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Commit cf26f127 authored by Jean  CURY's avatar Jean CURY
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Refactor Help pages

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......@@ -18,7 +18,7 @@ const props = withDefaults(defineProps<Props>(), {
density: "prominent",
drawer: true,
drawerEnabled: true,
title: "Knowledge database of all known anti-phage systems"
title: "Knowledge database of all known defense systems"
});
const emit = defineEmits(['update:drawer'])
function toggleTheme() {
......@@ -38,7 +38,7 @@ const sections = ref([
{ id: "wiki", label: "Wiki", to: '/', },
{ id: "refseq", label: "RefSeq DB", to: '/refseq/' },
{ id: "structure", label: "Structures DB", to: '/structure/' },
{ id: "help", label: "Help", to: '/help/' },
{ id: "help", label: "Help", to: '/help/defensefinder' },
]);
......
---
title: DefenseFinder Webservice
layout: article
---
# Documentation
## DefenseFinder
[DefenseFinder](https://github.com/mdmparis/defense-finder) is a software to detect defense systems in bacterial genomes.
It takes as input a fasta file, be it nucleic or protein (it will guess which).
On the web service page, users can upload (1) their fasta file(s). One can upload multiple fasta files at once, as many jobs will run.
Job are automatically launched once the upload is done. Jobs can be found in the analysis panel (2), and are named with the name of the input file. The job name can be changed.
Analyses are kept for 6 months, or with a maximum of 10 jobs.
![webservice_interface](/help/webservice_interface.jpg){max-width=750px}
In the Analyses panel, each past job is kept for 6 months. Next to the name of the input file (1) there is a rolling circle until the job finishes to run, which become a number. One can edit the job name (by default it's the file's name) by clicking on the small pen (2), or can delete a job (3). To visualize the results, one can click on Results (4) or on the job's name.
![analyses_interface](/help/analyses_interface.jpg){max-width=750px}
The result consists in 3 tables :
- Systems table : Shown by default. 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 (1).
- Genes table (2): 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 (3): 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.
![results_interface](/help/results_interface.jpg){max-width=750px}
---
title: Help
title: Contributing to the Wiki
layout: article
navigation:
icon: 'md:help'
---
# Documentation
# Contributing to the Wiki
## 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
## 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.
......@@ -43,7 +22,7 @@ Once your account is created, you need to request access to the project, on the
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).
......@@ -65,7 +44,7 @@ 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}
### 3/ Tips to write Markdown
## 3/ Tips to write Markdown
As a general advice, check an already written file to see how other pages are written.<br><br>
......
navigation.icon: "md:help"
......@@ -2,12 +2,15 @@
title: List of defense systems
layout: article-no-toc
relevantAbstracts:
- doi: 10.1101/2021.09.02.458658
- doi: 10.1038/s41467-022-30269-9
- doi: 10.1038/s41579-023-00934-x
---
# List of defense systems
The knowledge of anti-phage defense systems is ever expanding. The spectacular increase of the number of known systems in the past years suggests that many of them are still to be discovered. As of april 2022, 63 defense systems have been described.
The knowledge of anti-phage defense systems is ever expanding. The spectacular increase of the number of known systems in the past years suggests that many of them are still to be discovered. As of april 2022, 63 defense systems have been described. To our knowledge, there are currently in the following table, 151 systems.
This table summarizes some info for each systems (that can be search in the ***Search...*** field below), and contains link toward corresponding wiki page.
......
......@@ -5,19 +5,21 @@ navigation:
icon: "mdi-database"
---
# RefSeq DB
On this page, you'll find results of DefenseFinder on the entire Bacterial RefSeq database of complete genome (last updated in 05/2022).
Each line of the table corresponds to a system.
<br>
You'll find plot of the distribution of defense system per type and per various taxonomical levels. These plots are updated automatically according to the search of filter you used.
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<br><br>
::tip
One can search any text in the ***Search*** field or select a subset of the dataset based on a combination of condition in the ***Filter results*** field.
::
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<br>
::refseq-db
::
......
......@@ -5,10 +5,25 @@ navigation:
icon: "mdi-database"
---
# Structures' prediction DB
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In the following tables are various structures that were generated by Alphafold for all monomers, hetero- and homo-dimers for a given system.
In the page for each system is the structure for the monomers and real structure when it exists.
Scores are reported for each structure. Average pLDDTs for monomer and IPTM+PTM and pDock scores for multimers.
One can click on a given structure, it will show the structure colored by the pLDDT score at the amino-acid level, as well as the PAE matrix.
The structure can be downloaded when viewing the structure.
Some structures could not be determined for technical reasons and are in the process of being generated again (column *Completed*).
<br><br>
::tip
One can search any text in the ***Search*** field or select a subset of the dataset based on a combination of condition in the ***Filter results*** field.
Columns with score can be filtered with the sliders to filter scores within a given range.
::
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::structure-db
::
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