Supplementary package for COBRApy
Project description
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
- Make sure Jupyter is installed in your local machine
- Connect to the server using your account
ssh your_username@172.25.20.52
- Activate Jupyter Notebook in the server
jupyter notebook --no-browser --port=8889
- Connect your local machine to the remote jupyter notebook session
ssh -N -f -L localhost:8888:localhost:8889 your_username@172.25.20.52
- Open your browser and access
localhost:8888
- 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
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