Install Lattice Microbes and Jupyter Notebook

The first step is to install the software onto your Amazon machine instance. Depending on how you are connecting to your instance, follow one of the following sets of instructions.

Connecting via ssh

  1. Log in to your instance:

    ssh -i my_key_file.pem ubuntu@ipaddress

  2. Run the following command:

    curl -s https://s3.amazonaws.com/lm-deploy/install | bash

  3. Start the notebook by typing:

    sh start_notebook.sh
  4. Use a web browser to connect to the Jupyter notebook. The URL will be printed when you start the notebook, and the password is lm123.

  5. When you are finished, you can hit Ctrl+C in the termial, and press 'y' to confirm you wish to shut down the notebook.

Connecting via VNC

  1. Using DCV Endstation (or your VNC client of choice), connect to your instance, using the instance-id as the password.
  2. Open a terminal window (the icon in the bottom dock that looks like a black square with "$_" in it).

  3. Run the following command:

    curl -s https://s3.amazonaws.com/lm-deploy/install | bash
  4. Start the notebook by double-clicking on the 'Lattice Microbes Notebook' icon on the desktop, a terminal window will open to display messages from the notebook server.
  5. Use a web browser to connect to the Jupyter notebook. The URL will be printed when you start the notebook, and the password is lm123

  6. When you are finished, close the terminal window for the notebook server to shut it down.

Running the Tutorials

The tutorials are structured as Jupyter Notebooks, using Python. The interface is very similar to Mathematica, where you can interactively write and run code, and see the output immediately. If you are new to Jupyter, please take a look at the Jupyter tutorials on Notebook Basics and Running Code.

The tutorials follow the code listings in the Instruction Guide. You will likely also need to refer to the pyLM Reference.

Using VMD

The Lattice Microbes Plugin for VMD is now installed and can be used by launching VMD. The files generated during the tutorial are found in /home/ubuntu/notebook, and instructions using the plugin start on page 18 of the Instruction Guide. However, you are using a new version of the plugin that has new capabilities for loading lattice site data as volumetric datasets. Do not use the LM_CREATE_SITE_ATOMS as described in the Guide, but rather select the volumetric datasets when loading the .lm file. They can then be viewed by creating a volumetric representation with the Isosurface drawing method.