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Finished addition of rationale and workflow in readme.md

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2013-09-04 12:57:56 -04:00
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README.md
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The goal of this work is to provide a broad description of the population activity patterns that occur in developing cerebral cortex.
The main manuscript file is [wholeBrain_main.md][]
The main manuscript file is **[wholeBrain_main.md][]**
## Rationale
The idea is to provide a clear and beautiful representation of the visualized activity patterns in the developing brain.
The idea is to provide a clear and beautiful visualization of the immature activity patterns in the developing brain.
### Scientific importance
A comprehensive description of the spatiotemporal activity patterns in the immature brain will be crucial to understanding the developmental dynamics that exist between intrinsic and extrinsic factors that regulate circuit development.
* signature patterns that predict current or future behavior
* construction of self-organizing circuits (advanced robotics -- *Terminator, Skynet, Cylons*)
### Human health importance
* neurodevelopmental disorders (autism, schizophrenia, epilepsy)
* activity-dependent structural plasticity. Implications for brain repair.
* development of brain-machine interfaces
### Future work
More detailed descriptions of the nature and the functions of these activity patterns can and should be performed in parallel in ongoing and future studies.
For example:
* What is the intra- vs sub- cortical nature of barrel cortex activity (E.M.'s work)
* What is the intra- vs sub- cortical nature of ongoing activity in motor- associational-, and other non-primary sensory cortical areas?
* Relationship of imaged patterns to EEG patterns described in other studies?
* Extent to which functional correlations reflect direct synaptic connections?
* Retinal wave drive of other areas?
* Ontogenetic relationships of localized calcium domains?
* Development profile through first postnatal weeks
* Chronic developmental profile in individuals?
* Aberrant activity patterns in developmental disorder and seizure models?
We can do this because
## Workflow
Workflow will be similar to that used previously for [current opinion review][id3]. Some useful info in [currOpinRvw outline][id2].
Writing workflow will be similar to that used previously for [current opinion review][id3]. Some useful info in [currOpinRvw outline][id2].
Instructions for [converting multimarkdown to Word document][id4]
Image processing and dataset generation will utilize custom code in the [wholeBrainDX] software project.
Datasets, and exploratory data analysis will use R code that lives inside this wholeBrain project repository. Datasets and raw data to big too be inside this git repo will be stored on external servers and linked to accordingly.
[wholeBrain_main.md]: wholeBrain_main.md
@@ -25,4 +53,6 @@ Instructions for [converting multimarkdown to Word document][id4]
[id3]: https://github.com/ackman678/currOpinRvw/blob/master/README.md
[id4]: https://gist.github.com/ackman678/6391902
[id4]: https://gist.github.com/ackman678/6391902
[wholeBrainDX]: https://github.com/ackman678/wholeBrainDX/blob/master/README.md