Modeling Calcium Ion Transients in the Sarcoplasmic Reticulum

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Modeling Calcium Ion Transients in the
Sarcoplasmic Reticulum

• Arielle Yablonovitch
• Monash University, Melbourne, Australia
• July 4, 2008

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Proposed Research

• I plan to update a pre-existing mathematical
  model of the rabbit ventricular myocyte (Shannon
  et al, 2004). I will try to find parameters that
  accurately reflect Calcium ion concentrations in
  the sarcoplasmic reticulum of the myocyte during
  excitation-contraction coupling. These
  parameters will also be optimized so that the
  model comes to a steady state. The model code is
  written in MATLAB, and I will use Nimrod/G and
  Nimrod/O to find the appropriate parameters.

3
Progress

• Tested globus access and job submission
  successfully on most of the PRAGMA clusters,
  e-mailed the appropriate site administrators if
  there was a problem.
• Learned general information about how Nimrod/G,
  Nimrod/O, and Nimrod/E work.
• Ran practice experiments on Nimrod/G that
  involved varying sample parameters in the MATLAB
  code.
• E-mailed Cindy about which clusters have MATLAB
  installed.

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Short-term Goals

• Find out from my UCSD mentor (Anushka Michailova)
  which specific parameters I will be optimizing,
  along with the associated intervals and steps.
• Figure out how to generate output graphs of the
  model after running it through Nimrod.
• Learn how to run basic experiments on Nimrod/O.

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Pictures!
On the tram to St. Kildas pier.
Hiking in the Dandenong National Park
Melbourne Central
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Waiting for the train at South Yarra.
The seven of us, plus Rob Gray, at the Hotel
Claremont