Open Science Crash Course

background-image: url("https://raw.githubusercontent.com/EstherPlomp/PRES-data-software/main/images/OSC-data-software.jpg")
background-position: 80% 80%
background-size: 40%

## Open Science: Crash Course

#### Open Data/Software: What, when, how?

Slides by [**Esther Plomp**](https://estherplomp.github.io/) @ TU Delft, Faculty of Applied Sciences

License: CC-BY

[Link slides](https://estherplomp.github.io/PRES-data-software/)

---

# Open Science

---
# Open Science

.pull-left[
![TU Delft Open Science logo](https://d2k0ddhflgrk1i.cloudfront.net/Library/Themaportalen/Open.tudelft.nl/Homepage/OS_homepage_infographic_3.png)]

**Open Software**

**Open Education**

**Open Hardware**

**Open Methods**

**Open Publishing**

**Collaboration (community, inclusion)**

**Citizen Science**
]

---
class: inverse, middle, center

# Open Data

---

background-image: url("https://raw.githubusercontent.com/EstherPlomp/PRES-data-software/main/images/data-management-plan.jpg")
background-position: 80% 80%
background-size: 50%

# Planning for Open Data

**Data Management Plan (DMP)** to plan how to manage and share the data (see [The Turing Way for more information](https://the-turing-way.netlify.app/reproducible-research/rdm/rdm-dmp.html))

TU Delft has access to [DMPonline](dmponline.tudelft.nl/) with TU Delft specific templates and guidance

---

background-image: url("https://raw.githubusercontent.com/EstherPlomp/2022-PRES-Data/main/images/tidydata_3-small.jpg")
background-position: 100% 100%
background-size: 80%

# Data Organisation

---

## File naming
- 20220113-PRES-Data-V001
- [8 step guide](https://resolver.caltech.edu/CaltechAUTHORS:20200601-161923247) on how to set up your file naming convention
- [Presentation on file naming](https://speakerdeck.com/jennybc/how-to-name-files)
- [Stanford’s best practices](https://library.stanford.edu/research/data-management-services/data-best-practices/best-practices-file-naming)

## Folder structure
- Templates by [Colomb et al.](https://doi.org/10.5281/zenodo.4410128), [Nikola](http://nikola.me/folder_structure.html) and [Barbara Vreede](https://github.com/bvreede/good-enough-project) for [cookiecutter](https://github.com/cookiecutter/cookiecutter)
- [Find Files Faster](https://zapier.com/blog/organize-files-folders/): How to Organize Files and Folders
- [Data Management: File organisation](https://surfdrive.surf.nl/files/index.php/s/gJtISAQABapLvnI) by Christine Malinowski
- [Videos on project structure](https://www.youtube.com/watch?v=u6MiDFvAs9w&list=PLRPB0ZzEYegPiBteC2dRn95TX9YefYFyy&index=2) by Danielle Navarro
- Software: [Cookiecutter template by Barbara Vreede](https://github.com/bvreede/good-enough-project) based on [Wilson 2017](https://doi.org/10.1371/journal.pcbi.1005510)

---

# Data Organisation

.pull-left[
[![Friends meme on how Excel changes everything to a date](https://raw.githubusercontent.com/EstherPlomp/2022-PRES-Data/main/images/excel-dates.jpg)](https://twitter.com/mdancho84/status/1426970168660529153)]

- [Spreadsheet organisation tips](https://surfdrive.surf.nl/files/index.php/s/9aNX69fsWyAnMI8)
- [Broman and Woo 2018](https://doi.org/10.1080/00031305.2017.1375989)
- [Wickham 2014](https://vita.had.co.nz/papers/tidy-data.html)
- Use tools for data validation like [OpenRefine](https://openrefine.org/)

## Why? What could possibly go wrong? 
- [a lot](http://www.eusprig.org/horror-stories.htm)
]

---

# Data Documentation

.pull-left[
[![A pan filled with spaggethi on fire with the text: skimmed the protocol](https://raw.githubusercontent.com/EstherPlomp/2022-PRES-Data/main/images/skimmed-protocol.jpg)](https://twitter.com/thecrobe/status/1373590641012322306)]

.pull-right[
- (electronic) Labnotes: TU Delft provides [licenses for eLABjournal and Rspace](https://www.tudelft.nl/en/library/research-data-management/r/manage/electronic-lab-notebook)
- Readme files ([template](https://cornell.app.box.com/v/ReadmeTemplate))
- [Guide for data documentation](https://doi.org/10.5281/zenodo.1914401)
- [Data Dictionary](https://uf-repro.github.io/data-organization/slides.html)
- [Code Book](https://libguides.library.kent.edu/SPSS/Codebooks)

#### More information
- Book: Data Management for Researchers by Kristin Briney 
- [A Quick Guide to Organizing Computational Biology Projects](https://doi.org/10.1371/journal.pcbi.1000424) by William Noble
- [Some Simple Guidelines for Effective Data Management](https://doi.org/10.1890/0012-9623-90.2.205) by Borer et al.
]

---

background-image: url("https://raw.githubusercontent.com/EstherPlomp/PRES-data-software/main/images/fountain-of-open-data.jpg")
background-position: 100% 100%
background-size: 40%

# Open Data

made freely available for use and re-use by anyone and everyone

**Access** : Available (on the internet) to all on demand

**Reuse/distribution** : Provided under terms that permit reuse and redistribution

**Transparency** : Providing information about data generation/collection

**Interoperability** : Interoperability with other data, machine readable formats

**Participation** : Everyone must be able to use, reuse and redistribute

**Equity** : Data is not truly open if the research process is not open to all

.footnote[
[#bropenscience is broken science](https://thepsychologist.bps.org.uk/volume-33/november-2020/bropenscience-broken-science) by Kirstie Whitaker and Olivia Guest

[Open Science Beyond Open Access: For and with communities](https://doi.org/10.5281/zenodo.3946773)

image by [The Turing Way](https://doi.org/10.5281/zenodo.3332807)]

---

# Not Open Data

.pull-left[
[![Data being available upon request, with Agnes winking very obviously](https://raw.githubusercontent.com/EstherPlomp/2022-PRES-Data/main/images/upon-request.jpg)](https://twitter.com/MadS100tist/status/1366103674989277185)
]

.pull-right[
'[odds of obtaining the dataset] fell by 17% per year' [Vines et al. 2014](https://doi.org/10.1016/j.cub.2013.11.014)

‘research data cannot be reliably preserved by individual researchers’ - [Vines et al. 2014](https://doi.org/10.1016/j.cub.2013.11.014)

"We received no response to 41.3% of our data requests" - [Tedersoo et al. 2021](https://doi.org/10.1038/s41597-021-00981-0)

[Meme explanation](https://knowyourmeme.com/memes/agnes-harkness-winking)
]

---

# Open Data

.pull-left[
[![A tree with various pieces of documention in the branches and the text Repositree](https://pbs.twimg.com/media/EVzdm1nXQAI1fY_?format=jpg&name=900x900)](https://twitter.com/ErrantScience/status/1251118457279647746)
]

.pull-right[
## data repository
online archive that curates research datasets and provides long-term access
- Finalised datasets
- ~10-15 years (Long term preservation)
- Access
- DOI = more citations/visibility
- File format support

[How can you make research data accessible?](https://www.software.ac.uk/how-can-you-make-research-data-accessible) by Esther Plomp]

---

# Open Data

.pull-right[
## How to find a repository? 
- Check publications in your field
- [FAIRsharing](https://fairsharing.org/)
- [re3data](https://www.re3data.org/)

General repositories:
- [4TU.ResearchData](https://researchdata.4tu.nl/en/)
- [Zenodo](https://zenodo.org/)
]

---

# Open Data

A **Data Article** (also known as a Data Paper/Note/Release, or Database article) is a publication that is focused on the description of a dataset.

More information on [The Turing Way](https://the-turing-way.netlify.app/reproducible-research/rdm/rdm-article.html) and [TU Delft specific information](https://openworking.wordpress.com/2022/02/17/publishing-a-data-article/)

---
class: inverse, middle, center

# Open Software

---

background-image: url("https://raw.githubusercontent.com/EstherPlomp/PRES-data-software/main/images/recognition.jpg")
background-position: 100% 100%
background-size: 50%

#Open Software

Software in which the copyright holder has granted a license to **use, study, change, and/or distribute the source code.** - [opensource.org](https://opensource.org/definition)

Sharing Software allows for 
- Scrutiny of methods / increased **reproducibility**
  - see [Krafczyk et al. 2021](https://doi.org/10.1098/rsta.2020.0069) p5-11 for recommendations
- **Collaboration**
- **Credit**

See also: [Making software FAIR?](https://openworking.wordpress.com/2019/12/16/making-software-fair/) for more resources

---

# Version control

Version control allows you to **easily track changes**, both your own changes as well as those made by collaborators (for example, Git)

By configuring your version control system to use GitHub, GitLab or Bitbucket, you’ll have **backups** of every version. Follow this [webinar for an introduction to GitHub](https://www.youtube.com/watch?v=lRW8mlpTw5M). You can also use [TU Delft GitLab](https://gitlab.tudelft.nl/).

These platforms offer **collaboration tools** (issue tracker and project management tools), and you’ll be able to use third-party **services** such as code quality checkers, correctness checkers.

image by [The Turing Way](https://doi.org/10.5281/zenodo.3332807)
[![Version control allows you to easily access different versions of the same file](https://raw.githubusercontent.com/EstherPlomp/PRES-data-software/main/images/VersionControl.jpg)](https://doi.org/10.5281/zenodo.3332807)
]

---

# Also useful if you do not code

- Working together on projects ([Open Life Science](https://github.com/open-life-science/open-life-science.github.io), [The Turing Way](https://github.com/alan-turing-institute/the-turing-way))
  - [Live demo of collaborative working](https://youtu.be/KUgPlJIM6-E?t=1484) without code on GitHub
- Setting up your website (see [Esther’s website](https://estherplomp.github.io/))
- Making your work available to others (slides, [newsletters](https://github.com/EstherPlomp/TNW-PhD-Newsletters ))
- Keeping track of other projects (stars)
- Project management tools ([Project Boards](https://docs.github.com/en/issues/organizing-your-work-with-project-boards/managing-project-boards/about-project-boards), [Issues](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues))

---

# README

- Landing page for your repo (watch [this video](https://www.youtube.com/watch?v=Jgv34Kwgga8&list=PL1CvC6Ez54KDvJbbdLn5rPvf1kInifEh9&index=7) for more info)
- The 'Abstract' of your project
- Who is involved in the project?
- Invitation to others to contribute (what expertise is needed?)
- On GitHub this is rendered in Markdown (language to format text)
  - [Markdown Cheatsheet](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet)
  - [Emoji cheatsheet](https://www.webpagefx.com/tools/emoji-cheat-sheet)

### Examples:
- [Jupyter](https://github.com/jupyter/jupyter#readme) & [scikit-learn](https://github.com/scikit-learn/scikit-learn) (written in Python)
- [Matpower](https://github.com/MATPOWER/matpower) (written in MATLAB)
- [Examples and explanation by Alex Chan](https://alexwlchan.net/2021/10/readmes-for-open-science/)
- [Figures underlying Esther's article](https://github.com/EstherPlomp/Figures-Nd-data) 
- Templates: [#1](https://ha0ye.github.io/CW21-README-tips/template_README.html),[#2](https://github.com/othneildrew/Best-README-Template)

---

# Getting a DOI for your GitHub Repository

Summary of this [guide](https://guides.github.com/activities/citable-code/)
1. Have a repository in mind that you’re creating the identifier for
1. Set up an account at [Zenodo](https://zenodo.org/) (using your GitHub, email or [ORCID](https://orcid.org/))
1. Connect GitHub/Zenodo by authorizing Zenodo
1. On Zenodo, go to Settings -> GitHub, then toggle the button on for the repository that you want an identifier for
1. On GitHub: create a new release for your repository (snapshot that will be preserved on Zenodo)
1. On Zenodo: go to the Upload tab and add any additional information before publishing. 
1. On GitHub you can update your citation file with the DOI and add a DOI button in your Readme file

![](https://raw.githubusercontent.com/EstherPlomp/PRES-data-software/main/images/doi-repository.jpg)

---

# Software Citation

- Create a new file in your repository, name it CITATION.cff, select insert example, and fill out the template:

![](https://raw.githubusercontent.com/EstherPlomp/PRES-data-software/main/images/citationcff-make.jpg)

![](https://raw.githubusercontent.com/EstherPlomp/PRES-data-software/main/images/citationcff-result.jpg) More information: [The Turing Way](https://the-turing-way.netlify.app/communication/citable/citable-cff.html) / [video](https://youtu.be/6yhuHCEjPNU) (& [slides](http://doi.org/10.5281/zenodo.4706180)) with tips

---
background-image: url("https://raw.githubusercontent.com/EstherPlomp/PRES-data-software/main/images/software-publishing.jpg")
background-position: 50% 50%
background-size: 90%

# Options for software sharing/publishing

.footnote[ Slide by: Chue Hong, Neil (2021): Doing Science in the Digital Age (a personal journey as a data explorer). https://doi.org/10.6084/m9.figshare.17094365.v1 CC BY 4.0 ]

---
# Checklist for software sharing

- Have I assigned an **appropriate license** to my software?
- Have I **described my software properly**, using an appropriate metadata format, and included this metadata file with my software?
  - Have I given my software a clear **version number**?
  - Have I determined the **authors to be credited** for this release of my software, and included this in my metadata file?
- Have I procured a **persistent identifier** for this release of my software?
- Have I added my **recommended citation** to the documentation for my software?

####  Checklist for developers: https://doi.org/10.5281/zenodo.3482769

.footnote[ Slide by: Chue Hong, Neil (2021): Doing Science in the Digital Age (a personal journey as a data explorer). https://doi.org/10.6084/m9.figshare.17094365.v1 CC BY 4.0 ]

---

# If you’re reusing Software of others
- Have I **identified the software** which makes a significant and specialised contribution to my academic work?
- Have I checked if the software has a **recommended citation**?
  - If this is to a paper, have I also cited the software directly?
  - If there’s no recommended citation, have I **created as complete a citation as possible**?
      - Who created the software
      - When it was created
      - Title of the software (and version if available)
      - Where the software can be accessed
- Have I **referenced the software appropriately** in my academic work, complying with any citation formatting guidelines?

#### Checklist for authors: https://doi.org/10.5281/zenodo.3479199

.footnote[ Slide by: Chue Hong, Neil (2021): Doing Science in the Digital Age (a personal journey as a data explorer). https://doi.org/10.6084/m9.figshare.17094365.v1  CC BY 4.0 ]

---
class: inverse, middle, center

# Why not supplemental materials?

---
# Why not supplemental materials?

**Data control**: cannot be updated

**Interoperability**: not available in all formats which makes it difficult to integrate and interact with the data

**Availability**: Difficult to access if the article is behind the paywall (supplemental materials are not included in the DOI and therefore the links can also break!)

**Impact**: Data should be a primary research output

**Publisher requirements**: Some publishers recommend using a data repository instead

**Not FAIR**: Data/Software available in supplemental materials is not considered to be [FAIR](https://the-turing-way.netlify.app/reproducible-research/rdm/rdm-fair.html) (Findable, Accessible, Interoperable, Resuable)

See also: [The Push to Replace Journal Supplements with Repositories](https://www.the-scientist.com/news-opinion/the-push-to-replace-journal-supplements-with-repositories--66296)

---

## Sustainable access to data/code

---
class: inverse, middle, center

# Licenses

---
# Licenses

.pull-left[
![](https://raw.githubusercontent.com/EstherPlomp/2022-PRES-Data/main/images/cc-overview.jpg)
]

## Software
[Choose an open source license](https://choosealicense.com/)

####[Video on licenses](https://www.youtube.com/watch?v=xdBwuut6dRY&list=PL1CvC6Ez54KDvJbbdLn5rPvf1kInifEh9&index=5)
]

.footnote[Image [Source](https://foter.com/blog/how-to-attribute-creative-commons-photos/): CC-BY-SA]

---

# Software Licenses
.pull-left[

##Permissive

Open licenses that do not require derivative works to shared with the same license.

###Examples:
- CC BY
- MIT, BSD, APL-2.0

#### [TU Delft approved licenses](https://docs.google.com/presentation/d/1jYrjZMjuZ5RchjIC97JfLPvClnzfzbGTq0KnXk_zp10/) according to the [TU Delft Research Software Policy](http://doi.org/10.5281/zenodo.4629662) and [Guidelines](http://doi.org/10.5281/zenodo.4629635)

]

Open licenses that require all derivative works to be shared with the same license.

###Examples:
- CC BY-SA
- GPLv3, AGPL, LGPL, EUP]

---

# Sharing software according to TU Delft

Choose a pre-approved license (MIT, BSD, Apache, GPL, AGPL, LGPL, EUPL, CC0)

#### Use [4TU.ResearchData](https://researchdata.4tu.nl/en/)
- Log in (top right) using TU Delft credentials
- Create a new item or import from GitHub/GitLab
- Add relevant metadata in the information fields

#### OR

####Use another repository ([Zenodo](https://zenodo.org/)) AND register the software in [PURE](https://pure.tudelft.nl/admin/)
- Log in using TU Delft credentials
- Select Datasets/Software -> Software
- Fill out the metadata in the information fields and add DOI, select license and save the information

.footnote[Full [slidedeck](http://doi.org/10.5281/zenodo.4772235) + [recording](https://youtu.be/bPl5sdTvLMM?t=1394) of how to publish software (from 23:14 onwards)]

---
class: inverse, middle, center

# How to link your publication and data/code?

---

# How to link your publication and data/code?

- Publish the output before you publish the article

- Reserve the DOI

## Use the DOI/citation in your publication

Reference your data in the **Data Availability Statement** and the **References**

.footnote[ [The Turing Way: Linking Research Objects](https://the-turing-way.netlify.app/communication/citable/citable-linking.html)
]

---
# Publish or reserving a DOI

### [Zenodo](https://zenodo.org/) -> [Upload](https://zenodo.org/deposit/) -> [New Upload](https://zenodo.org/deposit/new)

![](https://raw.githubusercontent.com/EstherPlomp/2022-PRES-Data/main/images/data-zenodo-doi.jpg)

---
# Linking with publication

### Data accessibility/within table (descriptions)

[![A data accessibility table with information where the research outputs can be found](https://raw.githubusercontent.com/EstherPlomp/2022-PRES-Data/main/images/data-accessibility.jpg)](https://doi.org/10.1016/j.dib.2021.107375)

### Data availability statements (at the end)

[![Example of a data availability statement](https://raw.githubusercontent.com/EstherPlomp/2022-PRES-Data/main/images/data-availability-statement.jpg)](https://doi.org/10.1002/ajpa.24059)

---

# Linking with publication

![](https://raw.githubusercontent.com/EstherPlomp/2022-PRES-Data/main/images/data-references.jpg)

Always check the dataset's readme file or metadata on how the contributors prefer to be cited!

See [this document](https://surfdrive.surf.nl/files/index.php/s/IJt6nPbRf0G9zYZ) for more information about data/software citation.

---

background-image: url("https://raw.githubusercontent.com/EstherPlomp/2022-PRES-Data/main/images/schmid-2021.jpg")
background-position: 50% 50%
background-size: 50%

# Linking data/code/publication
.footnote[ [Publication](https://doi.org/10.1038/s41565-021-00958-5) // [Data & Code](https://doi.org/10.5281/zenodo.5059802)]

---
class: inverse, middle, center

# Where next? 
---

#Where next?

### **[TU Delft Open Science Community](https://osc-delft.github.io/)**
> [Sign up](https://osc-delft.github.io/join) for a 2-monthly newsletter, Slack channel and visibility on the website.

### **[Open Life Science Programme](https://openlifesci.org/)**
>  PhD candidates can follow this programme for 5 disciplinary specific credits. See [intranet](https://intranet.tudelft.nl/-/open-life-science-programme) for more information. New applications will open over the summer with the programme taking place around September-December.

### **[The Turing Way](https://the-turing-way.netlify.app/welcome)**

> There will be an online/hybrid event to contribute to the Turing Way in May/June. Contact Esther for more information.

---

background-image: url("https://raw.githubusercontent.com/EstherPlomp/PRES-data-software/main/images/thank-you.jpg")
background-position: 5% 2%
background-size: 40%

# Thanks!

Slides created via the R packages:

[**xaringan**](https://github.com/yihui/xaringan)<br>
[gadenbuie/xaringanthemer](https://github.com/gadenbuie/xaringanthemer)

[remark.js](https://remarkjs.com), [**knitr**](http://yihui.name/knitr), and [R Markdown](https://rmarkdown.rstudio.com)

images by [The Turing Way](https://doi.org/10.5281/zenodo.3332807)