Merge pull request #1 from liadomide/master

Work on Architecture and UI chapters
describe MATLAB interface
add details on GPU
Fills out details on the simulator
Minor modifications to contributed text by Lia
Add placeholder for Documentation section.
Two notes
Some notes and a few citations
Update pdf
Merge pull request #2 from stuart-knock/master

First pass -- notes, cite
Merge remote-tracking branch 'upstream/master'
Merge changes from upstream/master
Add ref and finish first section
excise matlab scripting section
Finish node models for the moment
update pdf
use TVB as normal acronym
miscellaneous modifications
begin profiling
add cprofiling
continue with profiling: memory