Merge pull request #53 from briandrawert/coral_model

Partially working periodic BCs
Working towards a 2D coral reef model
Fixed connectivity test
more coral model work
model change for a periodic domain
Having some issues with periodic subdomains
connectivity tests not working out
added dof mapping to example, I think it looks like the matrix is correct=does what's expected.
Rebased with develop, fixed merge conflicts
Fixed deprecation varning for dofmaps. Now attempts to use the new versions first.
Silence all dolfin logging below error level
Silenced annoying SparseEfficiencyWarning
actually silenced the warnings
started to add plots as particles
Merge branch 'periodic_bcs' into plotparticles
Plotting of particles work in 2D but is inefficient
turned off orbit controls
Merge branch 'coral_model' of https://github.com/briandrawert/pyurdme into briandrawert-coral_model
Merge pull request #55 from briandrawert/coral_model

G-protein cycle model and URDMEDataFunction class
updated setup.py, added js templates to package, removed dfsp data