Loop Designer: Getting Started

Installing LoopDB

LoopDB is available through PyPi, so you can just

pip install loopdb

Setting up a database

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

Install LoopDesigner

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

Starting the server

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.

Setting up a schema

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 file should define four collections:

• RE: Restriction enzymes used for an assembly, e.g:

{"name" : "BsaI", "seq" : "GGTCTCA"}

• RES: Pairs of restriction enzyme overhang sequences, which define either acceptors or recceivers, e.g.

{"name": "AF", "re": "BsaI", "site5": "GGAG" , "site3": "CGCT"},
{"name": "ab", "re": "SapI", "site5": "ATG" , "site3": "GCA" }

• BaseSeq: Plasmid sequence with one of the receiver sequence pairs, defined in RES section. This corresponds to different assembly levels, e.g. for an odd level (pOdd):

{"name": "pOdd-1", "receiver": "AF", "gbFile": "gb/pOdd-1.gb"}

where gbFile is the path to the plasmid sequence in the GenBank format.

• Backbone: A baseseq toogether with an adapter sequence, This corresponds to a particular vector, e.g. for pOdd-1

{"name": "pOdd-1", "baseSeq" : "pOdd", "adapter" : "ab" }

Once the schema file is complete, the schema can be applied to the database through an interactive python session:

>> 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