| Author(s) | C. Priami |
| Title | Stochastic π-Calculus |
| Published in | The Computer Journal 38(7), 1995 |
| Summary | Priami extends the syntax of the π-calculus by assigning a rate (a positive real number) to every action. On the semantic side, every action experiences a delay that is a random variable with the exponential distribution characterised by the rate. Finitely branching semantics are defined and thanks to the memorylessness of exponential distributions a Markov chain corresponding to the system can be given. |
| Case study | N/A |
| Link | ftp://ftp.di.unipi.it/Papers/priami/Spi.ps.Z |
| Index | 1 |
| Author(s) | C. Priami, A. Regev, E. Shapiro, W. Silverman |
| Title | Application of a stochastic name-passing calculus to representation and simulation of molecular processes |
| Published in | Information Processing Letters 80, 2001 |
| Summary | Stochastic π calculus of Priami is used to quantitatively model protein interaction networks. Rate of an action is interpreted as the basal rate of the biochemical reaction. Original semantics of Sπ are altered to correctly reflect changes in quantities after a reaction. Implemetation of the calculus, the BioPSI system, is described and used to analyse a simple biological system. |
| Case study | Simple generic gene expression regulation by positive feedback. |
| Link | http://www.wisdom.weizmann.ac.il/~aviv/ipl.pdf |
| Index | 2 |
| Author(s) | A. Regev, E. Shapiro, W. Silverman |
| Title | Representation and simulation of biochemical processes using the π-calculus process algebra. |
| Published in | Proceedings of the Pacific Symposium on Biocomputing 2001 |
| Summary | This paper introduces the application of the classical π calculus to pathway modelling. The π model of the analyzed system (RTK-MAPK pathway) is built from the top to the bottom, therefore gently introducing the reader to the π calculus (no formal exposition is given). The simulation of the behaviour of the system under different perturbations is performed and yields expected results. |
| Case study | RTK-MAPK signalling pathway |
| Link | http://www.wisdom.weizmann.ac.il/~biospi/regev_psb.ps |
| Index | 3 |
| Author(s) | A. Regev, E. Shapiro |
| Title | The π-calculus as an abstraction for biomolecular systems |
| Published in | G. Ciobanu, G. Rozenberg (eds.) Modelling in Molecular Biology, Natural Computing Series, Springer 2004 |
| Summary | This book chapter is an accessible introduction to the idea of modelling protein pathways with π and Sπ. |
| Case study | Some toy systems and glycogen biosynthesis |
| Link | http://www.wisdom.weizmann.ac.il/~udi/papers/pi_calculus.pdf |
| Index | 4 |
| Author(s) | A. Regev, E. M. Panina, W. Silverman, L. Cardelli, E. Shapiro |
| Title | BioAmbients: an abstraction for biological compartments |
| Published in | Theoretical Computer Science 325 (2004) |
| Summary | The molecule-as-process model of [2], [3] and [4] is extended with constructs to capture the idea of cellular compartments. Any process or collection of processes can be enclosed in an ambient. Every communication action can be labelled with a direction which determines the allowed location of the corresponding action w.r.t. the configuration of ambients. (e.g. the action labelled local can only be synchronised with a similarily labelled action in a process within the same immediate ambient). The ambient configuration is dynamic: an ambient can merge with another, enter another or leave the parent ambient. This behaviour is driven by synchronous communication of processes within reacting ambients. |
| Case study | Hypothalmic weight regulation system |
| Link | http://lucacardelli.name/Papers/BioAmbients an Abstraction for Biological Compartments.pdf |
| Index | 5 |
| Author(s) | C. Priami, P. Quaglia |
| Title | Beta Binders for Biological Interactions |
| Published in | Lecture Notes in Computer Science 3082 (Proceedings of CMSB 2004), 2005 |
| Summary | Beta binders are another extension of the π calculus designed to deal with biological compartments (see also [5]). A π-process can be prefixed with a beta binder that is an abstraction for a compartment. Every beta binder provides has a dynamic interface that describes the availability of its child processes for interaction with processes within other binders. The compartments (binders) themseleves can merge or split and this behaviour is controlled by two functions. Different definitions of these functions correspond to different assumptions about the interaction of compartments. |
| Case study | A simple abstract virus attack model |
| Link | [SpringerLink] http://www.springerlink.com/content/py3m20bgr7g9je7f/fulltext.pdf |
| Index | 6 |
| Author(s) | P. Lecca, C. Priami, P. Quaglia, B. Rossi, C. Laudanna, G. Constantin |
| Title | A Stochastic Process Algebra Approach to Simulation of Autoreactive Lymphocyte Recruitment. |
| Published in | Simulation, vol 80, 2004 |
| Summary | This paper is a case study in modelling with stochastic pi. A medium-sized, standard model of a system is given and analysed. The study is particularly interesting because it shows how to obtain quantitative data that does not follow directly from the simulation: the authors are able to analyse the evolution of the system depending on the diameter of the blood vessel, while the diameter is not a parameter of the model. |
| Case study | see title |
| Link | |
| Index | 7 |
| Author(s) | M. Calder, J. Hillston, S. Gilmore |
| Title | Automatically deriving ODEs from process algebra models of signalling pathways |
| Published in | Proceedings of CMSB 2005 (ed. G. Plotkin) |
| Summary | The paper gives a method of obtaining a system of ODEs (without the reaction rates)
that describe the dynamics of a biomolecular system modelled in
J. Hillson's PEPA (Performance Evaluation Process Algebra). A PEPA model gives
rise to a |
| Case study | The ERK pathway |
| Link | http://www.dcs.gla.sc.uk/pepa/highlowodes.pdf |
| Index | 8 |
| Author(s) | M. Calder, J. Hillston, S. Gilmore |
| Title | Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA |
| Published in | Proceedings of BioConcur 2004 |
| Summary | This paper gives two models of the ERK pathway. The first is reagent-centric, what means that PEPA processes represent molecular species. The other is pathway-centric: processes denote subpathways. The two models turn out to be isomorphic (bisimilar) and the authors argue that the resulting freedom of switching between the two approaches is valuable for the understanding of the biological domain. Automated translation procedures between these modelling styles are given. The models are analysed using the PEPA Workbench suite to confirm the observed influence of the RKIP protein on the ERK pathway. |
| Case study | The ERK pathway |
| Link | http://www.dcs.gla.sc.uk/pepa/RKIPbioconcur04.pdf |
| Index | 9 |
| Author(s) | R. Blossey, L. Cardelli, A. Phillips |
| Title | A Compositional Approach to the Stochastic Dynamics of Gene Networks |
| Published in | TCSB 4, LNCS 3939, Springer 2006 |
| Summary | This paper introduces the idea of modelling gene regulatory networks as circuits comprising
of |
| Case study | repressilator and oscillator |
| Link | http://lucacardelli.name/Papers/Gene%20Networks%20(TCSB).pdf |
| Index | 10 |
| Author(s) | L. Cardelli |
| Title | Abstract Machines of Systems Biology |
| Published in | TCSB 3, LNBI 3737, Springer 2005 |
| Summary |
The author discusses abstract dynamic formalisms ( |
| Case study | viral infection |
| Link | http://lucacardelli.name/Papers/Abstract%20Machines%20of%20Systems%20Biology%20(TCSB).pdf |
| Index | 11 |
| Author(s) | Flemming Nielson, Hanne Riis Nielson, Corrado Priami and Debora Rosa |
| Title | Static Analysis for Systems Biology |
| Published in | ACM International Conference Proceeding Series, Vol. 58 |
| Summary | A short case study in static analysis for BioAmbients. |
| Case study | An ad-hoc, simple BioAmbient process |
| Link | |
| Index | 12 |
| Author(s) | Patrick Lincoln and Ashish Tiwari |
| Title | Symbolic Systems Biology: Hybrid Modelling and Analysis of Biological Networks |
| Published in | LNCS 2993 |
| Summary | A basic and very accessible discussion of hybrid modelling for biology. |
| Case study | |
| Link | |
| Index |