Skip to content

Instantly share code, notes, and snippets.

@stain

stain/corbelarate.md

Last active November 9, 2015 14:26
Show Gist options
  • Star 1 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save stain/53d25514e5992523e4ea to your computer and use it in GitHub Desktop.
Save stain/53d25514e5992523e4ea to your computer and use it in GitHub Desktop.
Download ZIP
Corbelerate work packages overview
Raw
corbelarate.md

Corbelerate work packages overview

.. and tasks that might be relevant to UNIMAN

Excelerate

  • WP1: Tools Interoperability & Registry
    • Leads: Søren Brunak (DK) and Alfonso Valencia (ES)
    • UNIMAN 0 PM
    • Task 1.1: Federated Registry Curation (EDAM)
    • Task 1.3: Workbench integration and interoperability
      • Technically, this service will translate the description of any tool or service that is registered in the Tools and Data Services Registry into the metadata format required by the existing major workbenches, including Mobyle, Galaxy and Taverna.
  • WP2: Infrastructure for Community-led Benchmarking
    • Leads: Alfonso Valencia (ES) and Søren Brunak (DK)
  • WP3: Data Resources and Services
    • Leads: Jo McEntyre (EMBL-EBI) and Christine Durinx (SIB)
  • WP4: Compute, Data access and exchange services
    • Leads: Tommi Nyrönen (FI) and Ludek Matyska (CZ)
  • WP5: ELIXIR Interoperability Backbone
    • Leads: Barend Mons (NL) and Carole Goble (UK)
    • UNIMAN: 30 PM (Note: PMs below split across 15 partners)
    • Task 5.1: FAIR Principle Interoperability Implementation Agreements (62PM)
      • Subtask 5.1.1: Use Cases (WP6 to 9) (26PM)
        • Common APIs/descriptors, first WP7 (Plant), WP8 (Rare disease), then WP8 (Marine).
      • Subtask 5.1.2 Core and Named Resources (WP3) (18PM)
        • Example: HCLS Dataset
      • Subtask 5.1.3 Global engagement: international organisations and multilateral forums (18PM)
        • IMI, RI, EUDAT, EUON, NIH B2DK, Ga4GH, Force11, W3C, DataCite, ORCID, VIVO, ORE, RDA
  • Task 5.2 FAIR Interoperability Implementation Services (65PM)
    • Subtask 5.2.1: Identity Management, Mapping and Tracking services (14PM)
    • Subtask 5.2.2: Reporting Guidelines, Formats, Controlled Vocabulary Services (10PM)
    • Subtask 5.2.3: Dataset publishing for API interoperability (13PM)
    • Subtask 5.2.4: Biological knowledgebase publishing for Linked Data interoperability (14PM)
    • Subtask 5.2.5: Sustainability of Interoperability Implementation Services (14PM)
  • Task 5.3: “Bring Your Own Data” (BYOD) & Capacity Building Workshops (125.2PM)
    • Subtask 5.3.1: Manage and Run BYOD Workshops (65PM)
    • Subtask 5.3.2: Create and manage BYOD training materials (24.2PM)
    • Subtask 5.3.3: Data Node Capacity Building (36PM)
  • D5.1: Interoperability Implementation Regulations.
    • A set of standards, rules, controlled vocabularies, authorized unique identifiers and interoperable service APIs for the data repositories and biological knowledge bases agreed and implemented in the field with WP6 to 9, and WP3; resources registered in BioSharing; BioCatalogue and BioRegistry (WP1); ontologies accessible via Ontology Lookup Services. (M18)
  • D5.2: Sustainability business cases
    • ..for Interoperability Implementation Services, including contractual arrangements with non-ELIXIR resources. Data stewardship agreements with major data interoperability activities in Europe [EGA, EUDAT etc.] USA [DataOne, BD2K] and globally [RDA, GA4GH, Force11]. (M36)
  • D5.3: Bring Your Own Data
    • 8 delivered workshops and established roll-out programme across WP10 Data Node capability network; materials deposited on WP11 TeSS. (M24)
  • WP6: Use Case A: Marine metagenomic infrastructure services as driver for research and industrial innovation
    • Leads: Nils P Willassen (NO) and Rob Finn (EBI)
    • Task 6.1: Development and implementation of a comprehensive metagenomics data standards environment for the marine domain
  • WP7: Use Case B: Integrating Genomic and Phenotypic Data for Crop and Forest Plants
    • Leads: Paul Kersey (UK) and José Leal (PT)
    • Task 7.1: Development/adoption of appropriate controlled vocabularies for annotating plant phenotypic data
    • Task 7.4: Development and implementation of agreed public APIs for access to data in participating repositories and exposure via public computational infrastructures
  • WP8: Use Case C: Integrating ELIXIR infrastructure for Rare Disease research
    • Lead: Ivo Gut (ES) and Marco Roos (NL)
    • UNIMAN 6 PM
    • Task 8.1: The ELIXIR portfolio of data resources developed in collaboration with the rare diseases communities.
      • Subtask 8.1.2: Creation of reference datasets adequate for the specific assessment of methods and standards in the area of rare-diseases.
    • Task 8.3: Training workshops targeting different user communities
  • WP9: Use Case D: An ELIXIR framework for secure archiving, dissemination and analysis of access-controlled human data
    • Leads: Justin Paschall (EBI) and Arcadi Navarro (ES)
    • Task 9.1: Enhanced secure data submission tools
      • Subtask 9.1.1: Support for large scale submission of -omics data and sample metadata to the EGA.
        • These tools will make use of table “spread-sheet” based views of data for submitters less comfortable with technologies such as XML. (RightField?)
      • Subtask 9.1.2: Portable submission toolkit
        • .. data format definitions and software components
        • .. validation of standardized data and metadata formats.
    • Task 9.3: Federated authentication, large scale data management, and secure clouds in practice.
      • Subtask 9.3.3: Data access APIs.
        • Develop and implement standard data access APIs to be to used for inter and intra cloud communication and for secure remote REST API access in coordination with the Global Alliance for Genomics and Health (GA4GH).
  • WP10: ELIXIR Node Capacity Building and Communities of Practice
    • Leads: Jiří Vondrášek (CZ) and Bengt Persson (SE)
  • WP11: Accelerating the ELIXIR Training Programme
    • Leads: Leads: Chris Ponting (UK) and Patricia Palagi (CH)
    • UNIMAN: 30.8 PM
    • Task 11.1: Building an ELIXIR Training Infrastructure
      • Subtask 11.1.1: Assessing training quality, good practice and impact (UNIMAN, EBI)
        • Subtask 11.1.2: TeSS Training Portal
    • Task 11.2: Delivering training to the ELIXIR-EXCELERATE community
      • Subtask 11.2.2: Train the Researcher
        • To become independent and savvy users of the ELIXIR resources training will be given in: scientific programming, statistics, HPC, ontologies, workflows, data curation and annotation (WP3), as well as in the effective use of standards and FAIR data.
  • WP12: Excellence in ELIXIR Management and Operations
    • Lead: Niklas Blomberg (ELIXIR Hub)
  • WP13: Communications, Industry and Community Engagement
    • Lead: Andrew Smith (ELIXIR Hub)

Corbel

  • WP1: Management and coordination
    • leader: Niklas Blomberg (EMBL-ELIXIR)
    • UNIMAN: 0.1 PM (3 days!)
  • WP2: Documentation, communication and outreach
    • leader: Erko Stackebrandt (DSMZ)
  • WP3: Community Driven Cross-Infrastructure joint research - Medical
    • Leader: Jacques Demotes (ECRIN-ERIC)
  • WP4: Community Driven Cross-Infrastructure joint research - Bioscience
    • Leader: Jan Ellenberg (EMBL-HD) and Jutta Steinkötter (MDC)
  • WP5: Enabling common solutions for user access
    • leader: Michael Raess (INFRAFRONTIER GmbH)
  • WP6: Data access, management and integration
    • leader: Helen Parkinson (ELIXIR / EMBL-EBI).
    • UNIMAN: 30.7 PM
    • Task 6.1 Identifier standards and infrastructure supporting data management, deposition an access. UNIMAN
    • Task 6.2 Access to semantic standards.
      • we will deliver an enhanced version of the Ontology Lookup Service to support integrated access to ontologies,
      • OLS will be aligned with BioMedBridges and projects such as Open PHACTS.
    • Task 6.3 Secure Access to Sensitive Data
      • ... Federated authentication **
    • D6.1 Review of identifier schemes, standards and interoperability maps and proposed harmonizatio strategy [M12, UNIMAN]
    • D6.2 Access to Sustainable cross infrastructure identifier service(s) through ELIXIR service registry [M36, UNIMAN]
    • D6.3 Delivery of Toolkit supporting community ontology mapping and development [M40, EMBL-ELIXIR]
    • D6.4 Report on models and pilot designs for sustainable scalable cloud-based provision of data access and compute across infrastructures [M12, UMCG]
    • D6.5 Prototype implementation of distributed automated data access request, review and authorization and delivery systems [M48, CSC]
  • WP7: Common services providing support with Ethical, Legal and Societal Issues
    • leader: Michaela Th. Mayrhofer (BBMRI-ERIC)
  • WP8: Accelerating innovation
    • leader: Anton Ussi (EATRIS-ERIC)
  • WP9: Training
    • leader: Markus Pasterk (BBMRI-ERIC)

BioExcel

  • WP1: Software Scalability & Usability
    • Lead: KTH
  • WP2: Portable Environments for Computing and Data Resources (read: Workflows)
    • Lead: IRB
    • UNIMAN: 12 PM
    • providing easy access to computing and data resources through a range of workflow environments and associated data management tools and portals.
    • ..building blocks enabling easier deployment and usage will be made available, suitable for target platforms, including pre-packaged** VM images** and similar concepts. (read: components)
    • T2.1: Application building blocks for data and computing environments (incl. UNIMAN)
    • T2.2: Optimization of transversal Workflow units
    • T2.3: Deployment, Verification and Benchmark
    • T2.4: Provisioning a Workflow Environment (incl. UNIMAN)
    • T2.5: Integrating Simulation Workflows with data resources (EBI, UNIMAN 12 PM)
      • .. The Open PHACTS Discovery Platform includes, at present, 49 feeder datasets, including: Ensembl, InterPro, Uniprot, KEGG Compound, PubChem-compound, Protein Data Bank Ligand, DrugBank and so on.
      • Provide workflow blocks for accessing chemical repositories. ChEBI and ChEMBL are two extensive databases of small molecules. Integration with these data repositories will allow user to search for chemical patters and compare activity (solubility, toxicity, etc.). The Open PHACTS Discovery Platform includes: ChEBI and ChEMBL, as well as ChemSpider.
    • D2.1: State of the art and Gap analysis (M5)
    • D2.2: First release of workflows blocks and portals (M14)
    • D2.3: User feedback and future roadmap (M24)
    • D2.4: Final release of workflows and modular tools for user services (M36)
    • MS13: Software and Environment Repository Created
    • MS16: First Release of Workflows blocks and portal
    • MS19: Final Release of Workflows and Tools
  • WP3: Consultancy & User Groups
    • Lead: UEDIN
    • UNIMAN: 20 PM
    • T3.1: Identification of target user communities (Leader: UNIMAN) .. For the initial list of user groups we have identified the following ESFRI initiatives and industrial participants as important partners for the success of the project: ESFRI initiatives - PRACE, INSTRUCT, ELIXIR, BBMRI, EU-OPENSCREEN, EURO-BIOIMAGING, ISBE; Industrial partners - Pistoia Alliance (Pharmaceuticals), FoodDrinkEurope (Food Industry), CEFIC (Chemical Industry).
    • T3.2: Establishment of set of user groups (incl. UNIMAN)
    • T3.3: Active user group engagement (incl. UNIMAN)
    • T3.4: Pilot activities
    • T3.5: Consultancy modalities and funding options
    • T3.6: Support for development of consultancy proposals (incl. UNIMAN)
    • T3.7: Feedback and improvement
    • D3.1: Selection and Establishment of User Groups (M5)
    • D3.2: Consultancy proposals (M18)
    • D3.3: Consultancy Modalities and Funding Options, Half-time Update (M18)
    • D3.4: Efficacy of Feedback Process (M24)
    • D3.5: Consultancy Modalities and Funding Options, Final Update (M36)
    • D3.6: Consultancy Proposals Update (M36)
    • MS3: Target Communities are identified
    • MS5: User Groups established
    • MS14: Consultancy modalities and options agreed
    • MS17: First consultancy projects
    • MS20: Consultancy Modalities and Funding Options
  • WP4: Dissemination and Training
    • Lead: KTH
    • Uniman: 4 PM
    • T4.2: Promotion and outreach (incl. UNIMAN)
    • T4.3: Knowledge preservation and transfer (incl. UNIMAN)
    • T4.4: User Training (incl. UNIMAN)
    • T4.5: Collaborations with national/international initiatives and industry (incl. UNIMAN)
  • WP5: Governance and Sustainability
    • Lead: FT
  • WP6: Management
    • Lead: KTH
Raw
workpackages.md

Excelerate

  • WP1: Tools Interoperability & Registry
  • WP2: Infrastructure for Community-led Benchmarking
  • WP3: Data Resources and Services
  • WP4: Compute, Data access and exchange services
  • WP5: ELIXIR Interoperability Backbone
  • WP6: Use Case A: Marine metagenomic infrastructure services as driver for research and industrial
  • WP7: Use Case B: Integrating Genomic and Phenotypic Data for Crop and Forest Plants
  • WP8: Use Case C: Integrating ELIXIR infrastructure for Rare Disease research
  • WP9: Use Case D: An ELIXIR framework for secure archiving, dissemination and analysis of
  • WP10: ELIXIR Node Capacity Building and Communities of Practice
  • WP11: Accelerating the ELIXIR Training Programme
  • WP12: Excellence in ELIXIR Management and Operations
  • WP13: Communications, Industry and Community Engagement

Corbel

  • WP1: Management and coordination
  • WP2: Documentation, communication and outreach
  • WP3: Community Driven Cross-Infrastructure joint research - Medical
  • WP4: Community Driven Cross-Infrastructure joint research - Bioscience
  • WP5: Enabling common solutions for user access
  • WP6: Data access, management and integration
  • WP7: Common services providing support with Ethical, Legal and Societal Issues
  • WP8: Accelerating innovation
  • WP9: Training

BioExcel

  • WP1: Software Scalability & Usability
  • WP2: Portable Environments for Computing and Data Resources (read: Workflows)
  • WP3: Consultancy & User Groups
  • WP4: Dissemination and Training
  • WP5: Governance and Sustainability
  • WP6: Management
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment