start to work on Help page

components/Nav/Navbar.vue

@@ -61,7 +61,7 @@ const computedNavigation = computed(() => {
     </template>
     <v-app-bar-title>
       <span class="d-flex align-center">
-        Knowledge database of all known anti-phage systems by
+        Knowledge database of all known anti-phage systems
       </span>
     </v-app-bar-title>
     <template #append v-if="!mobile">

content/1.help.md

 ---
-title: help
+title: Help
 layout: article
 navigation: 
     icon: 'md:help'
@@ -7,5 +7,152 @@ navigation:
 
 
 
-## test
-de l'aide
+
+# Documentation
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+
+## 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). 
+
+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). 
+Once a job is submitted, the page is redirected to the "Analyses" panel (4) where results of the past runs can be found.
+
+![webservice_interface](/help/webservice_interface.jpg){max-width=750px}
+
+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
+
+The wiki is based on gitlab pages, and we are using the gitlab's instance of the Pasteur Institute. To contribute, users need to be part of the project.
+
+On every page, there is a button at the bottom proposing to "Edit on Gitlab". It will allow anyone registered to edit a given page seamlessly.
+But on the first try, the following dialog will be prompted. If you have a Pasteur account, chose 1, otherwise chose 2. In External account, you can connect with a third-party account such as Github, bitbucket or google.
+If you have neither, register on Github first (it's always useful).
+
+![Register](/help/register_1.png){max-width=750px}
+
+Once your account is created, you need to request access to the project, on the [gitlab page of the wiki](https://gitlab.pasteur.fr/mdm-lab/wiki) of the repo, there is a small link to request access.
+
+![Request Access](/help/Request_access.png){max-width=600px}
+
+Click, and wait for an admin approval. 
+
+### 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 : 
+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")
+4. This field is for the branch name, you can let it with the default value, or specify a more meaningful name (note that it's good to have your user name in the branch name so we can)
+
+![Edit a page](/help/Edit_page.png){max-width=750px}
+
+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".
+
+![Create MR](/help/Create_MR.png){max-width=750px}
+
+
+### Tips to write Markdown
+
+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>
+
+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>
+
+```
+![Alt-text, get printed if image is not found](/path/within/public){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`)
+
+<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 :**
+
+```
+---
+title: Viperin
+tableColumns:
+    article:
+    doi: 10.1038/s41586-020-2762-2
+    abstract: |
+        <the abstract>
+    Sensor: Unknown
+    Activator: Direct
+    Effector: Nucleotide modifying
+    PFAM: PF04055, PF13353
+Contributor : 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>
+
+**2. In the relevant abstract section, only the doi is relevant :**
+
+```
+::article-doi-list
+---
+items:
+    - doi: 10.1038/s41586-020-2762-2
+---
+::
+```
+<br>
+
+**3. To display a protein structure, you can call the plugin as follows :**
+
+```
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls: 
+    - /avs/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
+---
+::
+```
+
+
+### 3/ 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. 
+
+![review a MR](/help/Review_MR.png){max-width=750px}
+
+If you want to modify further the file or other file within the same merge request, go to "Changes (1)", and then click on the 3 little dots (see arrow on image) and then "Edit in single-file editor", or "Open in Web IDE".
+
+![Edit_MR](/help/Edit_MR.png){max-width=750px}
+
+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).
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