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SciTog_openscience License: Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) license
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Authors (in alphabetical order of first name): Brigitta Sipocz, Daniel van Strien, Pen-Yuan Hsing ("Pen")

Title: What goes into a guide to doing open science?

Pen's reflection blog post:
We started the discussion around what makes a good booklet/guide on doing good science. We agreed that there are many broad good practices ("Good science is open science, closed science is not good science!"), such as open source code, open access publications, and open data. However, it becomes difficult if you want to gear the guide to specific scientific fields. The concerns of an astronomer might be different from a biologist, even the tools they use are different. So if the guide is too specific, then it might not get scientists in other disciplines interested. Eventually, we came up with a bullet point list of a rough outline for a broad (not discipline specific) guide below.

Brigitta had a great idea which is a "case studies" section. This puts a lot of the practices into context and show that open science can be good/successful science, contrary to what some people might say.

As part of our wide ranging discussion, we talked about the institutional and cultural issues around doing science. The scientific method is fundamentally about building on past work and making your results for others to build on. Don't forget that as scientists, we are always "standing on the shoulders of [other scientists]"! Unfortunately, the realities of academia today (tenure review, credit attribution, the publishing process (e.g. Elsevier!!!), etc.) often incentive us to do closed science. How do we solve this fundamental betrayal of science? This is a big problem that will take more than one person to solve. However, it is important for all of us to remember that we are ultimately responsible to science not politics and keep that in mind when we make decisions. For example, climate change is a huge global issue that will take an equally huge cooperative effort to solve, and it has taken decades and we are still not close to solving it. But that doesn't mean we shouldn't work hard on it! It is also true for advocating open science.

That said, for making a guide to open science, talking about such deep issues might lose a reader's interest because they might want to see specific things they can do, rather than a deep discussion. How do you strike a good trade-off between the two? This is a question that we leave to the reader of this Etherpad. Finally, I propose that while the big problems can be overwhelming, one thing we can do is to think about the baby steps we can take towards more honest/responsible science. Maybe every month you can pick one small good practice to put into action in your research workflow.

# Outline for general guide for doing open science and good practice

## What is open science? (general)

* Good science is open science, closed science is not good science!
* Report on science as an open enterprise by the Royal Society: https://royalsociety.org/topics-policy/projects/science-public-enterprise/Report/

## open literature review

https://pad.okfn.org/p/opendiscovery-mozfest

## cultural/political questions
* Science doesn't operate in a vacuum 
* Practices/norms in different research areas?
* how can you implemenet new ways of working?
* Problems with attribution/credit

## Publishing open access

* What does open access really mean -> definition.
* Maybe talk about copyright and licenses here?
* 

## Open data

* What does open data really mean -> definition.
* Licenses.
* Where to submit data
* Long term storage/retrieval issues

## Tools for doing open science

* forced/planned obsolescence
* "Open source" replacements for commonly used proprietary tools
Very general list of collaborative office tools:
    * Google Sheets replacement: EtherCalc (https://ethercalc.org/)
    * Google Docs replacement: EtherPad (https://etherpad.net/ or http://etherpad.org/ for more providers)
    * Google Drive replacements: Open Science Framework (https://osf.io/), create "projects" in which all of your project files reside with DOI provided , can pull and integrate files from Dropbox, GitHub, Google Drive, Mendeley, etc. Zenodo (http://zenodo.org/) is also good. Another non-academic solution is ownCloud, which is hosted by different providers (https://owncloud.org/providers/), some free of charge.
    * Basecamp, Slack, and Skype replacement: Riot (https://riot.im/) does everything Basecamp, Slack, and Skype does and more. Mobile app here: https://play.google.com/store/apps/details?id=im.vector.alpha
    * Instant messaging and Skype replacements: Signal (https://whispersystems.org/), Riot (https://riot.im/), Ring (https://ring.cx/), or Jitsi Meet (https://meet.jit.si/)
    * Trello replacement: Taiga (https://tree.taiga.io/discover)
    * Eventbrite replacement: eventyay (https://eventyay.com/) which can be self-hosted on your server (https://github.com/fossasia/open-event-orga-server)
    * Evernote replacements: Turtl (https://turtlapp.com/), Laverna (https://laverna.cc/)
    * Doodle poll replacements: Dudle (https://dudle.inf.tu-dresden.de/), Framadate (https://framadate.org/)
    * Surveymonkey and Google Forms replacements: LimeSurvey (https://www.limesurvey.org/), Journey (http://welcome.journeysurveys.com/)
    * Mendeley, EndNote, and RefWorks replacement: Zotero (https://www.zotero.org/)
    * General blogging: Wordpress (https://wordpress.com/)
    * URL/link shorteners: Framalink (https://frama.link/), 1n.pm (https://1n.pm/), there are many others or set up your own with YOURLS (https://yourls.org/)
    * Discussion forum hosting: Discourse (https://www.discourse.org/)
    * A general resource for more replacements: Libre Projects (http://www.libreprojects.net/)
    * Adobe Photoshop replacement: GIMP (http://www.gimp.org/)
    * Adobe Illustrator replacement: Inkscape (https://inkscape.org/)
    * Adobe InDesign replacement: Scribus (http://www.scribus.net/)
    * Apple iMovie, Final Cut, or Adobe Premiere replacements: OpenShot (http://openshot.org/), Blender (very advanced https://www.blender.org/)
    * Audio editing: Audacity (http://audacityteam.org/)
    * Microsoft Office replacement: LibreOffice (https://www.libreoffice.org/)
    * Microsoft Internet Explorer, Google Chrome, or Apple Safari replacement: Mozilla Firefox (https://www.mozilla.org/firefox/)
    * Proprietary fonts replacements: http://openfontlibrary.org/

Some things for which I have sadly not found good replacements:

    * Apple Keynote and Microsoft Powerpoint
    * YouTube/Vimeo
    * Flickr

What about field-specific tools? Need list of good examples!

* Matlab, SPSS, Stata, etc. replacements: Python, R

## Reproducible research

* Code
* Non-code methods
* Anything else? Documentation?

## New ways of disseminating research
- Not everything has to be a paper 
- exectuable papers which link software, data, and text




## Case studies

* Success stories
* Projects that went from closed to open
* Arxiv.org is a great example of open access publishing, and it works well with publishers, too.
* SAO/NASA Astrophysics Data System adsabs.harvard.edu for astronomy and physics papers
* Genbank
* Astrophysics Source Code Library/Zenodo

### Link dump:
How did the Human Genome Project make science more accessible?  
http://www.yourgenome.org/stories/how-did-the-human-genome-project-make-science-more-accessible

Public vs Private Efforts to Map the Human Genome
http://www.knowledgene.com/part2.html


https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki

https://royalsociety.org/topics-policy/projects/science-public-enterprise/report/

Lifting proprietary period for the K2 mission compared to Kepler, effects on author stats, accessibility
(no write up on it yet, just a few figures: https://github.com/barentsen/exoplanet-charts/tree/master/publication-stats)

## Checklist for doing open science (easy to hard)
* Publish papers open access [ ] 
* Publish underlying data [ ] 
* Publish code/analysis scripts [ ] 
* ???


Software use in astronomy (survey by Tollerud&Momcheva, 2015): https://arxiv.org/abs/1507.03989

How python became the No1 language in astronomy: https://www.youtube.com/watch?v=R_UcjjUC8bE and https://www.youtube.com/watch?v=uz53IV1V_Xo


[addition Bianca: also check out Jon Tennant @protohedgehog initiative for an collaboratively put-together Open Science MOOC http://fossilsandshit.com/building-an-open-science-mooc/ - might be worthwhile to collaborate / benefit from each other's ideas/materials)
[also added as asked by Pen: Utrecht Summer School Open Science & Scholarship (this also has Jeroen & Bianca's contact details):  https://www.utrechtsummerschool.nl/courses/science/open-science-and-scholarship-changing-your-research-workflow