Open Science
DR SANDER BOSCH WHO AM I?
Sander Bosch
2011-2015 PhD in cognitive neuroscience 2015-2018 Postdoc in artificial intelligence 2019-2020 Project manager VU Research Support 2020-present VU Open Science Coordinator
Member of the Accelerate Open Science-team (NPOS Project H) Member of the VU Committee for Recognition & Rewards Member of Young Science in Transition OPEN SCIENCE Preregistration
Initiation Public Engagement/
Citizen Science Outreach & Planning valorisation
RDM/ FAIR Data Academia is in & Software transition towards a
more transparent way Data acquisition, Evaluation of doing and sharing analysis & research Open Peer Review Publication documentation
Open Access (INTER)NATIONAL DEVELOPMENTS
Ambition 100% Open Access (government, VSNU, NWO/ZonMw) From 2021 onwards, publicly financed research articles should be openly accessible immediately upon publication, under an open license (Plan S)
Mandatory data management plans for grants “Data management plans need to be completed in consultation with research data management support staff at the home institution of the grant holder. ” (NWO)
Strategic Evaluation Protocol (SEP) 2021-2027 Open Science as a pillar for research assessment
VSNU position paper Room for everyone’s talent ”A system of rewards and recognition that encourages all aspects of open science” WHY OPEN SCIENCE?
Transparency about the research process
Public values Open Access, Public Engagement & Valorisation
Collaboration FAIR Data & Software, Public Engagement & Valorisation
Reproducibility/ scientific integrity Open Peer Review, Research Data Management, FAIR Data & Software SCIENTIFIC INTEGRITY
Fabrication/ Fraud/ Plagiarism: ~2%
Sloppy science: ~34% Poor replicability Selective reporting
https://doi.org/10.1371/journal.pone.0005738 https://doi.org/10.1017/S0033291718001873 REQUIREMENTS FOR OPEN SCIENCE
VU Open Science Programme (2021), figure based on https://www.cos.io/blog/strategy-for-culture-change
INFRASTRUCTURE
Virtual research environment (e.g. anDREa) Safe working environment Open Science Framework Preregistration/ project management/ publishing platform PROSPERO Registry for systematic reviews DMPonline Data management planning Castor Research Data Management (RDM) Electronic Lab Notebooks RDM Version control RDM iRODS/ YODA Storage/ RDM Preprint servers Publishing platform Zenodo Publishing platform … FULLY OPEN WORKFLOW?
adding alternative evaluation, e.g. with altmetrics communicating through social media, e.g. Twitter sharing posters & presentations, e.g. at FigShare using open licenses, e.g. CC0 or CC-BY publishing open access, ‘green’ or ‘gold’ using open peer review, e.g. at journals or PubPeer assessment sharing preprints, e.g. at OSF, arXiv or bioRxiv outreach using actionable formats, e.g. with Jupyter or CoCalc open XML-drafting, e.g. at Overleaf or Authorea publication sharing protocols & workfl., e.g. at Protocols.io sharing notebooks, e.g. at OpenNotebookScience writing sharing code, e.g. at GitHub with GNU/MIT license sharing data, e.g. at Dryad, Zenodo or Dataverse analysis pre-registering, e.g. at OSF or AsPredicted commenting openly, e.g. with Hypothes.is using shared reference libraries, e.g. with Zotero search sharing (grant) proposals, e.g. at RIO
Bianca Kramer & Jeroen Bosman https://101innovations.wordpress.com DOI: 10.5281/zenodo.1147025
SUPPORT, SKILLS & KNOWLEDGE
Data stewards Questions about data (management) Research software engineers Questions about software management Privacy officers Questions about handling personal data/ GDPR Ethical committee Ethical considerations Librarians Questions about Open Access/ Open Science (e.g. licensing) Policy officers Questions about national and institutional policies IT Questions about technical RDM issues FIND YOUR RESEARCH SUPPORT OFFICE!
APH https://aph-qualityhandbook.org/ | [email protected]
RIHS https://www.radboudumc.nl/en/research/radboud-technology-centers/data-stewardship
CAPHRI https://www.maastrichtuniversity.nl/research/open-science
NIVEL https://www.uu.nl/en/research/research-at-utrecht-university/support-for-researchers SUPPORT, SKILLS & KNOWLEDGE
Open Science skills & knowledge
https://online-learning.tudelft.nl/courses/open-science-sharing-your-research-with-the-world/ https://utrechtuniversity.github.io/workshop-computational-reproducibility/ https://opensciencemooc.eu/# https://www.lcrdm.nl/spring-training-days https://the-turing-way.netlify.app/welcome.html https://www.openaire.eu/how-to-make-your-data-fair
Software skills
https://www.esciencecenter.nl/events/ https://coderefinery.org/lessons/ https://software-carpentry.org/lessons/
COMMUNITY
“a bottom-up learning community of researchers and students to learn more about Open Science”
goals: o invite newcomers to Open Science
o increase engagement in Open Science practices
o serve as a breeding ground for Open Science initiatives
o interact with policy, infrastructure and support services
o foster interactions between academia and society INOSC OTHER COMMUNITIES
http://riotscience.co.uk/ https://reproducibilitea.org/ https://studentinitiativeopenscience.wordpress.com/ https://carpentries.org/ https://scienceintransition.nl/
RECOGNITION & REWARDS
November 2019: VSNU Position paper on academic reward system
Now: University/ UMC-committees create and implement vision
o Diversification and vitalisation of career paths
o Finding a balance between the individual and the collective
o Focus on quality
o Stimulating open science
o Encouraging academic leadership
https://vsnu.nl/files/documenten/Domeinen/Onderzoek/Position%20paper%20Room%20for%20everyone%E2%80%99s%20talent.pdf Register now!
Verander de footer tekst: menu > invoegen> kop en voettekst STRATEGY EVALUATION PROTOCOL
More focus on qualitative assessment
Broader definition of scientific output and success
Open Science as a pillar for assessment
https://www.vsnu.nl/files/documenten/Domeinen/Onderzoek/SEP
_2021-2027.pdf DORA
San Francisco Declaration on Research Assessment (https://sfdora.org/)
General Recommendation
1. Do not use journal-based metrics, such as Journal Impact Factors, as a surrogate measure of
the quality of individual research articles, to assess an individual scientist’s contributions, or in hiring, promotion, or funding decisions. CREDIT CONTRIBUTOR ROLES
Taxonomy of 14 Contributor Roles
Conceptualization
Data curation
Formal Analysis Software
Funding acquisition Supervision
Investigation Validation
Methodology Visualization
Project administration Writing – original draft
Resources Writing – review & editing
https://casrai.org/credit/
RESEARCH LIFE CYCLE
Initiation
Outreach & Planning valorisation
Data acquisition, Evaluation analysis &
Publication documentation
https://zenodo.org/record/3754459
1. DISCOVER & INITIATE
Looking for research information? Perhaps your subject-matter specialist librarians can help you!
LibGuides with tips & tricks on: Finding data - https://libguides.vu.nl/finding-data Systematic reviews - https://libguides.vu.nl/SystematicReviews Searching literature - https://libguides.vu.nl/PMroadmap ORCID
Find people/ papers/ datasets Profiles: ResearcherID, ScopusID, academia.edu, Mendeley, Publons
Open Researcher and Contributor ID: Efficiency Visibility and findability Personal and under your control Widely adopted in scholarly infrastructure Registering is easy and only takes a few minutes at https://orcid.org/signin
2. PLAN & DESIGN
Data Management Plan (DMP) - How will you manage your research data during and after your research
project?
Tool: https://dmponline.vu.nl/ (with guidance) PREREGISTRATION
Publish your hypotheses/ analysis plan/ protocol before starting your project
o Creates a distinction between exploratory and confirmatory research
o See https://osf.io/3tbwc/, https://www.protocols.io/ or https://aspredicted.org/
3., 4., 5. DOING YOUR RESEARCH
Many differences between research disciplines for the parts
3. Collect & Store
4. Process & Analyse
5. Document & Preserve
Questions about Research Data Management (RDM)?
Ask your data steward/ library/ research support team for help! FAIR PRINCIPLES
Why?
1. Increase visibility and findability of your work
2. Improve reproducibility and reliability
3. Foster collaboration with others
4. Achieve maximum impact
See https://www.go-fair.org/fair-principles/ and https://fair-software.nl/ FINDABLE
Make your data findable by ensuring:
o Data are described with rich metadata
o (Meta)data are assigned a globally unique and persistent identifier
o (Meta)data are registered or indexed in a searchable resource
Metadata is data about your data
o Project-level: Who is the responsible researcher? How to cite your data?
o File-level: Which file does what? (read-me files)
o Item-level: What is this variable?
https://www.uu.nl/en/research/research-data-management/guides/how-to-make-your-data-fair ACCESSIBLE
It should be possible for humans and machines to gain access to
your data, under specific conditions or restrictions where appropriate.
FAIR does not necessarily mean that data need to be open!
Make your data accessible by ensuring:
o The repository you are using to share your data assigns persistent
identifiers by which data can be retrieved
o The access procedure includes authentication and authorisation steps, if necessary
o Metadata are accessible, wherever possible, even if the data are not
https://www.uu.nl/en/research/research-data-management/guides/how-to-make-your-data-fair INTEROPERABLE
It should be easy to combine your data with other datasets, applications and
workflows, for humans as well as computer systems.
Make your data interoperable by using:
o When possible, well-known and preferably open formats and software
o Relevant standards for metadata
o Community agreed schemas, controlled vocabularies, keywords, ontologies
https://www.uu.nl/en/research/research-data-management/guides/how-to-make-your-data-fair REUSABLE
Research data should be ready for future research and future
processing.
Make your data reusable by ensuring the data:
o Is well-documented to support proper data interpretation
o Have a clear and accessible data usage license so others know what kinds of reuse are permitted
o Has provenance information on how, why and by whom the data have been created and processed
https://www.uu.nl/en/research/research-data-management/guides/how-to-make-your-data-fair FILE NAMING
Machine-readable
o No spaces! o Deliberate use of delimiters
Human-readable
o Info on content
Plays well with default ordering o Put something numeric first!
https://speakerdeck.com/jennybc/how-to-name-files VERSION CONTROL
Benefits:
History full record of changes to your files
Traceability where did the error occur (and who made it)?
Time machine revert back to earlier versions if you need to
Collaboration work efficiently on files together with others
Automatic cloud back-up!
http://phdcomics.com/comics/arc hive_print.php?comicid=1531 See http://swcarpentry.github.io/git-novice/ or https://coderefinery.github.io/git-intro/
6. PUBLISH & SHARE
You can find a list of preprint servers here ROUTES TO OPEN ACCESS
https://libguides.mines.edu/OA GOLD VS GREEN Gold Green
Published version of VOR or record (VOR) author-accepted manuscript (AAM)
CC-BY licence VOR: CC-BY licence not possible due to transfer agreement AAM: CC-BY often not possible
Immediate access VOR: embargoed AAM: immediate access possible
Publisher organizes Self-archiving access
Author-pay No extra costs for author
https://camacuk.zendesk.com/hc/en-us/articles/115005898287- What-is-the-author-accepted-manuscript-AAM- OA OPTIONS FOR YOU
Gold Open Access o Is your journal part of a big deal? Check: https://www.openaccess.nl/en o Questions? Contact your library!
Green Open Access o For older publications (more than 6 months), you can make your publications Open Access in accordance with Dutch copyright law o Uploading an AAM on bioRxiv upon publication, without delay and under an open licence (CC-BY), is compliant with Plan S/ Horizon Europe (bioRxiv is listed in the OpenDOAR list of trusted repositories) Publishers usually don’t allow you to do this due to the copyright agreement and may ask you to take this version offline
Diamond Open Access o Benefits of Gold OA, with an institution-pay model – e.g. openjournals LICENSES
License selector for publications, data, software: https://ufal.github.io/public- license-selector/
Questions? Contact your library
https://commons.wikimedia.org/wiki/File:Cr eative_Commons_Licenses.png OPEN PEER REVIEW
https://www.fosteropenscience.eu/learning/open-peer- review/#/id/5a17e150c2af651d1e3b1bce
OUTREACH/ VALORISATION
Public Engagement Faces of Science
Citizen Science
https://www.pintofscience.nl/ https://www.nemokennislink.nl/facesofscience/ https://en.wikipedia.org/wiki/Sea_Hero_Quest
Thank you for attending the online CaRe days 2021
We hope to see you again, next year, at the CaRe days 2022 in Eindhoven 11 & 12 May 2022