Enabling a federated environment to support biomedical research. Gianmauro Cuccuru CRS4
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1 Enabling a federated environment to support biomedical research Gianmauro Cuccuru CRS4
2 ELIXIR connects national bioinformatics centres and EMBL- EBI into a sustainable European infrastructure for biological research data medicine agriculture 2 environment bioindustries ELIXIR underpins life science research across academia and industry
3 ELIXIR: the European Research Infrastructure for biological data ELIXIR connects national infrastructures and EMBL- EBI 16 Member states + EMBL Belgium, Czech Republic, Estonia, Denmark, Finland, France, Israel, Italy, Netherlands, Norway, Portugal, Slovenia, Spain, Sweden, Switzerland, UK 2 countries working towards membership Greece, Ireland
4
5 A distributed infrastructure scales with the challenges ELIXIR deliver services through national ELIXIR Nodes ELIXIR Nodes build local bioinformatics capacity throughout Europe ELIXIR Nodes build on national strengths and priorities 5
6 ELIXIR Infrastructure Data Sustain core data resources Tools Services & connectors to drive access and exploitation Compute Access, Exchange & Compute on sensitive data Standards Integration and interoperability of data and services. Training Professional skills for managing and exploiting data 6
7 ELIXIR- ITA 7
8 ELIXIR AAI history where we are now Use case gathering - - Autumn 2014 h?ps:// europe.org/documents/elixir- aai- use- cases Requirements and design Spring 2015 h?ps:// europe.org/documents/aai- requirements- and- design Deployment starts Autumn 2015 EXCELERATE WP4.3.1 Part of ELIXIR Compute plaqorm First release - - August 2016 UnTl that ELIXIR AAI in pilot status Key components up and running already Mikael Linden, Michal Prochazka AAI workshop March 2016 Manchester
9 ELIXIR AAI design Relying services EGA elearning wiki Cloud Intranet Data archive Credential translation Step-up AuthN ELIXIR Proxy IdP edugain IdPs ELIXIR Directory Common IdPs Dataset authorisation management (REMS) Bona fide management ELIXIR AAI Group/role mgmt (PERUN) Attribute self-management External authentication (e-infrastructures)
10 ELIXIR AAI design Relying services EGA elearning wiki Cloud Credential translation Step-up AuthN ELIXIR Proxy IdP Intranet Data archive ELIXIR Proxy IdP - User has one ELIXIR identity - User can authenticate Dataset authorisation using management external identities ELIXIR AAI - Proxy IdP consolidates Group/role management the Ids - ELIXIR Acts as SAML Bona IdP fide management for Relying Directory services (later also OAuth2) Attribute self-management edugain IdPs Common IdPs External authentication (e-infrastructures)
11 ELIXIR AAI design Relying services EGA elearning wiki Cloud Intranet Data archive Credential translation Step-up AuthN ELIXIR Proxy IdP Step-up Authentication 1. User authenticates Dataset authorisation weakly management using external authentication ELIXIR AAI 2. User authenticates Group/role management with second factor ELIXIR Bona fide management Directory - e.g. SMS-OTP or a mobile app Attribute self-management edugain IdPs Common IdPs External authentication (e-infrastructures)
12 ELIXIR AAI design Relying services EGA elearning wiki Cloud Credential translation Step-up AuthN ELIXIR Proxy IdP edugain IdPs Intranet Data archive Credential translation - ELIXIR Proxy IdP is web ELIXIR AAI - Some services Dataset are authorisation non-web - Access to management cloud middleware - SSH access Group/role to management a cloud VM ELIXIR - Triggering file transfer Bona fide management - Directory X.509 (CILogon) Attribute self-management - SSH public key - Kerberos Common IdPs External authentication (e-infrastructures)
13 ELIXIR AAI design Relying services EGA elearning wiki Cloud Intranet Data archive Credential translation Group management (PERUN) - Users can Step-up create and manage AuthN groups ELIXIR - Add/Invite new members ELIXIR Proxy IdP Directory - Remove members - Etc - Access to services can rely edugain IdPs on group memberships Common IdPs Dataset authorisation management Bona fide management ELIXIR AAI Group/role management Attribute self-management External authentication (e-infrastructures)
14 Intranet and mailing lists EGA elearning wiki Current operational integration to ELIXIR Relying AAI. services Intranet Cloud (Drupal) Mailing lists (Mailman) Credential translation Step-up Authentication AuthN ELIXIR Proxy IdP edugain IdPs Group memberships (batch job) ELIXIR Directory Google Dataset authorisation management Bona fide management ELIXIR AAI Group management (Perun) Attribute self-management External authentication (e-infrastructures)
15 Galaxy Galaxy is an open, web- based platform for accessible,reproducible, and transparent computational biomedical research. Accessible: Users without programming experience can easily specify parameters and run tools and workflows. Galaxy integrates a multitude of different tools by giving them the same look and feel Reproducible: Galaxy captures information so that any user can repeat and understand a complete computational analysis. Transparent: Users share and publish analyses via the web and create Pages, interactive, web- based documents that describe a complete analysis.
16 Galaxy main usage Publicly accessible server
17 Galaxy
18 Galaxy
19 Galaxy - Pages
20 Galaxy - Histories
21 Galaxy - Workflows
22 Galaxy - Libraries
23 Galaxy Tool Shed
24 ITA microbiology, variant analysis and transcriptomics. EPIGEN flagship project. metagenomics oriented
25 NGalaxy? Local
26 NGalaxy? Local Federated
27 NGalaxy? Local Federated Federated+
28 NO
29 Thank you
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