# IBL Bioinformatics Wiki

Welcome to the Wiki page for all researchers doing or willing to do some bioinformatics.

This Wiki site prioritizes collaboration. We welcome your assistance in identifying typos, misinformation, faults, and any other issues. Your contributions and suggestions are highly valued; please share them by creating new "Issues" on our [GitHub page](https://github.com/snail123815/IBL-bioinformatics-wiki/issues). Thank you for your valuable input.

If you wish to contribute further, such as by writing a new section, kindly initiate the process by creating an issue beforehand. This ensures smooth coordination and alignment with the project's objectives.

```{toctree}
---
caption: IBL Servers
maxdepth: 2
---
IBL_servers/Intro.md
IBL_servers/Server configurations.md
IBL_servers/Execute programs.md
IBL_servers/Install programs.md
IBL_servers/Common questions.md
```

```{toctree}
---
caption: SSH access
maxdepth: 2
---
ssh access/ssh access.md
ssh access/ssh access mobaxterm.md
ssh access/ssh access command line.md
```

```{toctree}
---
caption: ALICE
maxdepth: 2
---
alice/alice_ibl.md
alice/gromacs-ALICE.md
alice/how_to_run_blastp.md
alice/AlphaFold3
```

```{toctree}
---
caption: IBL RDM Howtos
maxdepth: 2
---
rdm_howtos/Intro.md
rdm_howtos/ResearchDrive.md
rdm_howtos/ELN.md
rdm_howtos/GitHub_in_research.md
```

```{toctree}
---
caption: Tools
maxdepth: 2
---
basic_tools/package_management_concept.md
basic_tools/micromamba.md
basic_tools/blast.md
basic_tools/rstudio-web.md
basic_tools/tabular_output_guide.md
```

```{toctree}
---
caption: Admin tools
maxdepth: 2
---
admin_tools/admin_tools.md
admin_tools/ipa_commands.md
admin_tools/default_home_folder.md
admin_tools/maintain_the_system.md
```

## Report issue

If you find anything in this site that can be better, please create an "Issue" at [Issues page](https://github.com/snail123815/IBL-bioinformatics-wiki/issues).

How to do that:

1. You will need a GitHub account because this documentation repository uses GitHub Issues; a nickname is also fine 😊
2. Identify the page you find wrong, check the "Address bar" of your browser.
3. After you logged in GitHub, head to [Issues page](https://github.com/snail123815/IBL-bioinformatics-wiki/issues), click the green "New issue" button.
4. Write a "Title" and "description". Include the webpage "Address" if you are referring to it. Please check "Preview" when you finished.
5. (optional) You can @snail123815 if it is urgent.
6. (optional) You can add Labels by clicking the gear icon next to "Labels" on the right side.
7. Lastly, click the green "Submit new issue" button.

We (currently only @snail123815) will review it and correct asap.

## Contribute more

If you think I am too slow on responding your issues, you are more than welcome to contribute by making changes directly. It is a bit more work then you might think, but I am sure you will learn a lot from the process.

Check the [front page ("Code" tab if you in the "Issues" tab)](https://github.com/snail123815/IBL-bioinformatics-wiki) of our GitHub repository. I wrote a brief introduction on how to do this in README file.

## Maintainer(s)

*Chao Du [@snail123815](https://github.com/snail123815)*

Contributors:
- You!
- *Belmin Bajramovic [@B-Bajramovic](https://github.com/B-Bajramovic)*
- *Joost Willemse [@Karivtan](https://github.com/Karivtan)*
- *Nicole Schmidt-Hebbel [@nicoleyshebbel](https://github.com/nicoleyshebbel)*

Previously involved:
- *Edder Bustos Diaz [@EdderDaniel](https://github.com/EdderDaniel)*
- *Caspar Schmeits [@Capspar](https://github.com/Capspar)*