diff --git a/README.md b/README.md index 6e59dab..7806e9e 100644 --- a/README.md +++ b/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 diff --git a/docs/building_planet.md b/docs/building_conekt.md similarity index 96% rename from docs/building_planet.md rename to docs/building_conekt.md index e196d2b..60fc05a 100644 --- a/docs/building_planet.md +++ b/docs/building_conekt.md @@ -1,6 +1,6 @@ -# 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 @@ -8,7 +8,7 @@ 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. diff --git a/docs/install_linux.md b/docs/install_linux.md index eb9f27b..4958d87 100644 --- a/docs/install_linux.md +++ b/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 -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) \ No newline at end of file +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) \ No newline at end of file diff --git a/docs/install_windows.md b/docs/install_windows.md index 04555ff..8944c03 100644 --- a/docs/install_windows.md +++ b/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 -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) \ No newline at end of file +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) \ No newline at end of file diff --git a/docs/run_website.md b/docs/run_website.md index ac2a5fa..9aec3af 100644 --- a/docs/run_website.md +++ b/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