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@@ -12,13 +12,13 @@ navigation:
## DefenseFinder
DefenseFinder is a software to detect defense systems from bacterial genomes.
[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 their fasta file. A user can upload multiple fasta files at once.
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 being submitted before clicking on the submit button.
Once a job is submitted, the page is redirected to the Analyses panel where results of the past runs can be found.
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}
@@ -27,6 +27,7 @@ The result consists in 3 tables :
- 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
@@ -47,7 +48,7 @@ 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 (if you have question about something or remarks with anything from content to design).
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.
@@ -67,59 +68,72 @@ To do so, just fill in the description (1) of what you did, or anything that you
![Create MR](/help/Create_MR.png){max-width=750px}
**Tips to write :**
### 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>
As a general advice, check an already written file to see how other pages are written.
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>
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
To add images, you need to upload the image of the public folder (and possibly to put it in the corresponding folder of the system) and you can specify its path in the markdown file as follows :
`![Alt-text, get prints if image is not found](/path/within/public){max-width=750px}` where `/path/within/public` is the relative path to the `public` folder (the absolute path would be `/content/public/path/within/public`)
In addition to this, there are some specificities to this wiki.
1. First, 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:
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
---
```
2. In the relevant abstract section, only the doi is relevant :
```md
::article-doi-list
---
items:
- doi: 10.1038/s41586-020-2762-2
---
::```
3. To display a protein structure, you can call the plugin as follows :
```md
::molstar-pdbe-plugin
---
height: 700
dataUrl: /avs/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
---
::```
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
dataUrl: /avs/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
---
::
```
### 3/ Review a Merge Request