GitHub - ModelDBRepository/262060: Mesoscopic model of spontaneous synaptic size fluctuations (Hazan & Ziv 2020)

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Read me - Mesoscopic model of size dynamics.pdf		Read me - Mesoscopic model of size dynamics.pdf
Sim dynamics and FRAP.c		Sim dynamics and FRAP.c
rand.c		rand.c
rand.h		rand.h
readme.html		readme.html
standard.h		standard.h

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<p>Mesoscopic model of size dynamics
</p><p>Hazan L, Ziv NE (2020) Activity dependent and independent determinants of synaptic size diversity. J Neuroscience
</p><p>The model, written in C as a Win32 console application, is provided as two source files and two header files:
</p><ul>
  <li>Sim dynamics and FRAP.c
  </li><li>rand.c
  </li><li>standard.h
  </li><li>rand.h</li></ul>
<p>The latter 3 files are part of the cryptographic random number generator ISAAC (Indirection, Shift, Accumulate, Add, and Count) <a href="http://burtleburtle.net/bob/rand/isaacafa.html">http://burtleburtle.net/bob/rand/isaacafa.html</a> Used here to generate streams of pseudorandom numbers
</p><p>The code was compiled and run using Visual Studio 2017
</p><p>To compile using Visual C++:
</p><ol>
  <li>Create a new project (File--&gt;New--&gt;Project...)
  </li><li>Create a Visual C++, Empty Project
  </li><li>Add the four files to the project as Source Files and Header Files, respectively using the Solution Explorer
  </li><li>Compile and run</li></ol>
<p>Two tab delimited text files are generated:
</p><ol>
  <li>Synapse size trajectories for all synapses (rows) at all simulated time steps (columns). Synapse size is defined as the momentary # of molecules bound to the synapse's matrix
  </li><li># of bound 'fluorescent' molecules for the 'photobleached' synapses (rows) at all simulated time steps (columns) starting at the photobleaching time step</li></ol>
<p>All parameters and output file names are 'hardwired' into the code.
To modify these, edit the definitions at the top of the file "Sim dynamics and FRAP.c"
</p><p>
<pre>
MATRIXDIM Matrix dimension (matrix size will be MATRIXDIM x MATRIXDIM)
N_SYNAPSES Number of synapses (matrices) that will be simulated
STEPS Number of simulation steps to run
P_ON Maximal On rate (scales with # of free molecules)
P_OFF Maximal Off rate
ALPHA Non-specific binding rate (scales with # of free molecules)
TOTAL_MOLECULES Total amount of scaffold molecules in the 'cell'
FRAP_CYCLE Simulation cycle at which 'photobleaching' will occur
FRAP_SYNAPSES Number of synapses to photobleach
OUTPUTFILENAME Full path to simulation output file
FRAPOUTPUTFILENAME Full path to FRAP data output file
</pre>
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