Writing and Publishing Protocols Using GitHub

AUTHOR: Dr Asad Prodhan https://asadprodhan.github.io/

How to write a protocol or user-manual in GitHub

1. Open a GitHub account

2. Create a new repository

3. Write it up using the following Markdown format

Title

```

Title

```

AUTHOR: Name Website

```

AUTHOR: Name Website

```

Space

<br />

Text formating

Heading

```

Heading

```

Sub-headings

```

Sub-headings

```

• Bullet and sub-bullet

``` - Bullet

- Sub-bullet

```

Embedded text

```

Embedded text ```

Italic

*Italic*

Bold

**Bold**

Italic and Bold

***Italic and Bold***

Script

Script

Add a figure

```

Figure 1: Figure description".

```

Add a presentation link:

```

An introduction to Nanopore DNA sequencing and data analysis. Nanopore Workshop for Biosecurity, Curtin University, Perth, Australia, 27-29 June 2023. VIEW

```

The above code chunk will produce the following display in your GitHub repository

An introduction to Nanopore DNA sequencing and data analysis. Nanopore Workshop for Biosecurity, Curtin University, Perth, Australia, 27-29 June 2023. VIEW

Add a download button in your repository:

[DOWNLOAD](https://github.com/asadprodhan/blastn/blob/main/main.nf)

The above code chunk will produce the following display in your GitHub repository

DOWNLOAD

Add a Table of Content

```

Content

01. Blastn database download and update [NCBI tool]

```

The above code chunk will produce the following display in your GitHub repository

Content

01. Blastn database download and update [NCBI tool]

See some GitHub repository examples here (Prodhan, 2022, 2024)

Prodhan, M. A. (2022). An Introduction to R Coding. Zenodo. https://doi.org/10.5281/zenodo.5880043

Prodhan, M. A. (2024). About the PATH. Zenodo. https://doi.org/10.5281/zenodo.11068991

How to add a license to your GitHub repository

• Click on Add file

• Create a new file

• Type LICENSE in the "Name your file" box

• Choose a license

• Review and submit it

How to publish your GitHub repository

1. Create a Zenodo account

2. Log in in Zenodo using your GitHub account

3. Go to the drop-down menu at the top-right-hand corner displaying your name and select GitHub

4. Toggle the ON button

5. Go back to your GitHub repository and create a release

- On the right-hand side, click Create a new release


    - Chhose a tag and create a tag, e.g. v1


    - Click on Publish release

1. Come back to Zenodo and will now find your GitHub repository in Zenodo along with a DOI

How to add "Cite this repository" option to your GitHub repository

you can do this step after publishing it in Zenodo, beacuse you need a DOI for your repository

Step 1: Create a CITATION.cff file

Open a Notepad file and write the following details

``` cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Prodhan" given-names: "M. Asaduzzaman" orcid: "https://orcid.org/0000-0000-0000-0000" title: "About the PATH" version: 1 doi: 10.5281/zenodo.11068992 date-released: '2024-04-25' repository-code: "https://github.com/asadprodhan/About-the-PATH/tree/v1" preferred-citation: type: article authors: - family-names: "Prodhan" given-names: "M. Asaduzzaman" orcid: "https://orcid.org/0000-0000-0000-0000" doi: "10.5281/zenodo.11068992" journal: "Zenodo" title: "About the PATH" year: 2024

```

Step 2: Save as text file

Step 3: Rename the text file as CITATION.cff

Step 4: Add the CITATION.cff file to your GitHub repository

On the left-hand side, you will see a citation request added

How to add a DOI badge to your GitHub repository

You can add a DOI badge to your GitHub repository using the following code chunk

[![DOI](https://zenodo.org/badge/DOI/doi.org/10.5281/zenodo.11068991.svg)](https://doi.org/10.5281/zenodo.11068991)

The above code chunk will produce the following display in your GitHub repository

Final output

In text: (Prodhan, 2024)

In bibliography: Prodhan, M. A. (2024). About the PATH. Zenodo. https://doi.org/10.5281/zenodo.11068992

Now you have a publication, you can add it to your institutional research repository, Google Scholar etc

References

Prodhan, M. A. (2022). An Introduction to R Coding. Zenodo. https://doi.org/10.5281/zenodo.5880043

Prodhan, M. A. (2024). About the PATH. Zenodo. https://doi.org/10.5281/zenodo.11068991