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Active research management and sharing

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Open science framework – Jeff Spies, Centre for Open Science
Active research from lab to publication – Simon Coles, University of Southampton
Managing active research in the university – Robin Rice, University of Edinburgh
Making research available: FAIR principles and Force 11 - David De Roure, Oxford e-Research Centre

Jisc and CNI conference, 6 July 2016

Published in: Education
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Active research management and sharing

  1. 1. Active research management and sharing Chair: Professor David De Roure, OERC 14/07/2016 1
  2. 2. Introduction Chair: Professor David De Roure, OERC 14/07/2016
  3. 3. Open science framework Jeff Spies, Centre for Open Science 14/07/2016
  4. 4. Open Science Framework Jeffrey Spies @jeffspies Center for Open Science | University of Virginia
  5. 5. C E N T R E
  6. 6. Mission Increase openness, integrity, and reproducibility of scientific research.
  7. 7. Problem The gap between scholarly values and practices.
  8. 8. Incentives for individual success are focused on getting it published, not getting it right. Nosek, Spies, & Motyl, 2012
  9. 9. Key incentive = Publication What is published? Novel results Positive results Clean results What is not? Replications Negative/Nulls Mixed evidence
  10. 10. Norms Communality Open sharing Counternorms Secrecy Closed
  11. 11. Norms Communality Open sharing Universalism Evaluate research on own merit Counternorms Secrecy Closed Particularlism Evaluate research by reputation
  12. 12. Norms Communality Open sharing Universalism Evaluate research on own merit Disinterestedness Motivated by knowledge and discovery Counternorms Secrecy Closed Particularlism Evaluate research by reputation Self-interestedness Treat science as a competition
  13. 13. Norms Communality Open sharing Universalism Evaluate research on own merit Disinterestedness Motivated by knowledge and discovery Organized skepticism Consider all new evidence, even against one’s prior work Counternorms Secrecy Closed Particularism Evaluate research by reputation Self-interestedness Treat science as a competition Organized dogmatism Invest career promoting one’s own theories, findings
  14. 14. Norms Communality Open sharing Universalism Evaluate research on own merit Disinterestedness Motivated by knowledge and discovery Organized skepticism Consider all new evidence, even against one’s prior work Quality Counternorms Secrecy Closed Particularism Evaluate research by reputation Self-interestedness Treat science as a competition Organized dogmatism Invest career promoting one’s own theories, findings Quantity
  15. 15. Anderson, Martinson, & DeVries, 2007
  16. 16. Anderson, Martinson, & DeVries, 2007
  17. 17. Anderson, Martinson, & DeVries, 2007
  18. 18. Problem The gap between scholarly values and practices.
  19. 19. Solution Openness.
  20. 20. Openness • Increases process transparency • Increases accountability • Facilitates reproducibility • Facilitates metascience • Fosters collaboration • Fosters inclusivity • Fosters innovation • Protects against lock-in • Open Content + APIs + Open Source Services
  21. 21. Openness is a means to increase research quality and efficiency.
  22. 22. Solution Technology can operationalize and incentivize scholarly values.
  23. 23. Openness is the solution; Workflow makes it practical.
  24. 24. Publish Report Search/Discovery Develop Idea Design Study Collect Data Store Data Analyze Data Write Report
  25. 25. Publish Report Search/Discovery Develop Idea Design Study Collect Data Store Data Analyze Data Write Report
  26. 26. Let experts be experts.
  27. 27. Scholars should focus on scholarship.
  28. 28. Publish Report Search/Discovery Develop Idea Design Study Collect Data Store Data Analyze Data Write Report OS F
  29. 29. OSF Application Framework • Workflow • Authentication • Permissions • File Storage • File Rendering • Meta-database • Persistence • Integrations • Search • SHARE osf.io journals registries preprint servers grants management university systems
  30. 30. http://osf.io
  31. 31. Collaboration Documentation Archiving
  32. 32. Version Control
  33. 33. Other Features • Granular permissions • Analytics dashboards • Forking • Persistent, citable identifiers • Persistent content • Project snapshotting (i.e., registration)
  34. 34. Connects Services Researchers Use
  35. 35. Publish Report Search/Discovery Develop Idea Design Study Collect Data Store Data Analyze Data Write Report Now
  36. 36. OpenSesame Soon29 grants to develop open tools and services: https://cos.io/pr/2015-09-24/ Publish Report Search/Discovery Develop Idea Design Study Collect Data Store Data Analyze Data Write Report
  37. 37. http://osf.nd.edu
  38. 38. Let experts be experts.
  39. 39. OSF Application Framework • Workflow • Authentication • Permissions • File Storage • File Rendering • Meta-database • Persistence • Integrations • Search • SHARE osf.io journals registries preprint servers grants management university systems
  40. 40. http://osf.io/prereg
  41. 41. http://osf.io/prereg
  42. 42. Society for the Study of Autism Registry
  43. 43. <menu> <title> Society for the Study of... </title> <osf-search /> <osf-login /> </menu> <society-questionnaire> Author: <osf-user name /> Question 1: <osf-metadata /> Analysis code: <osf-file upload /> </society-questionnaire>
  44. 44. OSF Application Framework • Workflow • Authentication • Permissions • File Storage • File Rendering • Meta-database • Persistence • Integrations • Search • SHARE osf.io journals registries preprint servers grants management university systems
  45. 45. Let experts be experts.
  46. 46. OSF Application Framework • Workflow • Authentication • Permissions • File Storage • File Rendering • Meta-database • Persistence • Integrations • Search • SHARE registries
  47. 47. registries
  48. 48. OSF Application Framework • Workflow • Authentication • Permissions • File Storage • File Rendering • Meta-database • Persistence • Integrations • Search • SHARE preprint servers
  49. 49. preprint servers
  50. 50. preprint servers Coming soon: http://osf.io/preprints
  51. 51. OSF Application Framework • Workflow • Authentication • Permissions • File Storage • File Rendering • Meta-database • Persistence • Integrations • Search • SHARE osf.io journals registries preprint servers grants management university systems
  52. 52. Substantive experts shouldn’t deal with… • Workflow integration • Authentication • Permissions • File storage • File rendering • Database – Metadata/Annotations/Co mmenting • Persistence • External service integrations • Search • SHARE Data
  53. 53. …or scaling these: • Workflow integration • Authentication • Permissions • File storage • File rendering • Database – Metadata/Annotations/Co mmenting • Persistence • External service integrations • Search • SHARE Data
  54. 54. @jeffspies | jeff@cos.io Find this presentation at http://osf.io/u4gs7
  55. 55. Active research from lab to publication Prof. Simon Coles (s.j.coles@soton.ac.uk) Director, UK National Crystallography Service
  56. 56. What is “active” here? Continual management throughout the whole experimental process Immediate feedback during the experiment to inform next steps or direction
  57. 57. Operating a Service 66 Admin Reporting
  58. 58. Working Across Facilities 67 Conceive Research Propose Experiment Analyse Publish Approval Submissi on Experim ent Analysi s Publicati on Propos al Proposal Approv al Schedul e Experim ent Archi ve Analy se Publi sh NCS User NCS Central Facility
  59. 59. LIMS: Lifecycle Management 68 Admin Reporting
  60. 60. Getting Mobile in the Lab 69 Package & Sample Tube Bulk Sample & Manipulation Mounted Sample Trial Diffraction Pattern
  61. 61. 70 Unstructured data
  62. 62. Structured Data 71 http://ecrystals.chem.soton.ac.u k
  63. 63. In the context of ‘traditional’ publishing • ELN as Supplementary Information for conventional publication (Chemistry Central Journal 2013, 7:182 ) 72
  64. 64. Can we make metadata do more for us (actively)? Formal frameworks for real-time capture required…
  65. 65. A semantic framework for chemistry • Describes and relates different types of process information 74 elnItemManifest high-level semantic description of ELN record Core Scientific Metadata model SIMS Reaction Procedures S88 Analytical data Allotrope Foundation
  66. 66. elnItemManifest • Layered metadata model for description, export & packaging • This is the first (information) layer – leads into knowledge • Published through Dial-a-Molecule athttp://wp.me/p2JoQ6-xF & in J. ChemInf 2013, 5:52 75
  67. 67. Core Scientific Metadata model as a Starting Point • Doesn’t cover all, but… • Forms the basis for extensions: - To derived data - To laboratory based science - To secondary analysis data - To preservation information - To publication data 76 Investigatio n Publication KeywordTopic Sample Sample Parameter Dataset Dataset Parameter Datafile Datafile Parameter Investigator Related Datafile Parameter Authorisati on
  68. 68. SIMS: Sample Information Management System • A standard/format for crystallographic sample and experiment data management and archival • Supported by CrystalClear and NCS Portal, providing interaction between facility, instruments and CIF, ImgCIF etc 77
  69. 69. Standards for reactions: S88 78 • Group arising from Dial-a-Molecule consisting of Mettler Toledo, Pfizer, GlaxoSmithKline, AstraZeneca, Johnson & Johnson, Southampton University, NextMove, Royal Society of Chemistry looking to: – Provide guidance for S88 implementations for synthetic organic chemistry reaction procedures – Provide example set – Agree on controlled vocabularies for elements – Generate a schema – IUPAC uptake?
  70. 70. Standards for reactions: S88 79 • Group arising from Dial-a-Molecule consisting of Mettler Toledo, Pfizer, GlaxoSmithKline, AstraZeneca, Johnson & Johnson, Southampton University, NextMove, Royal Society of Chemistry looking to: – Provide guidance for S88 implementations for synthetic organic chemistry reaction procedures – Provide example set – Agree on controlled vocabularies for elements – Generate a schema – IUPAC uptake? 16 (0.101 g, 0.132 mmol) and Cu(OTf)2 (0.006 g, 0.01 mmol) were added to a round-bottom flask under a N2 atmosphere. In a separate vial, 2 (0.155 g, 0.753 mmol) was dissolved in C2H4Cl2 (1.3 mL) and transferred to the reaction flask. CF3CO2H (0.030 mL, 3 equiv) was added to the reaction mixture, which was refluxed at 100 °C for 1 h. The reaction mixture was washed with saturated NaHCO3 (15 mL) and extracted with C2H4Cl2 (3 x 5 mL). The organic fractions were collected, dried (MgSO4), and filtered to give a dark red solution. The solvent was removed, and the product was purified by column chromatography (SiO2, 30:70 CH2Cl2 : hexane) to yield 17 as a pale yellow powder (0.096 g, 68% yield).
  71. 71. Allotrope Foundation • Standards for analytical process in (pharma) industry 80
  72. 72. Allotrope Foundation 81
  73. 73. Allotrope Foundation 82
  74. 74. Research Data Alliance • Chemistry data interest group • Joint RDA/IUPAC Charter drafted – Characterise chemical data types – Leverage to establish standards – Examine workflows in disciplines interacting with chemistry – Cultivate a sharing culture 83
  75. 75. What about process?
  76. 76. Recording process • Plan (Prospective provenance) 85 • Enactment (Retrospective provenance) • Realisation
  77. 77. oreChem Plan for eCrystals • Machine-readable representation of methodology • Describes requirements for software and data products 86
  78. 78. CREAM: Collaboration for Research Enhancement using Active Metadata • How to collect and use metadata actively to capture tacit information • Active metadata: assemblage of metadata and annotations used actively within the process that generates it (capable of being reused by another process). • Central Facilities; Chemistry; Geosciences; Art; Music… • Uptake: CODATA; Research Data Alliance 87 https://blog.soton.ac.uk/cream/
  79. 79. Managing active research in the university Robin Rice, University of Edinburgh 14/07/2016
  80. 80. Managing active research in the University of Edinburgh Robin Rice University of Edinburgh (@sparrowbarley)
  81. 81. Elements of the presentation • Funded & unfunded research, PGR students, collaborators • Managing & support for … – research grants – research outputs – research data • Simplified research lifecycle – (before – during – after) 90
  82. 82. New Research Management and Administration System (grants) Worktribe - Empowering and supporting research administrators and investigators from idea through costing, approvals, award, post-award management and closure. • A recent requirements and procurement project focused on delivery of a new 'Worktribe Research Management' system to support improved pre-award and post-award business processes across the University. – 3 pilot schools / institutes November 2015 – Go-live across university April 2016 • The new 'Worktribe Research Management' system is integrated with the existing Finance, HR and PURE systems. • https://www.projects.ed.ac.uk/programme/rmas 91
  83. 83. Managing research outputs: guidance for authors; OJS 1. Make your work Open Access 5. Acknowledge your funder 2. Use your name consistently 6. Statement on research data 3. Use an ORCID identifier 7. Cite the DOI and OA links 4. Institutional affiliation 8. Claim your digital space ‘Ensure your research reaches the widest possible global audience, is eligible for submission in research assessment exercises, and fulfils funder requirements.’ 92
  84. 84. Type, format volume of data, chosen software for long-term access, existing data, file naming, structure, versioning, quality assurance process. Information needed for the data to be read and interpreted in future, metadata standards, methodology, definition of variables, format & file type of data. Restrict access to data, risks to data security, appropriate methods to transfer / share data, encryption. Secure & sufficient storage for active data, regular backups, disaster recovery Make data publicly available (where possible) at the end of a project, license data, any restrictions on sharing, access controls? Select data to keep, decide how long data will be kept, in which repository, costs involved in long-term storage? Day-to-daymanagementofdata Managing Research Data (from researcher training) 93
  85. 85. Who manages active data? • RDM Policy (2011) sets out roles and responsibilities for researchers & the institution – Researchers are responsible for their work – Enabling role of institution • Services, including stewardship • Monitoring compliance • Principal Investigators • Research Institutes & Schools 94
  86. 86. 95
  87. 87. From RDM programme to Research Data Service… • RDM programme a result of both bottom-up (‘action group’) activity and top-down policy implementation • Services had various providers and their purpose and names were confusing • New single service has SO & SOM with Virtual Team across Information Services 96
  88. 88. Before - 97
  89. 89. After (Simplified data lifecycle) 98
  90. 90. Tools & support for working with data 99
  91. 91. Finding and analysing data • What is Data Library & Consultancy? • The Data Library & Consultancy team assists researchers to discover and use datasets for analysis, learning and teaching. • Data librarians are available to help you find answers to data- related questions. • Tools include a data catalogue and the Survey Documentation and Analysis online data browser 100
  92. 92. Storing data • What is DataStore? • DataStore is file storage for active research data, and is available to all research staff and postgraduate research students (PGRs). • DataStore provides a free individual allocation for each researcher, as well as shared group spaces. Additional capacity of virtually any size is available. 101
  93. 93. Transferring data • What is DataSync? • DataSync is a tool to synchronise and share research data with collaborators. It has an app to synchronise data to computers and mobile devices, and a web interface to allow access to data from any web browser. • Data can be shared with anyone who has an email address, via the web interface. 102
  94. 94. Versioning software • What is Subversion? • Subversion is a version control tool which allows users to store code. It is also available as an extension called SourcEd which provides a web based collaboration tool integrated with your repository. • When documents stored in a Subversion repository are updated the old versions are kept so you can revert if necessary. The service also allows multiple people to collaborate on documents. 103
  95. 95. Data management support One-to-one support is available on the following areas of RDM: • Writing and reviewing DMPs; • Creating SOPs for metadata collection and publication; • Creating SOPs for good data management practice; • Choosing a data repository and preparing data for deposit and publication 104
  96. 96. Training - Online • MANTRA: MANTRA is a free, non-credit, self-paced course designed for postgraduate students and early career researchers which provides guidelines for good practice in research data management • Research Data Management and Sharing MOOC: This free five- week course - created by the Universities of Edinburgh and North Carolina - is designed to reach learners across disciplines and continents. 105
  97. 97. 106
  98. 98. MANTRA sessions by country 2012-2016 107
  99. 99. Sessions by city: January – June 2016 108
  100. 100. www.coursera.org/learn/data-management #RDMSmooc 109
  101. 101. MOOC’s contents • Understanding Research Data • Data Management Planning • Working with Data • Sharing Data • Archiving Data 110
  102. 102. 111
  103. 103. 112
  104. 104. Training workshops • Creating a data management plan for your grant application • Managing your research data: why is it important and what should you do? • Working with personal & sensitive research data • Good practice in research data management • Handling data using SPSS 113
  105. 105. RDM training take-up, 2014-2016 114
  106. 106. THANKS R.Rice@ed.ac.uk 115
  107. 107. Making research available - FAIR principles and Force 11 David De Roure, Oxford e-Research Centre 14/07/2016
  108. 108. David De Roure @dder Making research available: FAIR principles and FORCE11 DIRECTOR, UNIVERSITY OF OXFORD E-RESEARCH CENTRE
  109. 109. A Brief History of Force11 ● 2008/2009: – Elsevier Grand challenge ● 2010: – Found & connected to Phil Bourne – Planned Dagstuhl meeting ● 2011: – January: Beyond the PDF, San Diego: 97 Attendees – August: Force11 at Dagstuhl: 34 attendees – November: Manifesto is published >> Force11! ● 2012: Funding Sloan ● 2013: Beyond the PDF2, Amsterdam: – 148 attendees, great discussion ● 2014: Working groups take off: – Data Citation Principles Working group – Resource Identifier Working group ● 2015: Force15, Oxford: – 257 attendees ● 2015: Force 2016, Portland, Oregon
  110. 110. www.force11.org
  111. 111. 121https://www.force11.org/fairprinciples
  112. 112. A diverse set of stakeholders - representing academia, industry, funding agencies, and scholarly publishers - have come together to design and jointly endorse a concise and measureable set of principles, for those wishing to enhance the reusability of their data holdings Including, but not limited to: European Open Science Cloud – High Level Expert Group
  113. 113. These put emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individual NOTE: The Principles are high-level; do not suggest any specific technology, standard, or implementation-
  114. 114. Exemplar implementations, their (level of) FAIRness and resulting value-added
  115. 115. Findable Accessible Interoperable Reusable Thanks to Susanna Sansone
  116. 116. Active research management and sharing14/07/2016 126

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