-
Notifications
You must be signed in to change notification settings - Fork 1
Purkinje cell dendritic tree selection in early cerebellar development (Kato + De Schutter accepted)
ModelDBRepository/267591
Folders and files
| Name | Name | Last commit message | Last commit date | |
|---|---|---|---|---|
Repository files navigation
<html>
<body>
<p>
The listed files are associated with a paper entitled "Models of Purkinje cell dendritic tree selection during
early cerebellar development" by Mizuki Kato and Erik De Schutter.
</p>
<p>
The following python scripts are implemented for the NeuroDevSim software (De Schutter 2022,
<a href="https://github.com/CNS-OIST/NeuroDevSim">https://github.com/CNS-OIST/NeuroDevSim</a>), and set to run
with 64 cores.
</p>
<p>
1. <tt>Initial_environment.py</tt>
</p>
<p style="margin-left:2em">
The shared initial environment (cycle 1 to 70) for Purkinje cell models (except for <tt>S0C_noGranuleCell</tt>).
The
script initiates 6 out of 12 phases of Granule cell migrations and 5 cycles of dendritic growth of Purkinje
cells. It takes about 20 minutes to run a single simulation.
</p>
<p style="margin-left:2em">
20 database files for the initial environment with different seeds (1 to 20) are obtained by following
command:<br>
<code>for i in {1..20}; do python initial_environment.py $i; done</code>
</p>
<p>
2. <tt>Scenario0A_growOne.py</tt>
</p>
<p style="margin-left:2em">This script simulates the growths of Purkinje cell dendrites ignoring dendritic selection
processes by randomly choosing single tree out of five candidates at the very beginning of the simulation.
Running a single simulation with the script takes about 3 hours.
</p>
<p>
3. <tt>Scenario0B_growAll.py</tt>
</p>
<p style="margin-left:2em">The script simulates the dendritic growths when growing all five candidate dendritic
trees without the selection phase. Each simulation takes about 3.5 hours.
</p>
<p>
4. <tt>Scenario0C_noGranuleCell.py</tt>
</p>
<p style="margin-left:2em">The script simulates the dendritic growths with no granule cell as an environment. Thus,
the code does not use the database generated from <tt>initial_environment.py</tt>. A single simulation takes
about 16
hours.
</p>
<p>
5. <tt>Scenario1_fixedTimings.py</tt>
</p>
<p style="margin-left:2em">This script controls the dendritic retraction phase by triggering the retractions at two
fixed simulation cycles: at cycle 90 and cycle 97. At cycle 90, 3 out of 5 trees with smaller numbers of
synapses with parallel fibers retract.Then, 1 out of the rest 2 trees is selected as a primary tree based on the
number of synapses at cycle 97. A single simulation of this scenario takes around 3 hours.
</p>
<p>
6. <tt>Scenario2_1_maturationBySize.py</tt>
</p>
<p style="margin-left:2em">The script performs the selection by choosing a winner tree by size of each dendrite. The
first retractions are initiated when a total number of fronts (cylindrical agents constituting dendrites) in a
cell reaches 300, and the cell retracts trees not been comprised of more than 20 fronts. Then, the cell chooses
a tree with the largest numbers of fronts as its primary tree when a whole cell has 400 fronts. Each simulation
takes around 3 hours.
</p>
<p>
7. <tt>Scenario2_2_maturationBySynapses.py</tt>
</p>
<p style="margin-left:2em">This script manages the selection by choosing winners based on number of synapses with
parallel fibers. The first selection starts when a whole cell has 90 synapses in total from 5 trees, and the
cell retracts trees with less than 30 synapses. The second selection starts when a cell gets 180 synapses in
total, and choose a tree with the largest number of synapses as its primary tree. One simulation with this
script takes about 3 hours.
</p>
<p>
8. <tt>Scenario3_networkActivity.py</tt>
</p>
<p style="margin-left:2em">This scenario coordinates the tree selection by total strengths of synaptic signals. The
first retraction happens when signals summed for the whole cell reaches 500. Average signal for each cell is
calculated and trees with lower signals than the average retracts. When the summed signal of a cell hits 1,200,
the cell selects a tree with highest signals. Each simulation takes about 2.5 hours with the script.
</p>
</body>
</html>About
Purkinje cell dendritic tree selection in early cerebellar development (Kato + De Schutter accepted)