uLoopDesigner is a web app for interacting with LoopDB, based on the original LoopDesigner written by Mihails Delhmans from https://github.com/HaseloffLab/LoopDB/tree/loopdesigner. The schema has been implemented for a simplified syntax so that there's less redundancy in (u)Loop libraries.

You can try a public version at uloopdesigner.herokuapp.com

This section will explain how to install a local (u)LoopDesigner server.

There are several difficulties with the installation that will require basic coding and maybe (depending on the case) debugging. You need command-line skills and at this point I've been successful on running it in MacOS. Linux probably work but I'd suggest using the last version of Ubuntu/Debian.

LoopDB is available through PyPi, so you can just

pip install loopdb

LoopDB is based on [SQLAlchemy] (http://www.sqlalchemy.org), which allows to use most of the common database back-ends. We recommend using PostgreSQL. After you have installed PostgreSQL, or any other database server, create a new database. With PostgreSQL it can be done with

createdb loopdb

You'll need credentials.

Check out the loopdesigner branch:

git clone https://github.com/HaseloffLab/LoopDB.git -b loopdesigner LoopDesigner

This will clone the files to LoopDesigner folder. Now install the requirements:

cd LoopDesigner
pip install -r requirements.txt

Now you should be ready to start the LoopDesigning server by running

python server.py

If you didn't get any errors you should be able to access the LoopDesigner by navigating to

http://127.0.0.1:8000

in your browser.

The easiest way to define a schema is by using a JSON file. Have a look at the schema.json file for an example. The schema has already been included according to a simplified common syntax. Check out the file to see the logic.

The config file schema.py has some important details regarding the location of the databse and where to find the schema file.

>> from loopDB import LoopDB # Importing the LoopDB module

>> loopDB = LoopDB( 'postgresql:///loopdb', clean = True) # Establishing the connection to the database
>> loopDB.initFromFile('schema.json') # Initialising from the schema file

Initiate the database using

python initialise.py

sh load.sh load/