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-title: help
+title: Help
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-## test
-de l'aide
\ No newline at end of file
+
+# Documentation
+
+## DefenseFinder
+
+DefenseFinder 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.
+
+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.
+
+
+
+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
+
+### 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).
+
+
+
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