Submission code: Second order adjoint and hybrid profile calculation

Merge pull request #243 from ICB-DCM/feature_more_adjoint_options

Feature more adjoint options

AMICI 0.4.0

• First citable version of AMICI (via zenodo integration).
• Better support for standalone compilation
• Improved SBML import scripts
• General Code Cleanup

v0.3.0

This update comes with many improvements, bug fixes and several new features. Most notably:

1. AMICI should now run on older versions of MATLAB (back to R2014a)
2. AMICI now compiles using older versions of Visual Studio
3. AMICI now also supports second order adjoint sensitivities (full (via the o2flag = 1 and as a vector product via o2flag = 2)
4. AMICI now supports more SBML, SBML v2 and rate rules

v0.2.1

Bugfix release. This release also includes some changes that should improve the performance on the new R2016a release of MATLAB.

v0.2.0

This update comes with many improvements to the computation time for both compilation and simulation. Moreover several new features were included:

1. Hessian Vector products for second order forward sensitivities
2. Correct treatment of parameter/state dependent discontinuities for both forward and adjoint sensitivities

initial release

This is the initial release of the toolbox