changed name in docs

README.md

@@ -1,7 +1,9 @@
-# PlaNet
-Code to build PlaNet and set up the website. 
+# *CoNekT:* Coexpression Network Toolkit
 
-Setting up PlaNet
+
+Code to build CoNekT and set up the website. 
+
+Setting up CoNekT
 -----------------
 Below are the instructions to set up a new PlaNet version.
 
@@ -15,7 +17,7 @@ Below are the instructions to set up a new PlaNet version.
 [Setting up planet with apache and mod_wsgi](docs/apache_wsgi.md)
 
 
-[Build PlaNet](docs/building_planet.md)
+[Build CoNekT](docs/building_conekt.md)
 
 
 [Run website](docs/run_website.md)
@@ -24,12 +26,12 @@ Below are the instructions to set up a new PlaNet version.
 Instructions for Developers
 ---------------------------
 
-Basic information on how PlaNet 2.0 is designed can be found [Instructions for developers](docs/developer.md)
+Basic information on how CoNekT is designed can be found [Instructions for developers](docs/developer.md)
 
 Acknowledgements
 ----------------
 
-PlaNet 2.0 is based upon many open-source projects, check the full list [here](docs/acknowledgements.md)
+CoNekT is based upon many open-source projects, check the full list [here](docs/acknowledgements.md)
 
 
 Contact

docs/building_planet.md → docs/building_conekt.md

@@ -1,14 +1,14 @@
-# Building PlaNet
+# Building CoNekt
 
-## Using the admin panel to build PlaNet 2.0
+## Using the admin panel to build CoNekt
 
 Make sure *LOGIN_ENABLED=True* in *config.py* and the database was build 
 with and admin account. Next, 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.
 
 
-![Admin pane](./images/admin_home.png "admin panel")
+![Admin panel](./images/admin_home.png "admin panel")
 
 The Admin Panel will welcome you with a large warning. Deleting data, 
 overwriting or changing entries here can ruin a carefully set up 
@@ -99,7 +99,7 @@ To do so, in the 'Admin panel', under 'Add' -> 'InterPro genes' select a species
 
 Expression data should be processed using [LSTrAP](https://github.molgen.mpg.de/proost/LSTrAP), 
 this will generate the expression matrix, coexpression networks and 
-clusters that can be directly imported into PlaNet 2.0. Note that in 
+clusters that can be directly imported into CoNekt. Note that in 
 some cases additional files, containing meta information, need to be 
 provided.
 

docs/install_linux.md

@@ -1,4 +1,4 @@
-# PlaNet Linux Installation
+# CoNekt Linux Installation
 
 ## Getting Started
 
@@ -12,13 +12,13 @@ Install virtualenv
     sudo pip3 install virtualenv
 
 
-Clone the repository into a directory PlaNet
+Clone the repository into a directory CoNekt
 
-    git clone https://github.molgen.mpg.de/proost/PlaNet PlaNet
+    git clone https://github.molgen.mpg.de/proost/CoNekt CoNekt
 
 Set up the virtual environment
 
-    virtualenv --python=python3 PlaNet/
+    virtualenv --python=python3 CoNekt/
 
 Activate the virtual environment
 
@@ -50,4 +50,4 @@ Build initial database
     flask add_admin <new_username> <new_password> 
 
 
-You now have a fresh installation of PlaNet. How to fill it with your data is included in the section [Building PlaNet 2.0](./building_planet.md)
+You now have a fresh installation of CoNekt. How to fill it with your data is included in the section [Building CoNekt](building_conekt.md)

docs/install_windows.md

@@ -1,4 +1,4 @@
-# PlaNet Windows Installation
+# CoNekt Windows Installation
 
 ## Getting Started
 
@@ -49,4 +49,4 @@ Build initial database
     # Optional, create additional admin accounts
     flask add_admin <new_username> <new_password> 
 
-You now have a fresh installation of PlaNet. How to fill it with your data is included in the section [Building PlaNet 2.0](./building_planet.md)
+You now have a fresh installation of PlaNet. How to fill it with your data is included in the section [Building CoNekt](building_conekt.md)

docs/run_website.md

@@ -1,6 +1,6 @@
-# PlaNet Website
+# CoNekt Website
 
-PlaNet is a flask app, all that is required to start the website is running. Note that the virtualenv needs to be 
+CoNekt is a flask app, all that is required to start the website is running. Note that the virtualenv needs to be 
 set up and activated.
 
     python run.py