The systems approach to biology aims to address problems using a holistic approach that focuses on emergent properties, namely those that cannot be attributed to a single part of a biological system, but rather, arise from complex, collective processes at the molecular level. An important feature of these emergent properties is robustness— the emergent phenomena are, to a considerable extent, i...

Synthetic biology is focused on engineering biological organisms to study natural systems and to provide new solutions for pressing medical, industrial and environmental problems. At the core of engineered organisms are synthetic biological circuits that execute the tasks of sensing inputs, processing logic and performing output functions. In the last decade, significant progress has been made ...

Cell counts and viral load serve as major clinical indicators to provide treatment in the course of a viral infection. Monitoring these markers in patients can be expensive and some of them are not feasible to perform. An alternative solution to this problem is the observer based estimation. Several observer schemes require the previous knowledge of the model and parameters, such condition is n...

Unwinding conditions have been fruitfully exploited in Information Flow Security to define persistent security properties. In this paper we investigate on their meaning and possible uses in the analysis of biological systems. In particular, we elaborate on the notion of robustness and propose some instances of unwinding over the process algebra Bio-PEPA and over hybrid automata. We exploit such...

This is the first design document for the Generic Biological Simulator (GBS), the Kinetic Engine and the Biological Simulation Graphical User Interface (BioGUI). The aim of this document is to give an overall view of the three projects in order to facilitate their individual design and implementation. Since this a proposal, the design of the three tools described in this document may change in ...