Edit History

Wiki » History » Version 8

Padraig Gleeson, 30 Apr 2014 14:57

1 1 Padraig Gleeson
Towards community developed cerebellar granule cell models
2 1 Padraig Gleeson
----------------------------------------------------------
3 1 Padraig Gleeson
4 1 Padraig Gleeson
This project was started following the [2013 OSB kickoff meeting](http://www.opensourcebrain.org/projects/osb/wiki/Meetings). At that meeting it was decided that the development of individual cell models from the cerebellum would be a good test case for exploring the requirements on technical infrastructure and the social aspects of collaborative model development. Due to the many independent granule cell layer networks being developed by participants at the OSB meeting, the cerebellar granule cell was identified as a good first cell model to focus on.
5 1 Padraig Gleeson
6 1 Padraig Gleeson
This wiki is intended to help gather the following information/requirements:
7 1 Padraig Gleeson
8 3 Padraig Gleeson
-   ***What granule cell models are out there?***
9 3 Padraig Gleeson
-   ***What electrophysiological properties do labs wish to reproduce in their models?***
10 3 Padraig Gleeson
-   ***What experimental data is publicly available on the behaviour of the granule cell?***
11 3 Padraig Gleeson
-   ***How well do existing models reproduce these behaviours?***
12 1 Padraig Gleeson
13 1 Padraig Gleeson
Models of the cerebellar granule cell
14 1 Padraig Gleeson
-------------------------------------
15 1 Padraig Gleeson
16 3 Padraig Gleeson
### Models currently available on OSB
17 1 Padraig Gleeson
18 4 Padraig Gleeson
table{border:1px solid black}.
19 4 Padraig Gleeson
{background:\#ddd}. | **Model** | **Summary** |
20 4 Padraig Gleeson
| project:granulecell | Single compartment, conductance based |
21 4 Padraig Gleeson
| project:grancellsolinasetal10 | Single compartment, conductance based |
22 4 Padraig Gleeson
| project:granulecellvscs | Single compartment, conductance based |
23 4 Padraig Gleeson
| project:grancellrothmanif | Integrate and fire model |
24 6 Padraig Gleeson
| project:cerebellargainandtiming | Integrate and fire cell in network model |
25 1 Padraig Gleeson
26 3 Padraig Gleeson
### Other known granule cell models
27 1 Padraig Gleeson
28 2 Padraig Gleeson
*Links to entries on ModelDB or PubMed articles…*
29 3 Padraig Gleeson
30 3 Padraig Gleeson
Simões de Souza F, De Schutter E (2011) **Robustness effect of gap junctions between Golgi cells on cerebellar cortex oscillations** Neural Systems & Circuits 1:7:1-19 ([ModelDB](http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=139656), reuses project:grancellsolinasetal10 ?)
31 3 Padraig Gleeson
32 3 Padraig Gleeson
Diwakar S, Magistretti J, Goldfarb M, Naldi G, D\`Angelo E (2009) **Axonal Na+ channels ensure fast spike activation and back-propagation in cerebellar granule cells** J Neurophysiol 101(2):519-32 ([ModelDB](http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=116835))
33 1 Padraig Gleeson
34 1 Padraig Gleeson
Target electrophysiological properties of granule cells
35 1 Padraig Gleeson
-------------------------------------------------------
36 1 Padraig Gleeson
37 1 Padraig Gleeson
To facilitate comparison between granule cell models it would be good to quantify certain properties of the cell activity which labs find **in their experimental data** and which should be reproduced in models. An initial list of properties is:
38 1 Padraig Gleeson
39 1 Padraig Gleeson
-   Resting Potential
40 1 Padraig Gleeson
-   Input Resistance
41 1 Padraig Gleeson
-   Reversal potential of Na
42 1 Padraig Gleeson
-   Reversal potential of K
43 1 Padraig Gleeson
-   AP max depolarisation
44 1 Padraig Gleeson
-   Firing rate at ?? Hz
45 1 Padraig Gleeson
-   Total cell capacitance
46 1 Padraig Gleeson
-   Soma radius
47 1 Padraig Gleeson
-   More…
48 1 Padraig Gleeson
49 1 Padraig Gleeson
Different species, drugs, experimental conditions will lead to different values for these between labs. Nevertheless, it would be good to get input from as many labs as possible.
50 1 Padraig Gleeson
51 1 Padraig Gleeson
### D’Angelo lab
52 1 Padraig Gleeson
53 2 Padraig Gleeson
*Species: …
54 1 Padraig Gleeson
Experimental setup summary: …
55 2 Padraig Gleeson
Resting potential: …*
56 1 Padraig Gleeson
57 1 Padraig Gleeson
### Silver lab
58 1 Padraig Gleeson
59 8 Padraig Gleeson
These figures are mainly based on data obtained by Jason Rothman for the paper: [Synaptic depression enables neuronal gain control](http://www.nature.com/nature/journal/v457/n7232/full/nature07604.html) Nature 2009.
60 8 Padraig Gleeson
61 8 Padraig Gleeson
Species: **Sprague-Dawley rats**
62 8 Padraig Gleeson
Region: **Cerebellar vermis**
63 8 Padraig Gleeson
Method: **Whole-cell recordings \*
64 8 Padraig Gleeson
Full methods [here](http://www.nature.com/nature/journal/v457/n7232/full/nature07604.html#online-methods).
65 8 Padraig Gleeson
AP threshold:**~~38mV to~~42 mV\*
66 8 Padraig Gleeson
AP height (from threshold to peak): **72 mV**
67 8 Padraig Gleeson
AHP depth (from threshold to AHP minimum) **21 mV**
68 8 Padraig Gleeson
Time of AP threshold to time of AHP minimum: **0.9 ms**
69 8 Padraig Gleeson
70 8 Padraig Gleeson
![](http://www.opensourcebrain.org/attachments/download/81/JasonAPstats2.png)
71 1 Padraig Gleeson
72 1 Padraig Gleeson
73 1 Padraig Gleeson
Publicly accessible data on granule cell behaviour
74 1 Padraig Gleeson
--------------------------------------------------
75 1 Padraig Gleeson
76 1 Padraig Gleeson
### Links to electrophysiological data in public repositories
77 1 Padraig Gleeson
78 2 Padraig Gleeson
\_(Wishful thinking I know…)\_
79 1 Padraig Gleeson
80 1 Padraig Gleeson
### NeuroElectro properties of granule cells
81 1 Padraig Gleeson
82 1 Padraig Gleeson
http://www.neuroelectro.org/neuron/21/
83 1 Padraig Gleeson
84 1 Padraig Gleeson
How well do existing models reproduce these behaviours?
85 1 Padraig Gleeson
-------------------------------------------------------
86 1 Padraig Gleeson
87 1 Padraig Gleeson
Information on construction of tests for comparing model behaviour to experimental data
88 1 Padraig Gleeson
89 1 Padraig Gleeson
Much of this will be based on [NeuroUnit/SciUnit](http://www.opensourcebrain.org/projects/neuroelectrosciunit) and existing test scripts in neuroConstruct projects (e.g. [here](https://github.com/OpenSourceBrain/GranuleCell/blob/master/neuroConstruct/pythonScripts/RunTests.py)).