Merge remote-tracking branch 'origin/master'

command/docs/start.rst

@@ -6,8 +6,8 @@ Getting my user id and password
 
 You can log in to COMMAND>_ using:
 
-- user_id: command
-- password: command
+   - username: ``guest``
+   - password: ``demo``
 
 Now you can change the admin password, create new users and assign them privileges following the instructions in :doc:`admin_user`.
 
@@ -19,14 +19,16 @@ Now you can change the admin password, create new users and assign them privileg
 Set up and select a compendium
 ------------------------------
 
-The first thing to do is creating a new empty compendium. Go to Admin (top bar) > Compendium Manager > Create Compendium (bottom-left corner + icon) and follow the instructions at :doc:`admin_user`. <TO DO>
+The first thing to do is creating a new empty compendium. Go to Admin (top bar) > Compendium Manager > Create Compendium (bottom-left corner + icon) and follow the instructions at :doc:`admin_user`.
 
 .. _comp01:
 .. figure::  _static/comp01.png
    :align:   center
 
 Now that a new compendium has been set up you need to retrieve a FASTA file containing the gene ids and sequences for the species you want to study.
-_Tip_: Usually you can visit, for example, the NCBI Nucleotide database and get the coding sequences for the organism of interest. This file is mandatory for blasting and mapping respectively in either microarray or RNA-Seq experiments. In order to import it into COMMAND>_ go to Data collection (on the top-left corner) > Biological features, then select Import biological features from the bottom-left + icon.
+
+.. Tip::
+	For example you can visit the `NCBI Nucleotide database <https://www.ncbi.nlm.nih.gov/nucleotide/>`_ and get the coding sequences for the organism of interest. This file is mandatory for blasting and mapping respectively in either microarray or RNA-Seq experiments. In order to import it into COMMAND>_ go to Data collection (on the top-left corner) > Biological features, then select Import biological features from the bottom-left + icon.
 
 .. _comp02:
 .. figure::  _static/comp02.png
@@ -47,18 +49,21 @@ Go to > Data collection (on the top-left corner) then > Experiments > New Experi
    :align:   center
 
 - In the Search options field of the dialog 'Download from Public DB' select the DB (here GEO) and the term of interest, either a description (e.g. Leukemia b-cell, Vitis vinifera, erc.) or directly a GSE ID.
-- From the list select an experiment of interest and click the download button(_Tip_: you can download multiple experiments at the same time).
+- From the list select an experiment of interest and click the download button.
+
+.. Tip::
+	You can download multiple experiments at the same time.
 
 
 .. _search02:
 .. figure::  _static/search02.png
    :align:   center
 
-- After a while, depending of the number of samples in the selected experiment(s) 
-
+- After a while, depending of the number of samples in the selected experiment(s) you have your experiment downloaded.
 
 .. Tip::
-	check Message log frequently) you have your experiment downloaded (Tip: inspect the Experiments section to see which experiments are available, yet to be parsed or already imported).
+	- Check Message log frequently.
+	- Inspect the Experiments section to see which experiments are available, yet to be parsed or already imported.
 
 Now you can start parse and import some experiment (see :doc:`use_cases`).