SSIT bioRxiv Publication Release

This release provides minor improvements to SSIT robustness, efficiency and simplicity in preparation of the package for publication.

New Solvers

• Key bottlenecks of SSA and FSP solvers have been coded in C++ to improve efficiency.

Simpler Solver interface

• SSIT class now supports saving multiple solutions from different methods by calling the 'solve' method with different options.

More flexible plotting functions

• New functions to quickly generate plots using existing solutions.

More examples and improved navigation

• Approximately two dozen example scripts provide to illustrate key features of the SSIT package.
• New SSIT.Tutorial method to allow for ease in launching and viewing expected results for SSIT tutorial examples.

Important changes and compatibility issues:

• The default for SSIT.solve now returns an updated SSIT class object with the requested solution. For example: "Model = Model(solver='fsp')" will solve the model using 'FSP' approach and return the SSIT object "Model" with new solution contained in "Model.Solutions".
• If necessary, the previous functionality returning (solution, bounds, SSIT) can be obtained by calling SSIT.solve using the returnType argument, "(soln,bounds,Model) = Model.solve(returnType='soln').