publishing

4-1-licensing.qmd

@@ -1 +1,53 @@
-## Licensing
+## Licensing
+
+Reusing other researcher's work is inherent in science. Licensing plays a central role for reuse, so we should know how it works.
+
+
+
+In my workshops on open and reproducible research licensing often comes up as a topic of fear.
+
+*What am I allowed to do? Should I better let the legal department decide? How do I avoid going to jail?*
+
+Most of the time choosing a license is actually quite simple. So let me help you loose your fear of it! 🤗
+
+### Choosing a license for texts, data, media, ...
+
+I really like the Creative Commons licenses for most research outputs (and other things I produce, like this newsletter).
+
+They are easy to understand and to pick. On the CC-website you can find a simple tool to help you choose your license:
+
+https://creativecommons.org/choose/
+
+In research we want to almost always use the CC-BY or CC0 license.
+
+- [CC0](https://creativecommons.org/publicdomain/zero/1.0/) (also known as CC0 1.0 Universal) means that the output is in the public domain and can by used by everyone for anything.
+- [CC-BY](https://creativecommons.org/licenses/by/4.0/) (also known as Attribution 4.0 International) requires the user to give credit to the creator but gives freedom on what can be done with the output. This is the license I use 90% of the time.
+
+#### Why not non-commercial?
+
+[CC-BY-NC](https://creativecommons.org/licenses/by-nc/4.0/) is another license I often see used, but I do not like it in the context of research. Why? The "NC" for non-commerical prohibits commercial use for anyone but the owner. That means, for example, that educators (like me) cannot use it, if there are fees or commercial learning platforms involved. Even blogs and Wikipedia struggle with NC if there are commercial derivatives or components. Read more here.
+
+
+### Choosing a license for software
+
+Software needs specific licenses. So for software there is another website you can use for choosing a license.
+
+https://choosealicense.com
+
+Again there is a license that works for most open projects: the MIT license.
+
+::: captioned-image-container
+![https://choosealicense.com](images/mit-license.png){fig-alt="Screenshot of https://choosealicense.com section 'I want it simple and permissive'"}
+:::
+
+That seems pretty simple, right? For more complex situations and when you have to worry about license compatibility of your code with software components that you use, please check out:
+
+- The Turing Way chapter on [License Compatibility](https://the-turing-way.netlify.app/reproducible-research/licensing/licensing-compatibility)
+- Talk "[All you need to know about Software Licenses](https://zenodo.org/record/8246557)" by Tobias Schlauch
+
+### Other
+
+For other licenses, such as for hardware, choosealicense.com also has help for you:
+[choosealicense.com/non-software](https://choosealicense.com/non-software/)
+
+I hope this short intro to licensing was helpful to you! Please note that I am not a legal expert but a self taught open science enthusiast.

4-2-where-to-publish.qmd

@@ -1 +1,76 @@
 ## Where to publish
+
+When people write the following:
+
+> *The data/code will be made available upon request.*
+
+This usually means:
+
+> *Once the PhD student who wrote this paper leaves their position, the
+> data/code will be lost in space.*
+
+Am I right? But how can you do better? How can you make your research outputs
+available?
+
+### Publish in a repository
+
+Publish your research outputs in a repository. You basically have three
+options here:
+
+-   A general purpose service (e.g. [Zenodo](https://zenodo.org/) or
+    [Open Science Framework](https://osf.io/)),
+-   The service of your institution (e.g. [Open Data
+    LMU](https://data.ub.uni-muenchen.de/) or [ETH Zurich's Research
+    Collection](https://www.research-collection.ethz.ch/?locale-attribute=en)),
+-   A field or project specific service (e.g. a specific repository for
+    [high throughput sequencing data](https://www.ncbi.nlm.nih.gov/sra)
+    or [CRAN](https://cran.r-project.org/) for R-Packages)
+
+Please make sure to use a trustworthy service. How to check if a service
+is trustworthy? My rule of thumb is that services that have investor
+backing (e.g. Figshare) are less trustworthy than services backed by the
+research community (e.g. Zenodo, which is developed by OpenAIRE and
+CERN). Why? Well, I think an Open Science service should not be driven
+primarily by commercial goals. At some point commercial services will
+take money from you, if that may be by selling your data, by locking
+your uploaded material behind a pay wall, or in another way.
+
+### Publish with the paper
+
+Some journals offer to publish your research outputs with your paper. I
+will be honest, I have mixed feelings about this. Not all journals which
+offer this, really have the expertise to do so and they don't
+necessarily have the possibility to store data long term. For one of my
+papers we uploaded the material with the journal, but the link to the
+material keeps vanishing and I keep getting the confused emails of
+interested readers. So, make sure the journal you upload your material
+to, ensures long term storage and availability 🧐.
+
+### If your research outputs cannot be shared openly
+
+What should you do if you cannot publish your research outputs openly?
+
+If you have sensitive data (e.g. patient data) and no consent, do not publish the data! There
+are other options for you.
+
+If for any reason you cannot share your research outputs, think of
+options how you can still ensure that others can trust in the
+reproducibility of your research.
+
+- Can you maybe publish the metadata and the code? 
+- Can you publish a synthetic version of your data? 
+- Can you share the data with specific people (e.g. researchers in the same field)? 
+
+Brainstorm with your peers, librarians, or IT support. There
+are always solutions that are better than publishing nothing.
+
+
+### Further reading
+
+-   [Zenodo Guide](https://www.openaire.eu/zenodo-guide)
+-   [How create an OSF
+    project](https://help.osf.io/article/252-create-a-project)
+
+
+
+

4-3-fair-revisited.qmd

@@ -1 +1,3 @@
-## FAIR revisited
+## FAIR revisited
+
+TODO

4-publishing-research.qmd

@@ -19,6 +19,8 @@
 Read this chapter and watch this week's videos. 
 Afterwards go through the following assignments:
 
+- Discuss with your accountability buddy and/or your research team: what are good places to publish
+    your data, code and other research outputs in your field?
 - Upload something (e.g. data or a slide deck) to a repository of your choice. How FAIR can you make it?
 
 Discuss your progress with your accountability buddy. Bring any questions and

_quarto.yml

@@ -25,6 +25,10 @@ book:
     - 3-2-stabilize.qmd
     - 3-3-automate.qmd
   - part: 4-publishing-research.qmd
+    chapters:
+    - 4-1-licensing.qmd
+    - 4-2-where-to-publish.qmd
+    - 4-3-fair-revisited.qmd
   - part: summary.qmd
     chapters:
     - references.qmd