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    1. Open Principles
      1. Why Open Research
      2. The Open PhD Toolkit
      3. Open Research Glossary. “Open data and content can be freely used, modified, and shared by anyone for any purpose.” (The Open Definition)
      4. Winning Research Grants with Open Science
        doi.org/10.5281/zenodo.12247
      5. From Open Science to Open Innovation, Henry Chesborough 2015
      6. A list of resources from ongoing research in my lab — including: Todd. 2014. Anatomy of an open science paper. Blog post.
      7. Masuzzo P, Martens L. (2017). “Do you speak open science? Resources and tips to learn the language,” PeerJ Preprints 5:e2689v1, https://peerj.com/preprints/2689/
      8. Vienna Principles
      9. Utrecht Summer School Open Science course
      10. Transparent and Open Social Science MOOC
      11. The SV-POW Tutorials include a helpful definition of Open Access and clarifications on licensing, copyright and related topics (Tutorial 19).
      12. Barba, Lorena A. (2017): A short lecture on Open Licensing. Figshare, doi:10.6084/m9.figshare.4516892.v1  
        (presentation slides and presenter notes also on SpeakerDeck)
      13. Oct. 2015 4+1 Interview: Lorena Barba — final question “Why do you advocate so strongly for open-source technology in research and education?”
      14. Community Management for Teachers and a handbook for Troll Control (learn how to emoderate your MOOC)
      15. The Panton Principles of Open Science

    1. Collaborative Platforms
      1. Mozilla Science study group lessons
      2. Friendly GitHub Intro
      3. OSF YouTube archive & OSF webinar series
      4. Any functional VRE as an example of things to come
      5. Overleaf, Authorea (AU), PaperHive, Figshare, ScienceOpen, Hypothes.is, Protocols.io
      6. NMR Lipids Project
      7. Synapse – open source, free to use, goals of enabling open science and collaborative research in real-time, integrates with R/Python via analytic clients, and has advanced data access controls for sharing human subjects data

    1. Reproducible Research and Data Analysis
      1. OSF
      2. [other pre-registration sites – to add] asPredicted
      3. Jupyter notebooks & Rmarkdown
      4. Statcheck, GRIM
      5. VMs, Docker, Vagrant, binder, nteract.io
      6. Data hygiene and data provenance eg (link)
      7. R for Data Science r4ds
      8. Bookdown Yihui Bookdown
      9. Modern Drive Chester Ismay
      10. https://sites.trinity.edu/osl/data-sets-and-activities
      11. A Data Cleaner’s Cookbook
      12. ReproZip – Open source tool for full computational reproducibility
      13. Software Carpentry and Data Carpentry lessons
      14. Reproducibility PI Manifesto
      15. Initial steps toward reproducible research
      16. ROpenSci’s reproducibility guide
      17. Barba group Reproducibility Syllabus (summary of the group’s top-10 readings in reproducibility)
      18. Barba group’s onboarding course “Essential skills for reproducible research computing.” A four-day, intensive, hands-on workshop on the foundational skills that everyone using computers in the pursuit of scientific research should have.
      19. Barba, Lorena A. (2017): How to run a lab for reproducible research. Figshare, doi:10.6084/m9.figshare.4676170.v1 (presentation slides and presenter notes also on SpeakerDeck).
      20. Gathering for Open Science Hardware (GOSH, openhardware.science)
      21. Institutions/projects using open hardware/materials:
        1. CERN’s Open Hardware Repository (http://www.ohwr.org/) and Open Hardware License
        2. UFRGS Centro de Tecnologia Acadêmica (CTA, http://cta.if.ufrgs.br)
        3. Michigan Tech Open Sustainability Technology research group (http://www.mse.mtu.edu/~pearce/Index.html)
        4. Open Plant (https://www.openplant.org/)
        5. Trend in Africa (www.trendinafrica.org)
        6. Open Lab Tools Cambridge University (http://openlabtools.eng.cam.ac.uk/index.php)
        7. PhotosynQ (https://photosynq.org/)
        8. PublicLab (https://publiclab.org/)
      22. Online repositories for open hardware:
        1. PLOS open source toolkit channel (https://channels.plos.org/open-source-toolkit)
        2. Open Neuroscience (www.openeuroscience.com)
        3. Open Plant Science (http://openplant.science/)
        4. Appropedia (http://www.appropedia.org/Welcome_to_Appropedia)
        5. DocuBricks (http://www.docubricks.com/)
        6. Hackaday.io (https://hackaday.io/submissions/prize2016_citizen/list)
      23. Companies providing OScH
        1. BackyardBrains (https://backyardbrains.com/)
        2. OpenPCR (www.openpcr.org)
        3. OpenROV (https://www.openrov.com/)
        4. PhotosynQ (https://photosynq.org/buy-multispeq)
      24. Code Ocean (https://codeocean.com) open, cloud-based computational reproducibility platform

    1. Open Data
      1. Zenodo, Figshare, Dryad, Pangaea.de
      2. Could be a place to feature NIH Team collaboration manual
      3. FAIRsharing.org metadata standards
      4. Australian National Data Service Guides
      5. Australian National Data Service Sensitive Data Resources
      6. The Open Data Institute

    1. Open Research Software and Open Source
      1. Sustainable Software Institute: Neil Chue Hong & Co
      2. Software Carpentry
      3. Github’s Open Source Guide
      4. Software Citation Principles
      5. InsideDNA, Galaxy, GCE
      6. Can check with GCE and AWS teams on what their uptake can be

    1. Open Access to Research Papers
      1. SHERPA/RoMEO
      2. DOAJ
      3. Think, Check, Submit
      4. SPARC Author Addendum
      5. OpenDOAR
      6. Schimmer et al. 2015 report via the MPDL
      7. Compact on Open-Access Publishing Equity (http://www.oacompact.org/)
      8. OADOI
      9. Quality Open Access Market
      10. Open Library of Humanities
      11. ASAPBio
      12. PeerJ
      13. arXiv, and bio, engr, etc. spinoffs
      14. Metrics for openness
      15. OA Repository version

    1. Open Peer Review
      1. Open-UP H2020 training calendar

    1. Citizen Science and Science Communication
      1. That PLOS Biology paper (link)
      2. Guidelines for good science PR
      3. PLOS Paper conf-tweeting: (link)
      4. https://www.aaas.org/cefp/about
      5. European Citizen Science Association ECSA
      6. Alan Alda Center for Communicating Science
      7. https://www.meetup.com/
      8. https://jumpingrivers.github.io/meetingsR/r-user-groups.html
      9. eLife collection of articles about plain-language summaries of research

    1. Open Educational Resources
      1. OER Hub
      2. Modern Drive Chester Ismay
      3. Software and Data Carpentry lessons
      4. MERLOT (Multimedia Educational Resource for Learning and Online Teaching)

  1. Open Advocacy
    1. SPARC author addendum – advocate for your own rights as an author w/ a journal https://sparcopen.org/our-work/author-rights/
    2. Bolick et al. rebuttal article written in the Journal of Wildlife Management after a misleading / fearmongering article about OA https://kuscholarworks.ku.edu/handle/1808/22672
    3. Perhaps some of the Lingua / Glossa articles on their move away from Elsevier – their advocacy as editors with a publishing organization
    4. Another example of a letter to a scholarly society advocating for Open Access – Jackie Smith to the American Sociological Association: http://www.asanet.org/sites/default/files/savvy/footnotes/mayjun14/asaforum_0514.html
      (And another article done by the same person: https://www.opendemocracy.net/jackie-smith/defending-global-knowledge-commons )
    5. eLife ECRwednesday webinar, May 31, about advocating for open science – video will be available on YouTube shortly. Featured Gary McDowell, Nick Shockey, Osman Aldirdiri, Corina Logan, Brianne Kent. Advice pitched at early-career researchers.

  1. Key Resources
    1. E-book: Open Science, Open Data, Open Source
    2. https://courses.p2pu.org/en/courses/3230/open-research-2015/
      (accompanying textbook: Open Research)
    3. Konrad Förstner, GitHub https://github.com/OKScienceDE/Open_Science_101 (CC0)
    4. Mozilla Science Lab, GitHub
    5. https://www.zotero.org/groups/medsci736-uoa/items
    6. Primary feed of the Open Access Tracking Project
    7. http://openscienceasap.org/ (
    8. 101 Innovations: tools database / wheel of open science practices (and it moves!)
    9. Reproducible Research Workshop (CC-BY, April Clyburne-Sherin & Courtney Soderberg)
    10. Starting Open Projects From Scratch (CC0, Crowdsourced by OpenCon attendees)
    11. Open Research Advocacy Train-the-Trainer (CC0, by April @ Sense About Science USA)
    12. The Open Science and Reproducible Research course (CC-BY, Christie Bahlai)
    13. Collaboration and Team Science: A Field Guide. National Institutes of Health
    14. FutureLearn MOOC (link)
    15. Improving statistical inferences MOOC (link)
    16. Uni of Cambridge’s Office for Scholarly Comms has recently run a series of workshops introducing open science practises for ECRs e.g. https://www.training.cam.ac.uk/event/1986331 (contact Danny Kingsley and Marta Teperek)
    17. Addgene.org A good start to learn about open materials sharing
    18. Open Access Directory
    19. Open Science Framework
    20. Foster Open Science
    21. Mozilla Science Lab
    22. RRI Tools Toolbox
    23. http://www.opensciencetraining.com/content.php
    24. Leiden University Online Learning Lab MOOC Production Toolkit
    25. Leiden University Centre for Innovation Toolkit
    26. Public -Friendly Open Science
    27. Tag libraries from the Open Access Tracking Project:
    28. Scholarly Communications super collection
    29. 2017 Summerschool Open Science and Scholarship, Utrecht Univerisity (schedule + materials)