diff --git a/content/1.help.md b/content/1.help.md
index dcacae5c398ecc27a5cf312c63e936bad40ba29a..983201dec5cb751223131463c05bcd6da1b755c0 100644
--- a/content/1.help.md
+++ b/content/1.help.md
@@ -5,29 +5,26 @@ navigation:
icon: 'md:help'
---
-
-
-
# Documentation
-## DefenseFinder
+## DefenseFinder
-[DefenseFinder](https://github.com/mdmparis/defense-finder) is a software to detect defense systems from bacterial genomes.
-It takes as input a fasta file, nucleic or proteic (it will guess which).
+[DefenseFinder](https://github.com/mdmparis/defense-finder) is a software to detect defense systems from bacterial genomes.
+It takes as input a fasta file, nucleic or proteic (it will guess which).
On the web service page, users can upload (1) their fasta file. One can upload multiple fasta files at once, as many jobs will be run.
-Users need to provide a name for the job (2) being submitted before clicking on the submit button (3).
+Users need to provide a name for the job (2) being submitted before clicking on the submit button (3).
Once a job is submitted, the page is redirected to the "Analyses" panel (4) where results of the past runs can be found.
{max-width=750px}
-The result consists in 3 tables :
+The result consists in 3 tables :
+
- Systems table : One system per line. On the column type, there is the name of the system, and one can click on it to be redirected to the corresponding wiki page.
- Genes table : One gene per line. Those are genes from the aforementioned system, with some addition information on the quality of the hit. The key between both table is `sys_id`
- HMMER table : One gene per line. Here it's all the genes hit by a hmm profile, even when the gene is not part of a defense system.
-
## Contributing to the Wiki
### 1/ Create an account
@@ -44,15 +41,16 @@ Once your account is created, you need to request access to the project, on the
{max-width=600px}
-Click, and wait for an admin approval.
+Click, and wait for an admin approval.
-### 2/ Edit a page.
+### 2/ Edit a page
Once you have access to the project (the previous step is done once), you can edit easily each page of the wiki, and post [issues](https://gitlab.pasteur.fr/mdm-lab/wiki/-/issues) (if you have question about something or remarks with anything from content to design).
To edit a page, just click on the Edit on Gitlab button at the bottom of every page of the wiki, and it will lead you to the corresponding page of the wiki.
-From this page, you can :
+From this page, you can :
+
1. Edit the text you'd like
2. Preview the change you've done (final modification might a bit different, especially if you use plugins to view citations or pdb structures)
3. Once you've finished you edits, you can specify what you did (e.g. "Re-wrote history of defense systems")
@@ -60,40 +58,34 @@ From this page, you can :
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-Then it asks you to create a merge request.
+Then it asks you to create a merge request.
In other words, the modifications you made will not be reflected on the website until a few automatic checks passed (which should be ok since you modified only some text) and that another person reviewed the change, and accept the merge request.
To do so, just fill in the description (1) of what you did, or anything that you would like the person who will accept the merge request to know, and just hit (2) "Create a merge request".
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+### 3/ Tips to write Markdown
-### Tips to write Markdown
+As a general advice, check an already written file to see how other pages are written.<br><br>
-As a general advice, check an already written file to see how other pages are written.<br>
-<br>
The files you edit are in markdown, which is pretty basic language but that can let you do many things, such as tables, links and such with a particular syntax.
-You can check more about this syntax here : https://docs.gitlab.com/ee/user/markdown.html<br>
-<br>
+You can check more about this syntax here : <https://docs.gitlab.com/ee/user/markdown.html><br><br>
-To add images, you need to upload the image in the `/content/public` folder (and possibly in the corresponding folder of the defense system) and you can specify its path in the markdown file as follows :<br>
-<br>
+To add images, you need to upload the image in the `/content/public` folder (and possibly in the corresponding folder of the defense system)
+and you can specify its path in the markdown file as follows :<br>
-```
-{max-width=750px}
-```
-<br>
-
-where `/path/within/public` is the relative path to the `public` folder (the absolute path would be `/content/public/path/within/public`)
+```md
+
+```
-<br>
+where `/path/within/public` is the relative path to the `public` folder (the absolute path would be `/content/public/path/within/public`)<br>
-In addition to this, there are some specificities to this wiki :<br>
-<br>
+In addition to this, there are some specificities to this wiki :<br><br>
**1. Each system's page has *frontmatter*, which is a piece of code that will be used to populate the table of the list of system. It has the following syntax :**
-```
+```yaml
---
title: Viperin
tableColumns:
@@ -105,44 +97,111 @@ tableColumns:
Activator: Direct
Effector: Nucleotide modifying
PFAM: PF04055, PF13353
-Contributor : Florian Tesson, Aude Bernheim
+RelevantAbstracts:
+ - doi: 10.1038/s41586-020-2762-2
+ - doi: 10.1126/science.aba0372
+contributors :
+ - Florian Tesson
+ - Aude Bernheim
---
```
-Any new item in the `tableColumns` object will create a new column in the list of [defense system's table](/defense-systems).
-<br>
+Any new item in the `tableColumns` object will create a new column in the list of [defense system's table](/defense-systems).<br>
-**2. In the relevant abstract section, only the doi is relevant :**
+**2. To display a protein structure, you can call the plugin as follows :**
```
-::article-doi-list
+::molstar-pdbe-plugin
---
-items:
- - doi: 10.1038/s41586-020-2762-2
+height: 700
+dataUrls:
+ - /avs/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
---
::
```
-<br>
-**3. To display a protein structure, you can call the plugin as follows :**
+**Custom containers:**
+
+Custom containers can be defined by their types, titles, and contents.
+<u>Default title:</u>
+
+```md
+::info
+This is an info box
+::
```
-::molstar-pdbe-plugin
+
+```md
+::tip
+This is a tip box
+::
+```
+
+```md
+::warning
+This is a warning box
+::
+```
+
+```md
+::danger
+This is a danger box
+::
+```
+
+```md
+::expansion-details
+There is some details
+::
+```
+
+<u>The output:</u>
+
+::info
+This is an info box
+::
+
+::tip
+This is a tip box
+::
+
+::warning
+This is a warning box
+::
+
+::danger
+This is a danger box
+::
+
+::expansion-details
+There is some details
+::
+
+<u>Custom title:</u>
+
+```md
+::info
---
-height: 700
-dataUrls:
- - /avs/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
+title: my title info
---
+This is an info box
::
```
+::info
+---
+title: my title info
+---
+This is an info box
+::
-### 3/ Review a Merge Request
+### 4/ Review a Merge Request
You can review other person's merge request by going the [merge request's pages](https://gitlab.pasteur.fr/mdm-lab/wiki/-/merge_requests).
On a given page, you can see what modifications where made for this merge request (1), then you can comment if you have anything to say (2 and 3).
-And finally, you can approve (4) the MR if you find it worth publishing on the website.
+And finally, you can approve (4) the MR if you find it worth publishing on the website.
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@@ -152,7 +211,6 @@ If you want to modify further the file or other file within the same merge reque
The Web IDE editor allows you to edit multiple file at once for a given commit. This editor is also accessible from the merge request's page under the "Code" button in the upper right corner of the page.
-
## Contribute to the code
-Contribution to the code and design are open. Please read the [README](https://gitlab.pasteur.fr/mdm-lab/wiki) on how to deploy the website locally (and see the modification you're doing live).
\ No newline at end of file
+Contribution to the code and design are open. Please read the [README](https://gitlab.pasteur.fr/mdm-lab/wiki) on how to deploy the website locally (and see the modification you're doing live).
diff --git a/content/3.defense-systems/detocs.md b/content/3.defense-systems/detocs.md
index 028de448103f457b1351c16bebf4275d91030af0..7866d92dac225a20f86d0c218174ee751f0b0a5c 100644
--- a/content/3.defense-systems/detocs.md
+++ b/content/3.defense-systems/detocs.md
@@ -15,6 +15,8 @@ contributors:
# Detocs
+
+
## Description
Detocs (**De**fensive **T**w**o**-**C**omponent **S**ystem) is a family of 3-gene defense systems that mediate anti-phage activity by abortive infection.