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
Tags: Alchemist
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