docs + fix in SVG export (now uses best_name instead of gene_name to …

…match graph in browser

conekt/static/js/planet_svg.js

@@ -112,7 +112,7 @@ function writeSVG(data) {
             }
 
             text = node.data('name');
-            if (node.data('gene_name') !== '') { text = node.data('gene_name'); }
+            if (node.data('best_name') !== '') { text = node.data('best_name'); }
 
             group.text({y:6, fill:"none", stroke:'#888888'}).content(text)
                 .attr('text-anchor', 'middle')

docs/building/003_expression_profiles.md

@@ -33,7 +33,7 @@ SRR314816
 ...
 ```
 
-For profile plots on the website most likely a custum order of conditions
+For profile plots on the website most likely a custom order of conditions
 is preferred. (We usually order tissues from bottom to top) A file to 
 specify this needs to be provided, conditions need to be stated in the 
 orther they should appear in the plot.
@@ -57,4 +57,13 @@ If all files are selected click 'Add Expression Profiles' to upload the
 data and add everything to the database.
 
 
-![Add expression profiles](../images/add_expression_profiles.png)
+![Add expression profiles](../images/add_expression_profiles.png)
+
+## Adding summarized profiles
+
+In case the complete profile is to detailed and more general profiles need to be included 
+(useful for specificity searches), there is the option to combine multiple condition in one.
+
+## Calculating expression specificity
+
+*UNDER CONSTRUCTION*

docs/building_conekt.md

@@ -4,7 +4,14 @@
 
 Make sure *LOGIN_ENABLED=True* in *config.py* and the database was build 
 with and admin account (check [here](install_linux.md) for instructions 
-how to add an admin account). Next, go to the website, log in and (once logged
+how to add an admin account). 
+
+Make sure your server **doesn't time out requests**, some operations can take several 
+minutes. If your server is live already running build steps can result in issues for 
+active users. To avoid this consider running and extra CoNekT instance
+on the server using the built in web-server and connecting to it using an SSH tunnel.
+
+To start building, go to the website, log in and (once logged
 in) click on the username (admin) in the top right corner. Select 'Admin
 Panel' from the drop-down menu.
 
@@ -23,7 +30,7 @@ Step-by-step instructions
 
   * [Adding GO term and InterPro domain definitions](./building/001_GO_InterPro_domains.md)
   * [Adding a new species and functional data](./building/002_species_functional_data.md)
-  * [Adding expression profiles](./building/003_expression_profiles.md)
+  * [Adding expression profiles and specificity](./building/003_expression_profiles.md)
   * [Adding co-expession networks and clusters](./building/004_coexpression_network_cluster.md)
   * [Adding comparative genomics data](./building/005_comparative_genomics.md)
   * [Precomputing counts and more](./building/006_precomputing_counts_etc.md)