Track 4: Mesoscale Modeling of Cardiac Myocyte

Goal: At the end of the Summer Institute we expect participants to have an understanding of how to create and use geometries from imaging data and run computational models at the molecular and subcellular levels. Furthermore, we hope that students will be able to apply these tools not only to processes in cardiac ventricular myocytes but also in other cells (e.g. neurons).

Target Audience: The track is geared towards researchers in the computational biology field, who are interested in mesoscale modeling of cardiac myocytes and applications to other systems in translational research.

Prerequisites: Familiarity with UNIX is highly recommended, including basic scripting.

  • You will need VNC viewer installed on your laptop Free options:.
  • We encourage users to install paraview on their personal laptops to visualize simulated data.

Topics: The topics include use of finite element based tools; SubCell (FEniCS based ) and CSMOL (FETK based), for simulation of Ca2+ dynamics in cardiomyocytes; use of GAMER in the generation of high quality mesh representation of subcellular structures; such as the t-tubular network typical for cardiac ventricular cells..

Format: Presentations and hands on Tutorials.

Course Materials

Location: Atkinson Hall, room 6004
Time: 14:00 - 17:00, M-Th July 30 - August 2 Johan Hake, Ph.D.
Pete Kekenes-Huskey, Ph.D.
Anushka Michailova, Ph.D.
Zeyun Yu, Ph.D 

Each student is assigned an account, a VNC connection password and a compute node to connect to. Conventions:

  • account: aaXX - 4 character, 2 letters followed by 2 digits
  • password: WORDaaXX, instructor will give you a WORD
  • compute-0-YY: compute node, instrutor will give you an assigned compute node number.

Sequence of commands to use VNC connection from your laptop to the cluster during the tutorial.

  1. On your laptop: open an ssh tunnel to the cluster as
    ssh -L 5920:compute-0-YY:59XX rocce.ucsd.edu -l aaXX
    Provide correct values for aaXX, XX (as a numeric part of your account) and YY. Type your ssh key passphrase when prompted
  2. On the cluster: Once you login, start the vncserver by executing
    ./startVNC.sh
    You will see the output similar to:
    Using display :12 for vnc
    Warning: untrusted X11 forwarding setup failed: xauth key data not generated
    Warning: No xauth data; using fake authentication data for X11 forwarding.
    New 'compute-0-34.local:12 (ab12)' desktop is compute-0-34.local:12
    Starting applications specified in /home/ab12/.vnc/xstartup
    Log file is /home/ab12/.vnc/compute-0-34.local:12.log
  3. On your laptop: use your installed VNC client and open a new connection window.
    In the new window type the information requested for:
    • host: use localhost
    • display: use 20
    • password: type WORDaaXX (WORD given by instructor and your account as a suffix)
    Leave the rest of values default and click on connect button. If you are successful a cluster Desktop window will popup on your laptop and you will be able to start your class work.

After you finish your work

  1. On your laptop: close the cluster Desctop window
  2. On the cluster:
    ./stopVNC.sh
    exit