scobra 0.0.4

Supplementary package for COBRApy

scobra

Scobra is a supplementary package for COBRApy designed by Maurice Cheung used by the Yale-NUS Computational and Systems Biology team. This version is specifically for Python 3.

To install scobra, run this line:

pip install scobra -r requirements.txt

Accessing scobra through the server using Jupyter Notebook

0. Make sure Jupyter is installed in your local machine
   
1. Connect to the server using your account
   

ssh your_username@172.25.20.52

2. Activate Jupyter Notebook in the server
   

jupyter notebook --no-browser --port=8889

3. Connect your local machine to the remote jupyter notebook session
   

ssh -N -f -L localhost:8888:localhost:8889 your_username@172.25.20.52

4. Open your browser and access
   

localhost:8888

5. If this is the first time your browser opens the session, you may need to provide a token. The token is displayed in your terminal running jupyter notebook remotely. It should look something like this:
   

Copy/paste this URL into your browser when you connect for the first time, to login with a token:
        http://localhost:8889/?token=779c5074bbe9c26338a8760875e0c0ba3f77294201f61353

Copy everything after http://localhost:8889/?token= to the box provided and login.

Copying files to and from server

To copy files from local machine to server, run:

scp path/to/local/file username@172.25.20.52:path/to/remote/directory

To copy files from server to local machine, run:

scp username@172.25.20.52:path/to/remote/directory path/to/local/file

Note: to copy folders, use scp -r instead of scp