Call for SME proposals for projects accessing VI-SEEM Resources and Services

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, 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 is opening a specific continuous Call for Proposals for preparatory/development projects accessing the VI-SEEM services and associated infrastructure specifically for partnerships involving SMEs and academic/research institutions. The call is addressed to consortia of scientists and researchers and SMEs that work in academic/research institutions and SMEs located 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.

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 SMEs and scientists from the selected scientific fields to have access, via joint projects, 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. VI-SEEM Cloud and Grid services are not provided through this call.

Access to underlying computational and storage resources will be awarded for a maximum period of 3 months. Access to the VI-SEEM data repository service might be granted for up to 12 months (see the relevant section).

Access is provided for free for research purposes and as specified in this call. If applicants require extra support for services other than those that are specified in this call they can communicate with individual service providers to negotiate their access method. In case you are interested for paid services please contact individual service providers or send an email to: vi-seem-pmo@vi-seem.eu.

2. Scope and criteria of access

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

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

  • The need for usage of the selected services and resources.
  • The results of the project should be of no direct commercial value and should be publishable.
  • Feasibility of the project based on a technical evaluation and the availability of resources.

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.

3. 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.

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 (SMEs) – preferably from the eligible countries – are required to be participants in the proposals. They must be participating as collaborators, in proposals with academic or research institutions in the eligible countries, and only if the aims and objectives of the project are compatible with the criteria set in section 2 of this call.

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 areas:

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.

In the scientific field of Climate Research

  • CR Area A: Regional climate modeling to better understand and predict climate change and impacts, and phenomena such as dust storms.
  • CR Area B: Air quality modeling, 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.

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 and should make these results publicly available.

4. 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. It is advised that applicants aim for project with a maximum requirement of 100.000 CPU core hours or 6.500 GPU or Phi node hours.

In total 1.5 million CPU core hours, 150 million GPU core hours and 5 million Phi core hours will be available for this call. It is advised that applicants aim for project requesting 100.000 core hours in order to be able to maximise the projects that can be accepted. However large projects (with more than 100.000 core hours) can be accepted if there is enough justification in the application forms. Although this is a continuous Call for Proposals for preparatory/development projects accessing the VI-SEEM services and associated infrastructure, due to limited amount of available resources the consortium will support up to 15 projects in total. Detail description of particular HPC resource is available at https://vi-seem.eu/infrastructure/.

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 three months from the beginning of its project. 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.

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 1TB of disk space for up to one year from the initiation of the project in case of sharing open data within the whole of the VI-SEEM community. In the case that the data is not openly shared then storage is restricted to 3 months as with all other services offered in this call.

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 6 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 analyse 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, 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 – 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 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:

  • the radius of the nanosphere (nm), and
  • 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 modeling 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 will be importing our new code which enables the user to construct different crystal nanoparticle shapes based on Miller indices and the distance measure from the centre 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.

5. Application process

All proposals should be submitted electronically via the following link:

http://survey.ipb.ac.rs/index.php/934822

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.

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.

You can submit proposals at any time. The evaluation team should provide a final evaluation of the proposals within a months from application submission. The evaluation team has the right to ask the applicant for clarification during the evaluation process.

Application will stop being accepted 4 months before the end of the VI-SEEM project which is the end of September 2018. The VI-SEEM consortium might terminate this call and stop accepting further applications at any point by publishing this decision in the current web address of the call. This might mainly happen if demand for successful proposals exceeds the current resource availability.

6. Evaluation process

After the deadline for submitting proposals, each proposal is subject to a 3-step evaluation procedure:

  • Stage A: Completeness and eligibility check.
  • Stage B: Technical Assessment, based on the objectives and criteria of the call as outlined in paragraph 2 hereof.
  • Stage C: Final decision on the allocation of services and resources.

Stages A and B and C are conducted by the Technical Committee on the basis of paragraphs the criteria of the call. Step A aims to ensure the completeness, correctness and understanding of the application by the Technical Committee and to check that the eligibility criteria as outlined in paragraph 3 hereof are met. At Stage B, which concerns the technical evaluation of the proposals, only proposals that have passed successfully stage A take part.

Provided that the necessary conditions are met as set forth in paragraph 2 above, the assessment of the degree of necessity to use supercomputer resources according to the Technical Committee judgment is as follows:

  • “High necessity”, score 7-10
  • “Medium necessity”, score 5-7
  • “Low necessity,” score 0-4.

At Stage C proposals that are of medium necessity and higher (score > 5) are awarded the necessary resources. Note that resources awarded might be less than requested based on the suggestion of the evaluation at Stage B and the overall resource availability in the infrastructure.

Participants will be informed of the final evaluation results by email. The PI of the selected proposals will receive further information on their access to VI-SEEM infrastructure and the procedure for obtaining user accounts.

7. Contacts

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

8. 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.