CPU core hours, 370 million GPU core hours and 16 million Phi core hours will be provided in this call.

https://wiki.vi-seem.eu/index.php/Main_Page#HPC_Resources

 

Cloud Resources: The Cloud resources available in the call can be used in two ways. Those clouds that provide the ability to launch VMs with public IPs give the possibility to deploy VRE services for their main or backup/fail-over instance. VMs that possess only private IPs can be used for distributed data processing where necessary. Cloud resources are provided by the following countries: Albania, Armenia, Bosnia, Bulgaria, Cyprus, FYR of Macedonia, Greece, Israel, Moldova and Romania. In total around 300 VM cores are to be provided in this call.

https://wiki.vi-seem.eu/index.php/Main_Page#Cloud_Resources

 

Grid Resources: The Grid resources, available in this call, are provided mostly from smaller clusters. Grid resources for the VI-SEEM VRE are provided from the following countries: Bulgaria, FYR of Macedonia, Georgia, Greece, Moldova, Montenegro and Serbia.

https://wiki.vi-seem.eu/index.php/Main_Page#Grid_Resources

 

VI-SEEM Simple Storage Service: The VI-SEEM Simple Storage Service (VSS) is a secure data storage service provided to VI-SEEM users for storing and sharing research data as well as keeping it synchronized across different computers. Data sharing will be possible with other registered VI-SEEM users or with anyone else by using public links which can be protected with passwords if needed. Each user will be provided with 50 GB of storage for up to two years from the beginning of their project.

 

VI-SEEM Repository Service: The main storage service that will allow the users of the VI-SEEM VRE to deposit and share data is the VI-SEEM Repository Service (VRS). This is VI-SEEM main repository for hosting the Regional Community Datasets. It can also be used to host publications and their associated data, as well as software or references to software and workflows used to generate such data and publications. The VRS is also the service designated for storing simplified data formats such as images, videos or others formats suitable also for the general public. Each project is eligible for up to 10 TB of storage for up to two years from the start of the project.

 

VI-SEEM Archival Service: Data archiving is the practice of moving data that is no longer being used or are being used in a less frequent fashion into a separate storage service. It is a single set or a collection of historical records specifically selected for longer term retention and future reference. Additionally, data archives contain data that are important for future reference or it is important to preserve them for regulatory and audit purposes. In science, archived data are important for future reference and reproducibility of scientific simulations. Each project will be eligible for storing up to 10 TB in the archival service of the project for at up to two years from the start..

 

VI-SEEM work storage space / local storage and data staging: This service refers to storage space available by the computational resource providers to store temporary data for the purposes of processing them, or for storing results of computations. The service will be available for 12 months from the start of the project. The maximum capacity depends on the service provider.

 

Application Specific Services

 

The Live Access Server (LAS)

The Live Access Server (LAS) is a highly configurable server designed to provide flexible access to geo-referenced scientific data. It can present distributed data sets as a unified virtual data base through the use of DODS networking. Ferret is the default visualization application used by LAS, though other applications (Matlab, IDL, GrADS etc) can also be used.

LAS enables the web user to:

  • visualize data with on-the-fly graphics
  • request custom subsets of variables in a choice of file formats
  • access background reference material about the data (metadata)
  • compare (difference) variables from distributed locations

 

Clowder

Clowder is a research data management system designed to support any data format and multiple research domains. It contains three major extension points: pre-processing, processing and previewing. When new data is added to the system, pre-processing is off-loaded to extraction services for extracting appropriate data and metadata. The extraction services attempt to extract information and run pre-processing steps based on the type of the data, for example to create previews. This raw metadata is presented to the user in the Clowder web interface. Users can upload, download, search, visualize and get various information about these data.

Data in the case of VI-SEEM and more specifically in the field of Digital Cultural Heritage can be of very diverse types and formats.

More specifically users can upload massively (zipped) or individual files of:

  • 3D Models: where extractors clean up and prepare for visualization on the platform itself.
  • Scanned books and their metadata: OCR algorithms will be used to extract the text in the documents so that users can find books using both metadata information and the book’s contents.
  • Image, text and sound files and their metadata, organised in collections.
  • Advanced documentation data, such as Reflectance Transformation Imaging, and analysis of material properties of structures, works of art and artefacts.

 

ChemBioServer

ChemBioServer is a web-application for effectively mining and filtering chemical compounds used in drug discovery. ChemBioServer allows for pre-processing of compounds prior to an in silico screen, as well as for post-processing of top-ranked molecules resulting from a docking exercise with the aim to increase the efficiency and the quality of compound selection that will pass to the experimental test phase.

It provides researchers with the ability to:

  • browse and visualize compounds along with their properties
  • filter chemical compounds for a variety of properties such as steric clashes and toxicity
  • apply perfect match substructure search
  • cluster compounds according to their physicochemical properties providing representative compounds for each cluster
  • build custom compound mining pipelines
  • quantify through property graphs the top-ranking compounds in drug discovery procedures.

 

Finally, successful applicants will get access to all public services, data sets, workflows and codes available in the VI-SEEM VRE – https://vre.vi-seem.eu.

 

The number of accepted projects will depend on the technical and scientific merit of the proposals and the availability of resources. HPC projects are expected to be assigned a maximum of 3 Million core hours. A larger number of requested core hours will require elaborate and well documented justification.

 

Application process

 

All proposals should be submitted electronically via the following link:

 

http://survey.ipb.ac.rs/index.php/112349?lang=en

 

The application form is also available in pdf format in order for applicants to have the full list of questions available. Please note that you have to fill in the on line form for your application to be taken into account.

 

VI-SEEM Access Team will be available to answer questions while the call is open. You can contact the access team by sending e-mail to: service-access@lists.vi-seem.eu

 

Deadline for submission of proposals to the 1st call is Monday the 14th of November 2016 at 18:00 CEST

 

Process details and deadlines

 

After the deadline of the call on the call organizing committee will validate the applications, and if any clarifications are needed, they will have to be provided by the 18th of November 2016.

 

The proposals will undergo a technical review and a lightweight scientific review in order to determine the eligibility and suitability of applications for the requested services and systems. Applications that are successful at this stage will undergo scientific peer review by scientific experts in all countries of the region. Reviewers are allowed to ask applicants for clarifications.

 

The VI-SEEM access committee comprising of the VI-SEEM project technical board will prioritize the applications based on the criteria set in Section “Scope and criteria of access” of this document.

 

The applicants will be notified of the final results of the evaluation. Successful applicants will receive further details regarding the services and resources and the process to obtain user accounts.

 

Important Dates:

 

  • Opening date: 14th October 2016
  • Closing Date: 14th November 2016
  • Clarification provided by applicants if needed: 18th November 2016

 

  • Allocation decision: January 2017
  • Allocation Start Date of awarded proposals: January 2017
  • Allocation end date of award: January 2018 for computational services, January 2019 for some data services.
  • Final report from successful projects: May 2018

 

Contacts

 

For any queries related to applications please contact: service-access@vi-seem.eu

 

About

 

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.