Cyano2017

"Open​ ​Science​ ​-​ ​The​ ​future​ ​of​ ​science?" session/workshop at the 2​nd​​ ​Early​ ​Career​ ​Researcher​ ​Symposium​ ​on​ ​Cyanobacteria (http://schmelling.github.io/cyano2017.html) on the 14th of September 2017.

This talk is a short introduction into Open Science from a microbiologist's perspective. It includes a collection of Open Science ideas and resources, gives examples of biologists's Open Science activities, and should serve a thought-provoking purpose.

Authors:
Andreas Leimbach, University of Münster, Institute of Hygiene (ORCID: https://orcid.org/0000-0001-9077-1041)

Talk licensed under Creative Commons Attribution 4.0 International License (CC BY 4.0): https://creativecommons.org/licenses/by/4.0/

Source links for pictures with non-CC0 licenses are given. Non-licensed are the Cyano2017, University of Göttingen, G2L, UKM, and the University of Würzburg logos, as well as Rosie Redfield’s portrait.

Transcript

1. OPEN SCIENCE The future of science? Cyano 2017 Andreas Leimbach @aleimba #cyano2017 The opinions expressed here represent my own and not those of my affiliations. Talk licensed under CC-BY. Source links for pictures with non-CC0 licenses are given. Non-licensed are the Cyano2017, University of Göttingen, G2L, UKM, and the University of Würzburg logos, as well as Rosie Redfield’s portrait.
2. About myself CC-BY https://commons.wikimedia.org/wiki/ File:Karte_Bundesrepublik_Deutschland.svg
3. About myself Microbial Genome Plasticity CC-BY https://commons.wikimedia.org/wiki/ File:Karte_Bundesrepublik_Deutschland.svg
4. About myself Microbial Genome Plasticity CC-BY https://commons.wikimedia.org/wiki/ File:Karte_Bundesrepublik_Deutschland.svg
5. About myself CC-BY https://commons.wikimedia.org/wiki/ File:Karte_Bundesrepublik_Deutschland.svg Microbial Genome Plasticity CC-BY https://github.com/OKScienceDE/ AG_Open_Science_Logo/blob/master /AG_Open_Science_Logo.png
6. Outline 1. Short introduction to Open Science 2. Collecting ideas with the audience 3. Summary and examples 4. What can you do right now for the future of (Open) Science? 5. (References)
7. Scientific progress relies on sharing of both scientific ideas and scientific methodology “If I have seen further, it is by standing on the shoulders of giants” -- Isaac Newton 1676 Robert Koch Fanny Angelina Hesse
8. Research cycle
9. What is Open Science? • Open science is the concept of making all aspects of scientific research publicly accessible, to allow others to follow the process and collaborate/discuss – Transparency in methods, data, and analyses – Public availability and reusability of scientific methods, data, and analyses published hidden CC-BY https://github.com/OKScienceDE/AG_Open_Science_Logo/ blob/master/AG_Open_Science_Logo.png
10. Open Science promotes Open communication Integrity and quality Reproducibility Reusability CC-BY-SA https://commons.wikimedia.org/wiki/ File:4_pillars_from_the_inner_court_of_the_Bel_Temple_Palmyra_Syria.JPG CC-BY https://github.com/OKScienceDE/AG_Open_Science_Logo/ blob/master/AG_Open_Science_Logo.png (O pen) Science
11. Open Science promotes Open communication Integrity and quality Reproducibility Reusability CC-BY-SA https://commons.wikimedia.org/wiki/ File:4_pillars_from_the_inner_court_of_the_Bel_Temple_Palmyra_Syria.JPG CC-BY https://github.com/OKScienceDE/AG_Open_Science_Logo/ blob/master/AG_Open_Science_Logo.png (O pen) Science Good scientific practice
12. Innovations in scholarly communication CC-BY-SA https://en.wikipedia.org/wiki/ File:Angela_Merkel_Juli_2010_-_3zu4.jpg CC-BY https://101innovations.wordpress.com/outcomes/ “Neuland” tools
13. Innovations in scholarly communication “Neuland” tools See the poster “Open Science 4.0 - Transforming the Way We Do (Open) Science Using Digital Tools” from Nicolas Schmelling CC-BY-SA https://en.wikipedia.org/wiki/ File:Angela_Merkel_Juli_2010_-_3zu4.jpg CC-BY https://101innovations.wordpress.com/outcomes/
14. Open science intents to lower barriers • Many barriers for scientific advancement: – Economic: Paywalls – Cultural: Peer review delays – Methodological: incomplete methods description – Systemic: Incentives to hide data and methods • Value of reuse
15. Why are scientists not doing Open Science? • Cost of sharing • Lack of training and conservatism of practice • No incentives (no metrics for evaluation) • Reputation “game” • Commercial interests (publishers) • Minimal accountability John R. McKiernan CC-BY http://whyopenresearch.org
16. Reproducibility crisis • Foremost psychology, e.g. about two thirds of 100 high-impact studies non-reproducible: http://go.nature.com/1JBe4Yo • “Arsenic-life” bacterium GFAJ-1 – Wolfe-Simon F. et al. (2011) “A bacterium that can grow by using arsenic instead of phosphorus”. Science 332(6034): 1163-1166. • STAP cells (Stimulus-Triggered Acquisition of Pluripotency) – Obokata H. et al. (2014) "Stimulus-triggered fate conversion of somatic cells into pluripotency". Nature 505(7485): 641-647. – Obokata H. et al. (2014) "Bidirectional developmental potential in reprogrammed cells with acquired pluripotency". Nature 505(7485): 676-680. • Plant scientist Olivier Voinnet – 8 retractions, 17 corrections – Science, PNAS, EMBO Journal etc. – EMBO gold medal revoked
17. The rise of retractions Brembs B, Button K, Munafò M. 2013. Deep impact: unintended consequences of journal rank. Front Hum Neurosci 7:291.
18. If you could start the scientific process from scratch, how would you imagine it for the advancement of science and for individual scientists? CC-BY-SA https://en.wikipedia.org/wiki/ File:Blue-green_algae_cultured_in_specific_media.jpg
19. Idea collection
20. Facets of Open Science
21. Microbiologists’ Open Science examples (1) 1,094
22. Microbiologists’ Open Science examples (1) 637
23. Microbiologists’ Open Science examples (2) Leimbach A. 2016. bac-genomics-scripts: Bovine E. coli mastitis comparative genomics edition. Zenodo. http://dx.doi.org/10.5281/zenodo.215824. https://github.com/aleimba/bac-genomics-scripts
24. Microbiologists’ Open Science examples (2) Leimbach A. 2016. bac-genomics-scripts: Bovine E. coli mastitis comparative genomics edition. Zenodo. http://dx.doi.org/10.5281/zenodo.215824. https://github.com/aleimba/bac-genomics-scripts
25. Microbiologists’ Open Science activities (1) Rosie Redfield’s ‘open science’ research blog, amongst others about the “Arsenic-life” bacterium GFAJ-1: http://rrresearch.fieldofscience.com/ Reaves ML. et al. (2012) “Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells.” Science 337(6093): 470-473.
26. Microbiologists’ (biologists’) Open Science activities (2) • #MICROJC online microbiology journal club https://gplusmicrojc.wordpress.com/ • Ethan White’s collection of publicly available grant proposals in the biological sciences https://jabberwocky.weecology.org/2012/08/ 10/a-list-of-publicly-available-grant-proposals- in-the-biological-sciences/
27. What can you do right now? • Use/promote – open access journals – preprint servers (and publish freely accessible post-prints, e.g. http://dissem.in) – data repositories for your research data • Document and release code • Use the reviewing process to promote open science (e.g. “The Open Science Peer Review Oath”) • Interact with colleagues and public via social media (blogs, Twitter etc.) • Integrate Open Science in your classes/meetings (e.g. “The Open Science and Reproducible Research course”) – Do replication studies with students: Data available?, Code available and usable?, Methods detailed enough? • Organize Trainings: Software/Data/Library Carpentry, Hackathons etc. • Abandon the broken "journal prestige" system to influence university administration on matters of research evaluation and tenure (e.g. Felix Schönbrodt University of Munich, http://www.nicebread.de/open-science-hiring-practices/), and on grant panels and editorial boards
28. What can you do right now? • Use/promote – open access journals – preprint servers (and publish freely accessible post-prints, e.g. http://dissem.in) – data repositories for your research data • Document and release code • Use the reviewing process to promote open science (e.g. “The Open Science Peer Review Oath”) • Interact with colleagues and public via social media (blogs, Twitter etc.) • Integrate Open Science in your classes/meetings (e.g. “The Open Science and Reproducible Research course”) – Do replication studies with students: Data available?, Code available and usable?, Methods detailed enough? • Organize Trainings: Software/Data/Library Carpentry, Hackathons etc. • Abandon the broken "journal prestige" system to influence university administration on matters of research evaluation and tenure (e.g. Felix Schönbrodt University of Munich, http://www.nicebread.de/open-science-hiring-practices/), and on grant panels and editorial boards Create a reward system that promotes openness and has incentives to share methods/data/results
29. You can get involved OKF (Open Knowledge foundation) Open Science Working Group: http://science.okfn.org/ German Speaking Open Science group of the OKF: https://www.ag-openscience.de/ CC-BY https://github.com/OKScienceDE/AG_Open_Science_Logo/ blob/master/AG_Open_Science_Logo.png
30. When will the ‘future of science’ become simply ‘science’? CC-BY https://github.com/OKScienceDE/AG_Open_Science_Logo/ blob/master/AG_Open_Science_Logo.png Watson M (2015) When will ‘open science’ become simply ‘science’? Genome Biol. 16(1): 101.
31. Slides available at https://speakerdeck.com/aleimba/cyano2017 or http://bit.ly/2x29dQe
32. Further information/References (1) Background links • Konrad Förstner’s and Andreas Leimbach’s Open Science workshop template: https://github.com/konrad/Open_Science_Workshop_Toolbox • Open Research Glossary: https:// figshare.com/articles/Open_Research_Glossary/1482094 • Prof. Titus C. Brown “What is open science?”: http://ivory.idyll.org/blog/2016-what-is-open-science.html • Dr. Graziella DiRenzo "Open science: why is everyone talking about it?": http://grazielladirenzo.weebly.com/bayes-the-way/open-science-why-is-everyone-talki ng-about-it • Prof. Dan Gezelter “What, exactly, is Open Science?”: http://www.openscience.org/blog/?p=269 • F1000 blog Eva Amsen “What is open science?”: https://blog.f1000.com/2014/11/11/what-is-open-science/ • Reproducibility Project: Cancer Biology https://elifesciences.org/collections/9b1e83d1/reproducibility-project-cancer-biology
33. Further information/References (2) Background Publications • McKiernan EC et al. 2016. How open science helps researchers succeed. eLife 5:e16800. • Fang FC, Casadevall A. 2015. Competitive science: is competition ruining science? Infect Immun 83:1229–1233. • Edwards MA, Roy S. 2017. Academic Research in the 21st Century: Maintaining Scientific Integrity in a Climate of Perverse Incentives and Hypercompetition. Environ Eng Sci 34:51–61. • Munafò MR et al. 2017. A manifesto for reproducible science. Nature Human Behaviour 1:21. • Barone L et al. 2017. Unmet Needs for Analyzing Biological Big Data: A Survey of 704 NSF Principal Investigators. bioRxiv. https://doi.org/10.1101/108555 • McKiernan EC. 2017. Imagining the “open” university: Sharing science to improve research and education. e2711v1. PeerJ Preprints. • Markowetz F. 2015. Five selfish reasons to work reproducibly. Genome Biol 16:274.
34. Further information/References (3) General • Open Science Radio: http://www.openscienceradio.de/ • Center for Open Science (COS): http://centerforopenscience.org/ • Mozilla Science Lab: https://www.mozillascience.org/ • Open source/data licenses: https://choosealicense.com/ • F1000 Research “Guide to open science publishing”: http:// f1000.com/resources/F1000R_Guide_OpenScience.pdf • 101 Innovations in Scholarly Communication: https://101innovations.wordpress.com/ Alternative measures of impact • Leiden manifesto for research Metrics: http://www.leidenmanifesto.org/ • San Francisco Declaration on Research Assessment (DORA): http://www.ascb.org/dora/ • Unique Researcher ID for all research output, ORCID: http://orcid.org/ • Contributorship badges/CRediT taxonomy: – https://badges.mozillascience.org/ – http://dictionary.casrai.org/Contributor_Roles • Altmetric: http://www.altmetric.com • Impactstory: https://impactstory.org
35. Further information/References (4) Open Access • open-access.net: https://www.open-access.net/DE-EN/germany-english/ • Directory of Open Access Journals (DOAJ): https://doaj.org/ • Find open access versions of articles – Open Access Button: https://openaccessbutton.org/ – Unpaywall: http://unpaywall.org/ • Raphaël Lévy (2015) “Where to Publish Our Next Paper? – Letter to a Group Member” JUnQ, 5, 1 • Schloss PD. 2017. Preprinting Microbiology. bioRxiv. https://doi.org/10.1101/110858 • Preprint server: – bioRxiv: http://biorxiv.org/ – arXiv: http://arxiv.org/ – PeerJ preprints: https://peerj.com/preprints/ • Journal preprint/post-print policies: – SHERPA/RoMEO rchiveit wrapper: http://rchive.it/ – https://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy
36. Further information/References (5) Open Data • Publish the whole research cycle: – Open Science Framework (OSF): https://osf.io/ – Research Ideas and Outcomes (RIO) Journal: http://riojournal.com/ • DataONE Best Practices Database for Data/Open Data: https://www.dataone.org/best-practices • Data repositories: – Dryad: http://datadryad.org/ – Zenodo: http://www.zenodo.org/ – Figshare: http://figshare.com/ – Treebase: http://treebase.org/treebase-web/home.html – re3data.org – Registry of Research Data Repositories: http://www.re3data.org/ • Data journals (later publication in a “normal” journal still possible): – NPG’s Scientific Data: http://www.nature.com/sdata/ – GigaScience (“Big Data” Journal): http://www.gigasciencejournal.com/ • Publish protocols: https://www.protocols.io/
37. Further information/References (6) Open Source • Code repositories/collaborative coding: – GitHub: http://github.com/ – Bitbucket: http://bitbucket.org/ – SourceForge: http://sourceforge.net/ • Get a citable DOI (digital object identifier) for your source code with: – Figshare: http://figshare.com/ – Zenodo: http://www.zenodo.org/
38. Further information/References (7) Open Peer Review • Aleksic J et al. 2015. An Open Science Peer Review Oath. F1000Research 3:271. • Open Peer Review Journals: – The EMBO Journal: http://emboj.embopress.org/ – PeerJ: http://peerj.com – GigaScience: http://www.gigasciencejournal.com/ – etc. • Post-publication peer review – F1000 Research: http://f1000research.com/ – ScienceOpen: https://www.scienceopen.com/ • Discuss published articles: – PubPeer: https://pubpeer.com/ – RetractionWatch: http://retractionwatch.com/ – PubMed Commons: http://www.ncbi.nlm.nih.gov/pubmedcommons/ – Blogs etc. • Take credit for Peer Review – Publons: http://publons.com/
39. Further information/References (8) Open Educational resources • Data Carpentry: http://datacarpentry.org/ • Software Carpentry: https://software-carpentry.org/ • Rosalind: http://rosalind.info/ • Dr. Christie Bahlai “The Open Science and Reproducible Research course” (for organismal ecologists, but generally applicable): https:// github.com/cbahlai/OSRR_course • Massive open online courses (MOOCs): – MIT OpenCourseWare: http://ocw.mit.edu/index.htm – Udacity: https://www.udacity.com/ – edX: https://www.edx.org/ – Coursera: https://www.coursera.org/ – etc. Open Notebook • OpenWetWare: http://openwetware.org/ • Jupyter Notebook: https://jupyter.org/ • R Markdown: http://rmarkdown.rstudio.com/