Sign In
New ItemNew Item

Full name

Thomas Anung Basuki 


Modelling Biological Systems Using Calculi of Looping Sequences and Maude 

Start Time





Technology has helped biologists to observe biological
systems at microscopic level, down to the molecular level.
More knowledge has been gained about cell structure and
behaviour. Natural observation and experiments contribute to
give an accurate description of all phenomena observable at
cellular level. Although it is possible to track the causes
of certain phenomena at cellular level down to specific
biochemical reactions occurring at molecular level, we are
still far from being able to entirely explain cell behaviour
in terms of the biochemical reactions occurring within the
cell and its environment.

In my thesis I am developing an approach for modelling
biological systems using two levels of representation:
a purely formal representation, which we call molecular
level, models the biochemical dynamics of the system;
visualisation-oriented representations, which we call visual
levels, provide views of the biological system at a higher
level of organisation and are equipped with the necessary
spatial information to generate the appropriate

The approach is based on Calculi of Looping Sequences,
a class of formalisms based on rewriting logic, and has been
implemented using the Maude System. The resultant tool
supports simulation by combining molecular representation
and a visualisation-oriented representations of the cell
cycle. It also supports property checking at molecular level
and provides a 3D visualisation of cell proliferation.


Systems Biology, rewriting logic, visualisation 


Antonio Cerone, Andrea Maggiolo-Schettini 




Created at 8/29/2009 1:32 AM  by Thomas Basuki 
Last modified at 8/31/2009 11:44 AM  by Cristian Dittamo