Fixed problem of the noise ordering. Nsig is not scaled by the length and dt anymore... To fix

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5216 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Add a constant history length to scale the drift term of the diffusion process used to define the default initial history. See NOTE in initial. Next step: strictly bound the diffusion process to the sv ranges

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5217 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Clean pdb trace and print lines

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5218 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Can't sleep ... Correct nsig scaling factor from steps to time

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5219 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
begin http api

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5223 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
add function for URL

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5224 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
move matlab toolbox to separate Git repo

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5225 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
remove api module

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5226 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
add accelerated JansenRit model

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5227 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
add local coupling

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5228 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Use CSR format for local coupling

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5229 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Hide the newly added model (JRFast) from UI appearence, due to not being tested enough.
Comment recent change done by MM, as tests are failing.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5230 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Add a new analyzer that contains the bold balloon model(s). Needs cleaning and more testing before making it available through the interaface. Also consider directly including directly in the monitors module...

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5232 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Added 'truncated' noise for initial method in models. This noise bounds the initial history values to the state variable ranges. TODO: so many things like independent random streams and even different models/approaches to fill the initial history. However, for the moment I'll content myself with the current fix ...

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5233 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Update balloon model... 

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5234 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
UpdateLarterBreakspear model. Added table with the parameters they used in Alstott et al.  One little step, two little steps... toward reproducible science :) ...

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5235 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Modified hyperbolic tangent coupling function. We can select to normalise the connectivity  matrix ...

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5236 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Fix the documentation on model parameters.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5238 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
TVB-1049
correct path towards phase_plane-interactive
class_diagrams.sh works now, but is not generating images for the new models (Liley Stayns Ross).

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5239 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1
Update simulator diagrams for the api documentation.

git-svn-id: https://repo.thevirtualbrain.org/svn/tvb/trunk/scientific_library@5240 1c0e02f0-7929-43c0-8fb3-3293bf43b0d1