In this thesis, the goal is to explore the suitability of Alchemist as a biochemical simulator. A mapping for each concept in biology to the Alchemist model will be needed in order to provide the widest set of features a stochastic simulator ever had. Moreover, some improvements will be needed to ease and improve the chemistry incarnation of Alchemist. After that, many lines can be explored:

• A new, easy language will be needed, in order to write complex simulations within few simple lines
• A graphical editor would be a great tool
• CellML to AlchemistXML (useful for import)
• SBML to AlchemistXML (useful for import)
• BioAlchemist to SBML/CellML (useful for export)
• Comprehensive graphical interface

Mirko Viroli (Contact)

Mirko Viroli (Supervisor)

Danilo Pianini (Co-supervisors)