Competence centre BBMRI

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BBMRI.jpg


CC Coordinator: Petr Holub

CC members' list: cc-bbmri AT mailman.egi.eu

CC meetings: http://indico.egi.eu/indico/categoryDisplay.py?categId=140


Introduction

Thousands of biobanks in Europe have been collecting data, samples and images of millions of individuals in different stages of their lives, during disease and after recovery. Biobanking is currently evolving from local repositories to a pan-European RI the BBMRI-ERIC (Biobanking and BioMolecular resources Research Infrastructure – European Research Infrastructure Consortium). The BBMRI CC facilitates the implementation of big data storage in combination with data analysis and data federation by integrating technologies from community projects, EGI and other e-Infrastructures. The CC will capture requirements and provide technology demonstrators to:

  • Increase biobank interoperability and data discovery in BBMRI community by providing a secure and standard way to share biobank high-throughput data.
  • Provide biobanking community with a federated infrastructure for big data storage and intensive data analysis.
  • Facilitate the efficient use of bio-resources by supporting visibility and sharing, while also respecting the protection level required by owners of the data and samples.
  • Facilitate the efficient use of economic resources in BBMRI by providing a common infrastructure for storage and processing of big data.

OSG, as an associated partner will provide interoperability mechanisms for the virtual organisations of the BBMRI competence centre to use OSG resources, and will organise a joint information sharing workshop to discuss interoperability and new technologies that may affect international resource sharing.

  • CC project duration: 24 months, from M7 until M30 of EGI-Engage (1. September 2015 - 31. August 2017)
  • CC members from the EGI-Engage project:
  1. BBMRI-ERIC (coordinator) - 4PM
  2. BBMRI-CZ - 3PM
  3. BBMRI-NL - 5PM
  4. BBMRI-SE - 1PM
  5. CESNET, Czech Republic - 5PM
  6. SURFsara, The Netherlands - 5PM
  7. KTH, Sweden - 6PM
  8. University of Indiana representing Open Science Grid (Unfunded)

The CC is open for other members to join.


Concept and approach

This CC will build upon the EGI federated cloud (IaaS), the BiobankCloud Platform as a Service (PaaS), and EUDAT’s services and technologies to support local biobanks by connecting data resources in a federated cloud infrastructure in coordination with the ELIXIR cloud working group and BBMRI-ERIC Common Service IT.

We will first collect and publish requirements in terms of data security, storage and federation, including implementation of use cases to facilitate policy making and training activities. In this CC we will explore how the EGI IaaS cloud, BiobankCloud PaaS and EUDAT platform could work together to (i) support biobanks with a locally deployable cloud infrastructure for data and Virtual Machines (VMs) that can be accessed by remote sites and (ii) connected into trusted workspaces for research communities that embark on trans-national and multi-center studies across biobanks. The CC will be involved in providing requirements and testing services and technologies.


Tasks

Task 1 - Technology exchange, training, outreach and support

Goal: technology exchange within the Competence Centre, and training, outreach and support on Biobank joint infrastructure to the BBMRI-ERIC community

Related internal deliverables and milestones:

  • Regular technology exchange / project meetings
  • Coordination with ELIXIR EGI-Engage Competence Centre
  • User documentation for services and technologies M13-M30
  • Outreach and training material on services M13-30

Task 2 - AAI integration

Lead: KTH

Goal: Integration of existing services and technologies from the BiobankCloud and the EGI Federated Cloud infrastructure. Attention will be especially paid to the required 'authentication and authorisation infrastructure' (AAI), including security levels and encryption.

Task 3 - Data identification, storage, provenance

Lead: BBMRI-ERIC

This task will evaluate data identification, storage and provenance services from EGI and third party e-infrastructure/technology providers, such as EUDAT and iRODS. Evaluation will be performed with respect to functionality and usefulness for BBMRI-ERIC goals.

Task 4 - Integration & pilot deployment

Goals: Exploitation of Task 2 and 3. Enabling research consortia to implement integrated data analysis across BBMRI biobanks, central public repositories and their own ‘study’ data. We will deploy tools to support heterogeneous data processing workflows in the EGI Cloud. This includes Virtual Machines (VMs) with tools for data staging (e.g. B2STAGE, B2SHARE from EUDAT), for connectivity to relevant data providers (ranging from de-centralized data with access restrictions such as individual biobank data to data from central repositories such as ENA/EGA) and for platform facilities executing analysis workflows (e.g. BiobankCloud).

Milestones and deliverables

(To report to the European Commission by EGI-Engage)

  • M6.2 Security and privacy requirements and secure storage architectural design are agreed
    • Date: Feb.2016
    • Description: Requirements are approved by the BBMRI Research Infrastructure community and the developers of the secure storage solution verified and accepted the design
  • D6.8 Analysis of requirements on biobank and study workflows (R)
    • Delivery date: Oct 2016
    • Description: This document provides a summary and an analysis of the requirements captured by the BBMRI-ERIC Competence Centre for workflows from the biobank community.
  • D6.11 Security toolset release for BBMRI-ERIC (OTHER)
    • Delivery date: Nov 2016
    • Description: The final version of the toolset and security libraries released by the BBMRI-ERIC Competence Centre. This includes implementation and testing of the AAI in the project.
  • D6.16 Evaluated cloud environment and demonstrator of analysis workflow for biobank studies (DEMONSTRATOR)
    • Delivery date: Aug 2017
    • Description: A demonstrator of a biobank research workspace running in the EGI cloud, together with an evaluation of its suitability in a typical NGS use case.

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