Wiki » History » Version 1
Padraig Gleeson, 30 Apr 2014 14:57
| 1 | 1 | Padraig Gleeson | Towards community developed cerebellar granule cell models |
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| 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 | 1 | Padraig Gleeson | - What granule cell models are out there? |
| 9 | 1 | Padraig Gleeson | - What electrophysiological properties do labs wish to reproduce in their models? |
| 10 | 1 | Padraig Gleeson | - What experimental data is publicly available on the behaviour of the granule cell? |
| 11 | 1 | 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 | 1 | Padraig Gleeson | ### Models on OSB |
| 17 | 1 | Padraig Gleeson | |
| 18 | 1 | Padraig Gleeson | project:granulecell |
| 19 | 1 | Padraig Gleeson | project:grancellsolinasetal10 |
| 20 | 1 | Padraig Gleeson | project:granulecellvscs |
| 21 | 1 | Padraig Gleeson | |
| 22 | 1 | Padraig Gleeson | ### Other known models |
| 23 | 1 | Padraig Gleeson | |
| 24 | 1 | Padraig Gleeson | Links to entries on ModelDB or PubMed articles… |
| 25 | 1 | Padraig Gleeson | |
| 26 | 1 | Padraig Gleeson | Target electrophysiological properties of granule cells |
| 27 | 1 | Padraig Gleeson | ------------------------------------------------------- |
| 28 | 1 | Padraig Gleeson | |
| 29 | 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: |
| 30 | 1 | Padraig Gleeson | |
| 31 | 1 | Padraig Gleeson | - Resting Potential |
| 32 | 1 | Padraig Gleeson | - Input Resistance |
| 33 | 1 | Padraig Gleeson | - Reversal potential of Na |
| 34 | 1 | Padraig Gleeson | - Reversal potential of K |
| 35 | 1 | Padraig Gleeson | - AP max depolarisation |
| 36 | 1 | Padraig Gleeson | - Firing rate at ?? Hz |
| 37 | 1 | Padraig Gleeson | - Total cell capacitance |
| 38 | 1 | Padraig Gleeson | - Soma radius |
| 39 | 1 | Padraig Gleeson | - More… |
| 40 | 1 | Padraig Gleeson | |
| 41 | 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. |
| 42 | 1 | Padraig Gleeson | |
| 43 | 1 | Padraig Gleeson | ### D’Angelo lab |
| 44 | 1 | Padraig Gleeson | |
| 45 | 1 | Padraig Gleeson | Species: … |
| 46 | 1 | Padraig Gleeson | Experimental setup summary: … |
| 47 | 1 | Padraig Gleeson | Resting potential: … |
| 48 | 1 | Padraig Gleeson | |
| 49 | 1 | Padraig Gleeson | ### Silver lab |
| 50 | 1 | Padraig Gleeson | |
| 51 | 1 | Padraig Gleeson | … |
| 52 | 1 | Padraig Gleeson | |
| 53 | 1 | Padraig Gleeson | Publicly accessible data on granule cell behaviour |
| 54 | 1 | Padraig Gleeson | -------------------------------------------------- |
| 55 | 1 | Padraig Gleeson | |
| 56 | 1 | Padraig Gleeson | ### Links to electrophysiological data in public repositories |
| 57 | 1 | Padraig Gleeson | |
| 58 | 1 | Padraig Gleeson | (Wishful thinking I know…) |
| 59 | 1 | Padraig Gleeson | |
| 60 | 1 | Padraig Gleeson | ### NeuroElectro properties of granule cells |
| 61 | 1 | Padraig Gleeson | |
| 62 | 1 | Padraig Gleeson | http://www.neuroelectro.org/neuron/21/ |
| 63 | 1 | Padraig Gleeson | |
| 64 | 1 | Padraig Gleeson | How well do existing models reproduce these behaviours? |
| 65 | 1 | Padraig Gleeson | ------------------------------------------------------- |
| 66 | 1 | Padraig Gleeson | |
| 67 | 1 | Padraig Gleeson | Information on construction of tests for comparing model behaviour to experimental data |
| 68 | 1 | Padraig Gleeson | |
| 69 | 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)). |