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RDM@Edinburgh_interoperation_IDCC2015

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Historic Environment Scotland
Historic Environment Scotland

The document discusses integrating the RSpace electronic lab notebook (ELN) with the University of Edinburgh's research data management services. It describes how RSpace can link to files stored in Edinburgh's DataStore storage system, export data and metadata to the DataShare research data repository, and archive data long-term in the future DataVault archive. The integration helps researchers manage and share their data across different projects and institutions while complying with the university's RDM policy. RSpace provides a convenient interface for researchers, while the services help institutions meet requirements for data storage, publication, and preservation.

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Service Integration to Enhance RDM: RSpace electronic laboratory notebook (ELN) case study Stuart Macdonald (RDM Services Coordinator, University of Edinburgh) stuart.macdonald@ed.ac.uk Rory Macneil (CEO, Research Space) rmacneil@researchspace.com 10th International Digital Curation Conference, London, 10 February 2014
University of Edinburgh RDM Policy  University of Edinburgh is one of the first Universities in UK to adopt a policy for managing research data: http://www.ed.ac.uk/is/research- data-policy  The policy was approved by the University Court on 16 May 2011.  It’s acknowledged that this is an aspirational policy and that implementation will take some years.
Policy implementation: RDM Roadmap Colleagues in IS developed a roadmap to deliver a suite of services that will meet: • RDM policy objectives • the needs of our researchers Cross-divisional collaboration  3 Phases (Aug. 2012 – May 2015) Services already in place: o Data management planning o Active working file space = DataStore o Data publication repository = DataShare Services in development: o Long term data archive = DataVault o Data Asset Register (DAR) RDM support: Awareness raising, training & consultancy http://edin.ac/1u3sKqy Before research During research After research
Research Data Management Planning Customised instance of DCC’s DMPonline toolkit for Univ. of Edinburgh use: A range of funders and local (non-funder) DMP templates Institutional guidance (storage, services, support) Tailored DMP assistance for researchers submitting research proposals (F-2-F) DataStore NAS facility to store data that are actively used in current research activities 0.5 TB (500GB) allocated per researcher (incl. PGRs) Up to 0.25TB can be used for “shared” group storage Extra storage costs: £200 per TB per year incl. back-up and DR copies Infrastructure in place. Allocation of space devolved to School IT departments overseen by Heads of IT from each College.
DataShare  Edinburgh DataShare is the University’s OA multi-disciplinary data repository hosted bt the Data Library : http://datashare.is.ed.ac.uk  Assists researchers who want to share their data, get credit for data publication, and preserve their data for the long-term (DOI, licence, citation) Data Vault  Safe, private and secure long-term data archive  Current focus on front-end application requirements (authorisation, retention & deletion, file structure, file transfer, integration) Data Asset Register (DAR)  Using PURE as the catalogue of data assets produced by Edinburgh researchers for discovery, access, and re-use as appropriate. Interoperation  Systems are more likely to be used if some or all of the components are integrated and developed to minimise ‘duplication’ of effort
RDM Support • RDM team work with Research Administrators , Academic Support Librarians and IT staff in each of the 22 Schools. • Queries can be sent to the IS Helpline who will direct them to appropriate RDM staff via CMS. • Introductory sessions on local RDM services and support for researchers and research administration staff in Schools / Institutes • RDM website: http://www.ed.ac.uk/is/data-management • RDM blog: http://datablog.is.ed.ac.uk • RDM wiki: https://www.wiki.ed.ac.uk/display/RDM/Research+Data+Management+Wiki
Training: Tailored Courses Formal and bespoke training in the form of workshops, seminars and drop in sessions to help researchers with RDM issues.  Creating a data management plan for your grant application  Handling data using SPSS  Managing your research data: why it is important and what should you do? NEW  Publishing and sharing sensitive data (pilot) NEW  MANTRA - http://datalib.edina.ac.uk/mantra  An internationally recognized free online RDM training course for researchers - developed by the Data Library  Software-specific data handling exercises  CC License & embed units in VLE’s e.g. Moodle
Service Integration examples • DataShare is a customised DSpace instance with OAI-PMH compliant DCMI metadata fields for data discovery through Google and other search engines • Records are harvested by Thomson-Reuters Data Citation Index • SWORD API utilised for batch deposit of large and/or many files from computers (‘Push using http’) • Internal batch ingest of many/large files to circumvent 2.1GB limit via interface (‘Pull via command line interface’) • checksums determine that delivered object mirrors deposited object • DSpace GITHUB plugin* - allows software used in research to be from GitHub (or similar) source code repository into DataShare, which then be assigned a DOI to facilitate citation - using the SWORD deposit protocol
DataSync – a secure dropbox-like facility for synchronising data on DataStore with desktop and mobile machines: • uses open source ‘ownCloud’ technology Refresh of ECDF Computing Cluster (‘Eddie’) complete with ‘Data Centric Computing’ business model – integrate Eddie storage & HPC, parallel and cloud computing layers with DataStore for data sharing i.e. data transferred from DataStore for analysis run on Eddie and then data ported back to DataStore (DataVault) Linking of SDA toolkit with numeric ASCII data held in DataShare for the purposes of analysis (re-use) Facility to embargo variables within numeric files (in statistical analysis package formats) for subsequent open deposit into DataShare of de-sensitised version Research data deposit directly from RSpace Electronic Lab Notebook (ELN) interface into DataShare and Datastore (& Data Vault) using SWORD protocol
Who and what is driving demand for ELNs? ● Researchers – Utility and convenience of paper lab book + online capabilities – On multiple devices – File management/integration ● Groups/PIs – Controlled sharing – Collaboration – Group management – File management/integration ● Institutions: data librarians, research admins, IT, commercialisation offices – Enterprise features: Scalable deployment, Single Sign On – IP protection: audit trail, signing – Publishing – Archiving – Repository integration – File management/integration
RSpace RSpace First electronic notebook for research institutions
Business Model ● Free public cloud for labs and individuals ● Institutional deployments @$100/user/year ● Seamless movement of groups and data between different RSpaces Researchers Institutions Funders Value Edinburgh Public Cloud Stanford Lab LabLab Convenience Productivity Portability Control Compliance Data mining Data mining
RSpace at Edinburgh – Linking to files in Edinburgh DataStore – Depositing content in Edinburgh DataShare – Archiving in Edinburgh DataVault
Linking to DataStore “My plan for workflow would be generally to deposit my data in DataStore either from the wet lab instruments (gel photos, elisa data, etc, and also possibly directly from an iPad) or from in silico data analysis I’ve been doing, and then link to it from within RSpace.”
Linking to DataStore Experiment Procedure ~~~~~~~~~~ ~~~~~~~~~~ Results ~~~~~~~~~~ Results.xls ELN UoE DataStore
Exposing DataStore File Roots
Linking to a DataStore File
Linking to a DataStore File
Linking to a DataStore File
Exporting to DataShare RSpace UoE DataShare
Adding metadata
Archiving in Edinburgh DataVault ● DataVault functionality/API not yet specified ● Anticipate use of XML zip archive ● Many requirements to be determined – e.g., searching, restoration
RSpace and Edinburgh RDM RSpace server DataShareDataStore DataVault User / Browser
Thanks! Acknowledgements: Sunny Yang, Richard Adams, Nigel Goddard Robin Rice, Kevin Tomlinson, George Hamilton, Orlando Richards

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RDM@Edinburgh_interoperation_IDCC2015

  • 1. Service Integration to Enhance RDM: RSpace electronic laboratory notebook (ELN) case study Stuart Macdonald (RDM Services Coordinator, University of Edinburgh) stuart.macdonald@ed.ac.uk Rory Macneil (CEO, Research Space) rmacneil@researchspace.com 10th International Digital Curation Conference, London, 10 February 2014
  • 2. University of Edinburgh RDM Policy  University of Edinburgh is one of the first Universities in UK to adopt a policy for managing research data: http://www.ed.ac.uk/is/research- data-policy  The policy was approved by the University Court on 16 May 2011.  It’s acknowledged that this is an aspirational policy and that implementation will take some years.
  • 3. Policy implementation: RDM Roadmap Colleagues in IS developed a roadmap to deliver a suite of services that will meet: • RDM policy objectives • the needs of our researchers Cross-divisional collaboration  3 Phases (Aug. 2012 – May 2015) Services already in place: o Data management planning o Active working file space = DataStore o Data publication repository = DataShare Services in development: o Long term data archive = DataVault o Data Asset Register (DAR) RDM support: Awareness raising, training & consultancy http://edin.ac/1u3sKqy Before research During research After research
  • 4. Research Data Management Planning Customised instance of DCC’s DMPonline toolkit for Univ. of Edinburgh use: A range of funders and local (non-funder) DMP templates Institutional guidance (storage, services, support) Tailored DMP assistance for researchers submitting research proposals (F-2-F) DataStore NAS facility to store data that are actively used in current research activities 0.5 TB (500GB) allocated per researcher (incl. PGRs) Up to 0.25TB can be used for “shared” group storage Extra storage costs: £200 per TB per year incl. back-up and DR copies Infrastructure in place. Allocation of space devolved to School IT departments overseen by Heads of IT from each College.
  • 5. DataShare  Edinburgh DataShare is the University’s OA multi-disciplinary data repository hosted bt the Data Library : http://datashare.is.ed.ac.uk  Assists researchers who want to share their data, get credit for data publication, and preserve their data for the long-term (DOI, licence, citation) Data Vault  Safe, private and secure long-term data archive  Current focus on front-end application requirements (authorisation, retention & deletion, file structure, file transfer, integration) Data Asset Register (DAR)  Using PURE as the catalogue of data assets produced by Edinburgh researchers for discovery, access, and re-use as appropriate. Interoperation  Systems are more likely to be used if some or all of the components are integrated and developed to minimise ‘duplication’ of effort
  • 6. RDM Support • RDM team work with Research Administrators , Academic Support Librarians and IT staff in each of the 22 Schools. • Queries can be sent to the IS Helpline who will direct them to appropriate RDM staff via CMS. • Introductory sessions on local RDM services and support for researchers and research administration staff in Schools / Institutes • RDM website: http://www.ed.ac.uk/is/data-management • RDM blog: http://datablog.is.ed.ac.uk • RDM wiki: https://www.wiki.ed.ac.uk/display/RDM/Research+Data+Management+Wiki
  • 7. Training: Tailored Courses Formal and bespoke training in the form of workshops, seminars and drop in sessions to help researchers with RDM issues.  Creating a data management plan for your grant application  Handling data using SPSS  Managing your research data: why it is important and what should you do? NEW  Publishing and sharing sensitive data (pilot) NEW  MANTRA - http://datalib.edina.ac.uk/mantra  An internationally recognized free online RDM training course for researchers - developed by the Data Library  Software-specific data handling exercises  CC License & embed units in VLE’s e.g. Moodle
  • 8. Service Integration examples • DataShare is a customised DSpace instance with OAI-PMH compliant DCMI metadata fields for data discovery through Google and other search engines • Records are harvested by Thomson-Reuters Data Citation Index • SWORD API utilised for batch deposit of large and/or many files from computers (‘Push using http’) • Internal batch ingest of many/large files to circumvent 2.1GB limit via interface (‘Pull via command line interface’) • checksums determine that delivered object mirrors deposited object • DSpace GITHUB plugin* - allows software used in research to be from GitHub (or similar) source code repository into DataShare, which then be assigned a DOI to facilitate citation - using the SWORD deposit protocol
  • 9. DataSync – a secure dropbox-like facility for synchronising data on DataStore with desktop and mobile machines: • uses open source ‘ownCloud’ technology Refresh of ECDF Computing Cluster (‘Eddie’) complete with ‘Data Centric Computing’ business model – integrate Eddie storage & HPC, parallel and cloud computing layers with DataStore for data sharing i.e. data transferred from DataStore for analysis run on Eddie and then data ported back to DataStore (DataVault) Linking of SDA toolkit with numeric ASCII data held in DataShare for the purposes of analysis (re-use) Facility to embargo variables within numeric files (in statistical analysis package formats) for subsequent open deposit into DataShare of de-sensitised version Research data deposit directly from RSpace Electronic Lab Notebook (ELN) interface into DataShare and Datastore (& Data Vault) using SWORD protocol
  • 10. Who and what is driving demand for ELNs? ● Researchers – Utility and convenience of paper lab book + online capabilities – On multiple devices – File management/integration ● Groups/PIs – Controlled sharing – Collaboration – Group management – File management/integration ● Institutions: data librarians, research admins, IT, commercialisation offices – Enterprise features: Scalable deployment, Single Sign On – IP protection: audit trail, signing – Publishing – Archiving – Repository integration – File management/integration
  • 11. RSpace RSpace First electronic notebook for research institutions
  • 12. Business Model ● Free public cloud for labs and individuals ● Institutional deployments @$100/user/year ● Seamless movement of groups and data between different RSpaces Researchers Institutions Funders Value Edinburgh Public Cloud Stanford Lab LabLab Convenience Productivity Portability Control Compliance Data mining Data mining
  • 13. RSpace at Edinburgh – Linking to files in Edinburgh DataStore – Depositing content in Edinburgh DataShare – Archiving in Edinburgh DataVault
  • 14. Linking to DataStore “My plan for workflow would be generally to deposit my data in DataStore either from the wet lab instruments (gel photos, elisa data, etc, and also possibly directly from an iPad) or from in silico data analysis I’ve been doing, and then link to it from within RSpace.”
  • 17. Linking to a DataStore File
  • 18. Linking to a DataStore File
  • 19. Linking to a DataStore File
  • 22. Archiving in Edinburgh DataVault ● DataVault functionality/API not yet specified ● Anticipate use of XML zip archive ● Many requirements to be determined – e.g., searching, restoration
  • 23. RSpace and Edinburgh RDM RSpace server DataShareDataStore DataVault User / Browser
  • 24. Thanks! Acknowledgements: Sunny Yang, Richard Adams, Nigel Goddard Robin Rice, Kevin Tomlinson, George Hamilton, Orlando Richards

Editor's Notes

  1. Edinburgh Data Science Institute Centre for Doctoral Training in Data Science (School of Informatics) Data Lab Innovation centre
  2. Designed and developed over three years with teams at three leading global research institutions The first and only ELN developed to meet the needs of research institutions – third generation supplanting second generation lab-focused ELNs. Comparison with major competitor, Lab Archives, shows dominance of RSpace for institutional requirements. Individual features not remarkable; advantage comes from the combination. Sustainable advantage from relationships with three partners, long head start and difficulty/impossibility of discovering and implementing detailed requirements of this customer set. Result: no real contest – like Man U vs. Cambridge United!