# Publishing your research output
## Being open in your work
### Luke Johnston

---

---

- Benefits to open science

- Publishing services and archives

- Copyright and licensing

- Challenges
]]

---

# Get credit for all your work!

---

## Publish your:

---

# But why bother publishing anything other than research papers?

## (besides getting credit for all aspects of your work...)

---

.pull-left[.footnote[Source from [Open Science Training Manual](https://open-science-training-handbook.gitbook.io/book/open-science-basics/open-research-software-and-open-source).]]

---

## There are enormous benefits to being open!

.pull-left[
- Sharing code and/or data:
    - Pushes you to make things correct, understandable, organized
    - Gets more visibility, potential collaborations [1]
    - Better science with more transparency
    - Your work doesn't rot away if you move elsewhere
]

.pull-right[
- Using preprints [2]:
    - More impact to you and your career
    - Sooner release of research, sooner on your CV
    - More citations, visibility, scientific priority/precedence [3]
    - Funders increasingly requesting it (e.g. Plan S from EU)
]

.footnote[
[1] See DOI: [10.1101/183814](https://www.biorxiv.org/content/10.1101/183814v1)  
[2] Preprints are articles on an archive that aren't peer reviewed  
[3] See DOI: [10.7554/eLife.16800](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973366/)
]

---

## Possible hosting services and archives to use

- [Zenodo]
- [GitHub] (and [releases])
- [Open Science Framework]
- [JOSS], [JSS], [R Journal], [JORS]

For data [1]:

- [Open Science Framework]
- [Dryad]
- [figshare]
]

- [Open Science Framework] 
    - [Pre-registration](https://cos.io/prereg/)
    - [Registered Reports](https://cos.io/rr/)
- [eLife Registered Reports](https://elifesciences.org/articles/registered-report)

For posters, slides, papers:

- [figshare]
- [PeerJ Preprints]
- [bioRxiv]
]

.footnote[
[1] Depends on the field, which may have their own repositories. See this
[list of repositories](https://www.nature.com/sdata/policies/repositories)
to use. Also, make sure your data conforms to GDPR (pseudoanonymization,
anonymization) before sharing.  
[2] Pre-registering makes science better: More [null findings](https://www.nature.com/articles/d41586-018-07118-1) 
from studies that pre-registered... which is a *great thing*!!
]

[JORS]: https://openresearchsoftware.metajnl.com/about/
[JOSS]: https://joss.theoj.org/
[JSS]: https://www.jstatsoft.org/index
[R Journal]: https://journal.r-project.org/
[Zenodo]: https://zenodo.org/
[GitHub]: https://github.com/
[releases]: https://help.github.com/en/articles/about-releases
[Dryad]: https://datadryad.org/
[figshare]: https://figshare.com/
[PeerJ Preprints]: https://peerj.com/preprints/
[bioRxiv]: https://www.biorxiv.org/

---

---

### Is our obsession healthy, scientific, moral, or ethical?
]

---

.pull-left[.footnote[Source from [Open Science Training Manual](https://open-science-training-handbook.gitbook.io/book/open-science-basics/open-licensing-and-file-formats).]]

---

]

???

Anyone think that's... weird or wrong?

Journals don't need to do that. There is nothing legally necessary for them to 
take your copyrighted work.

---

- Code: **[MIT] (recommended)** or [GPL]

- Posters, slides, manuscripts: [CC-BY] \[1\]

- Data [2]: [CC0] or [Open Data Commons]

.footnote[
[1] As best you can, don't give away the copyright of *your* research and work
to journals! Lots of great journals out there that don't do that.  
[2] See the [Open Science Framework] on [licensing data].
]
]

[MIT]: https://opensource.org/licenses/MIT
[GPL]: https://opensource.org/licenses/gpl-license
[CC0]: https://creativecommons.org/share-your-work/public-domain/cc0/
[Open Data Commons]: https://opendatacommons.org/index.html
[CC-BY]: https://creativecommons.org/licenses/by/4.0/
[Open Science Framework]: https://osf.io/
[licensing data]: http://help.osf.io/m/bestpractices/l/611430-licensing

---

## But, there are many challenges

- Mostly [cultural] pushback
    - Traditional scientists may not understand
    - Fear of "scooping", no strong incentives (yet)
    - Lots of new things to learn

- Lack of awareness that data and code are foundation of good science...
    - Not the publication, the findings, or journal "impact factor"
    - [Awareness even less for code](https://www.nature.com/articles/nn.4579)

- It's hard to do open and reproducible science
    - Those who do open data and are rigorous about it, but don't share code,
    [only 35% were easily reproducible](https://royalsocietypublishing.org/doi/full/10.1098/rsos.180448)

- What really is stopping you?
    - 50-80% of PhD and post-docs move into industry [1]
    - Being open and showing your work can *only help!*

> But, the key is that this **is** the future of science

???

Question: How many intend to stay in academia?

[cultural]: https://www.software.ac.uk/blog/2018-11-20-main-obstacles-better-research-data-management-and-sharing-are-cultural-change-our

.footnote[
[1] See [here](https://www.the-scientist.com/careers/addressing-biomedical-sciences-phd-problem-32258),
[here](https://smartsciencecareer.com/become-a-professor/), and 
[here](http://www.sgs.utoronto.ca/Documents/SGS_Overview_10KPhDsProject.pdf).
]

Notes for current slide

Notes for next slide

Publishing your research outputBeing open in your workLuke Johnston1 / 14

Outline

Outputs to publish
Benefits to open science
Publishing services and archives
Copyright and licensing
Challenges

2 / 14

Get credit for all your work!

3 / 14

Publish your:

Code!

4 / 14

Publish your:

Code!

Posters and slides!

4 / 14

Publish your:

Code!

Posters and slides!

Data!

4 / 14

Publish your:

Code!

Posters and slides!

Data!

Papers! (of course)

4 / 14

But why bother publishing anything other than research papers?

(besides getting credit for all aspects of your work...)

5 / 14

Source from Open Science Training Manual.

6 / 14

There are enormous benefits to being open!

Sharing code and/or data:
- Pushes you to make things correct, understandable, organized
- Gets more visibility, potential collaborations [1]
- Better science with more transparency
- Your work doesn't rot away if you move elsewhere

7 / 14

There are enormous benefits to being open!

Sharing code and/or data:
- Pushes you to make things correct, understandable, organized
- Gets more visibility, potential collaborations [1]
- Better science with more transparency
- Your work doesn't rot away if you move elsewhere

Using preprints [2]:
- More impact to you and your career
- Sooner release of research, sooner on your CV
- More citations, visibility, scientific priority/precedence [3]
- Funders increasingly requesting it (e.g. Plan S from EU)

[1] See DOI: 10.1101/183814
[2] Preprints are articles on an archive that aren't peer reviewed
[3] See DOI: 10.7554/eLife.16800

7 / 14

Possible hosting services and archives to use

For code and code papers:

For data [1]:

For pre-registration of analysis [2]:

For posters, slides, papers:

[1] Depends on the field, which may have their own repositories. See this list of repositories to use. Also, make sure your data conforms to GDPR (pseudoanonymization, anonymization) before sharing.
[2] Pre-registering makes science better: More null findings from studies that pre-registered... which is a great thing!!

8 / 14

Question:

What does "high impact journal" mean to you?

9 / 14

Question:

Why does academia have a fascination with "high impact" journals?

Is our obsession healthy, scientific, moral, or ethical?

10 / 14

Source from Open Science Training Manual.

11 / 14

Question:

How many have published something and signed their copyright over to the journal?

12 / 14

Anyone think that's... weird or wrong?

Journals don't need to do that. There is nothing legally necessary for them to take your copyrighted work.

Licensing

Make sure to consider licensing and copyright for maximum impact

Code: MIT (recommended) or GPL
Posters, slides, manuscripts: CC-BY [1]
Data [2]: CC0 or Open Data Commons

[1] As best you can, don't give away the copyright of your research and work to journals! Lots of great journals out there that don't do that.
[2] See the Open Science Framework on licensing data.

13 / 14

But, there are many challenges

Mostly cultural pushback
- Traditional scientists may not understand
- Fear of "scooping", no strong incentives (yet)
- Lots of new things to learn

14 / 14

But, there are many challenges

Mostly cultural pushback
- Traditional scientists may not understand
- Fear of "scooping", no strong incentives (yet)
- Lots of new things to learn

Lack of awareness that data and code are foundation of good science...
- Not the publication, the findings, or journal "impact factor"
- Awareness even less for code

14 / 14

But, there are many challenges

Mostly cultural pushback
- Traditional scientists may not understand
- Fear of "scooping", no strong incentives (yet)
- Lots of new things to learn

Lack of awareness that data and code are foundation of good science...
- Not the publication, the findings, or journal "impact factor"
- Awareness even less for code

It's hard to do open and reproducible science
- Those who do open data and are rigorous about it, but don't share code, only 35% were easily reproducible

14 / 14

But, there are many challenges

Mostly cultural pushback
- Traditional scientists may not understand
- Fear of "scooping", no strong incentives (yet)
- Lots of new things to learn

Lack of awareness that data and code are foundation of good science...
- Not the publication, the findings, or journal "impact factor"
- Awareness even less for code

It's hard to do open and reproducible science
- Those who do open data and are rigorous about it, but don't share code, only 35% were easily reproducible

What really is stopping you?
- 50-80% of PhD and post-docs move into industry [1]
- Being open and showing your work can only help!

14 / 14

But, there are many challenges

Mostly cultural pushback
- Traditional scientists may not understand
- Fear of "scooping", no strong incentives (yet)
- Lots of new things to learn

Lack of awareness that data and code are foundation of good science...
- Not the publication, the findings, or journal "impact factor"
- Awareness even less for code

It's hard to do open and reproducible science
- Those who do open data and are rigorous about it, but don't share code, only 35% were easily reproducible

What really is stopping you?
- 50-80% of PhD and post-docs move into industry [1]
- Being open and showing your work can only help!

But, the key is that this is the future of science

14 / 14

Question: How many intend to stay in academia?

[1] See here, here, and here.

Outline

Outputs to publish
Benefits to open science
Publishing services and archives
Copyright and licensing
Challenges

2 / 14

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