3rd Call for Proposals for projects accessing the VI-SEEM services and associated infrastructure.

  1. 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 supports open calls to scientific communities in the region in the form of resource pooling between the resource providers.

VI-SEEM opens the third Call for Proposals for projects accessing the VI-SEEM services and associated infrastructure. The call is addressed to scientists and researchers that work in academic/research institutions in the region of South Eastern Europe and Eastern Mediterranean. More specifically countries are (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.

The project proposals should address non-proprietary/open research topics in the 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. Access to the VI-SEEM data repository service might be granted for up to 2 years (see the relevant section).

  1. Scope and criteria of access

The third call enables researchers from selected countries and applications fields to obtain access to the advanced services of the VI-SEEM Virtual Research Environment. 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.
  • Innovation potential.
  • Scientific and/or social impact of the proposed research.
  • The need for usage of the selected services and resources.
  • The ability to provide the 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 the using the selected resources and services.
  • Feasibility of the project based on a technical evaluation and the availability of resources.
  • Potential for the collaboration among scientists in the eligible countries 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.

  1. 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 centers that offer resources in the various resource-providing countries.

Industrial partners may participate only as collaborators in proposal that are 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.

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

In the scientific 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.
  • LS Area F: Reconstruction of medical imaging data.

In the scientific 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 scientific field of Digital Cultural Heritage

  • DCH Area A: Online services and access to repositories in order to enable studies of the immense cultural heritage assets in the region (e.g., searchable digital libraries; with support of meta-data and OCR for Latin characters).
  • DCH 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).
  • DCH Area C: Unsupervised feature learning in photogrammetric techniques, data processing for image classification; semantic referencing; and geo-referencing.
  • DCH Area D: Architecture, Urban Modelling and Planning.
  • DCH Area E: Bioarcheology and Natural Sciences.
  • DCH Area F: Material Science.

In the Cross-disciplinary scientific field:

  • CD Area A: Data Visualization
  • CD Area B: Data Analytics and Processing
  • CD Area C: Remote Sensing and Photometric Techniques

or any other combination of above

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, users should acknowledge the use of the VI-SEEM VRE services in all publications presenting results obtained from using the allocated resources.

  1. Application process

All proposals should be submitted electronically via the following link:

http://survey.ipb.ac.rs/index.php/292255

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.

Only complete, good quality applications will be considered by the reviewers. For an example of a successful application please refer to this PDF. The length of the answers should follow more or less the provided example.

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 3rd call: Monday the 12th of March 2018 at 18:00 CEST

Deadline for submission of proposals to the 3rd call has been extended to Monday the 26th  of March 2018 at 18:00 CEST

  1. Process details and deadlines

After the deadline, the call organizing committee will validate the applications, and if any clarifications are needed, they will have to be provided within 5 working days of receipt of the request for clarifications.

The proposals will  initially 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 independent scientific experts. 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.

  1. Important Dates:

  • Opening date: 12th February 2018
  • Closing Date: 12th March 2018  26th March 2018
  • Allocation decision: latest April 2018
  • Allocation Start Date of awarded proposals: latest April 2018
  • Allocation end date of award: April 2020 for computational projects, April 2021 for some data projects.
  • Final report from successful projects: May 2020
  1. Contacts

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

  1. 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.

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, FYROM, Greece, Hungary, Jordan, Romania and Serbia. In total 15 million CPU core hours,300 million GPU core hours and 15 million Phi core hours will be available for this call. 7 out of 15 million CPU core hours are at a Blue Gene supercomputer.

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, FYROM, Greece, Israel, Moldova and Romania. In total, 300 VM cores are to be provided in this call.

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

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. The service is able to support up to 16 TB of data, and in this call each user will be provided with 50 GB of storage for up to two years from the beginning of its 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 suitable also for the general public. The service is connected with 2 x 10Gbit/s connections, and it is able to support 1 PB of data. Each project is eligible to use up to 10TB of disk space for up to two year from the initiation 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 initiation of the project.

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.

VI-SEEM data analysis service: This service provides the capability to the VRE users to carefully and efficiently investigate and analyze even very large, unstructured datasets. The VI-SEEM data analysis service is based on Hadoop technology, and provides access to 60 CPU cores, 180 GB of RAM and 5.3 TB of storage in HDFS.

Application Specific Services

The Live Access Server (LAS) – http://las.vi-seem.eu

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, …) 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 – http://dchrepo.vi-seem.eu

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 – http://bioserver-3.bioacademy.gr/Bioserver/ChemBioServer/

ChemBioServer is a publicly available web application for effectively mining and filtering chemical compounds used in drug discovery. 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.

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.

Furthermore, 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.

AFMM – http://afmm.vi-seem.eu

AFMM provides an automated platform with which the users can generate parameters for modeling small molecules with Molecular Dynamics simulations. The method used fits the molecular mechanics potential function to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. The program optimizes an initial parameter set (either pre-existing or using chemically-reasonable estimation) by iteratively changing them until the optimal fit with the reference set is obtained. By implementing a Monte Carlo-like algorithm to vary the parameters, the tedious task of manual parameterization is replaced by an efficient automated procedure. The program is best suited for optimization of small rigid molecules in a well-defined energy minimum, for which the harmonic approximation to the energy surface is appropriate for describing the intra-molecular degrees of freedom.

Due to the abundance of organic molecules, no parameters have been created for the full chemical space. Thus, there is a great need for molecule parameterization before proceeding to Molecular Dynamics calculations. AFMM allows users to access parameters for their Molecular Dynamics simulation of small organic molecules that can be used as drugs or materials.

NANO-Crystal – http://nanocrystal.vi-seem.eu

NANO-Crystal is a web-based tool, is implemented for the construction of spherical nanoparticles of a given radius.

More specifically, our goal is to find the number and the Cartesian coordinates of smaller spheres that fit on the surface of the nanoparticle and visualize the output morphology. The home page menu allows two selections for the user:

  • (i) the radius of the nanosphere (nm), and
  • (ii) the radius of smaller spheres (nm), that will cover the surface of the nanoparticle

The program computes the number of smaller spheres that fit on the bigger surface and the user can download their Cartesian coordinates (output format .xyz). The program code is implemented using PHP server-side scripting language, which is embedded into the HTML and CSS code. JQuery, a cross-platform JavaScript library, is also used. For local host of the webpage tool, the Wamp server is used. Moreover, we have developed a crystal computational morphology toolbox for constructing and modelling different crystal nanoparticle shapes. We use computational approaches for computing the macroscopic morphology of any periodic crystal by forming different shapes based on Miller indices and the distance measure from the center of the crystal and visualizing the resulting crystal. That crystal is a polyhedron that is created as the intersection of multiple polyhedra and individual planes via the steps that follows. This tool is planned to be imported in the NANO-Crystal webserver within 2017.

This tool enables users to construct spherical nanoparticles. Moreover, within 2017 we imported our new code which enables the user to construct different crystal nanoparticle shapes based on Miller indices and the distance measure from the center of the crystal.

Subtract – http://subtract.vi-seem.eu

Subtract is an online tool that can calculate the volume of a binding site found in a protein. Subtract accepts an atom selection in the form of a PDB file and computes the three-dimensional convex hull of the atoms points with the help of SciPy library. The next step of the algorithm is to compute the volume of the convex hull and the volume of the atoms that are included in the solid based on their van der Waals radii. The subtraction of those two volumes yields the volume of the investigated cavity. The algorithm computes cavity volumes of trajectory frames in parallel for maximum efficiency and speed. It requires minimal usage of memory due to the fact that it follows a buffering strategy of reading file chunks and therefore there is no need to load the entire file into memory. There is a wide support of trajectory formats like Gromacs trajectory files and multi-model PDB files due to its dependency to the MDTraj library.

The measurements are evaluated for statistical significance using Wilcoxon Signed-Rank test and had their null hypothesis rejected (p-value < 0.005). Subtract is a tool that has been created to solve the problem of accurate measurement of the protein binding sites, and works both for crystal structures downloaded from the Protein Data Bank and for protein structures arising from Molecular Dynamics simulations trajectories.

  1. 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.