Merge pull request #9 from mauriceling/master

1. Files for analytical functions and general commandline interface. 2. Closing logging database after reading simulation data for revival
Merge pull request #10 from mauriceling/master

1. connect to simulation database from shell. 2. save history and workspace
Reconstructed writing of parameters to print all keys in sim_parameters of all simulations
Merge pull request #67 from clarencecastillo/master

Reconstructed writing of parameters to print all keys in sim_parameters of all simulations