GitHub - ModelDBRepository/245411: Striatal Spiny Projection Neuron, inhibition enhances spatial specificity (Dorman et al 2018)

ModelDBRepository / 245411 Public

Notifications You must be signed in to change notification settings
Fork 2
Star 0

Striatal Spiny Projection Neuron, inhibition enhances spatial specificity (Dorman et al 2018)

modeldb.science/245411

Notifications

Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
InOut		InOut
MScell		MScell
PSim_ConstrainUp_GABA.g		PSim_ConstrainUp_GABA.g
PSim_ConstrainUp_NoGABAControl.g		PSim_ConstrainUp_NoGABAControl.g
PSim_Params.g		PSim_Params.g
README.html		README.html
SimParams.g		SimParams.g
constrainup_GABA.py		constrainup_GABA.py
figure7.py		figure7.py
graphics7.g		graphics7.g
screenshot.png		screenshot.png

Repository files navigation

<html>
<p>This is the ModelDB repository for:
</p>
<p>Dorman, Daniel B., Joanna Jedrzejewska-Szmek, and Kim T. Blackwell. "Inhibition
  enhances spatially-specific calcium encoding of synaptic input patterns in a
  biologically constrained model." <a href="http://dx.doi.org/10.7554/eLife.38588">eLife</a> 7 (2018): e38588.[<a href="https://www.ncbi.nlm.nih.gov/pubmed?holding=modeldb&term=30355449">PubMed</a>]
</p>
<p>The GENESIS Simulator code was contributed by Daniel Dorman.
</p>
<p>The model is a spiny projection neuron of the striatum. It includes 4 primary,
8 secondary, and 16 teriary dendritic branches, with more than 3000 explicitly
modeled dendritic spines.
</p>
<p>It includes known ion channels for this neuron type, including NaF, KaF, KaS,
Krp, KIR, CaL1.3, CaL1.2, CaR, CaN, CaT3.2, CaT3.3 voltage gated channels.
</p>
<p>It includes calcium dynamics using the GENESIS difshell/difbuffer objects,
which model calcium buffering and diffusion within subdivided volumes of the
dendritic and spine compartments.
</p>
<p>This model version is a modification/further development of a previously
published model in ModelDB: <a href="http://modeldb.yale.edu/189153">http://modeldb.yale.edu/189153</a>
</p>
<p>The top-level simulation script can be run by:
</p>
<p>    genesis PSim_ConstrainUp_GABA.g
</p>
<p>The top-level parameter file is PSim_Params.g, which overrides
parameters set in other files (e.g. Sim_Params.g, MScell/globals.g).
</p>
<p>The following python script will run several simulations to reproduce data for
Figure 7A-B:
</p>
<p>    python constrainup_GABA.py
</p>
<p>After about 1 hour 13 minutes (on a 2012 MacBook Pro) the output data will be saved in ./SimData
</p>
<p>After running constrainup_GABA.py, Figure 7A-B can be regenerated from output
data using the python script: figure7.py</p>
python figure7.py<p/>
which in less than a minute should generate:</p>
<img src="./screenshot.png" alt="screenshot">
</body>
</html>