APICe » Theses » AlchemistBioLanguage

Alchemist based biochemical simulator with multiple mobile compartments 

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)