Section: New Results
Analysis of Biological Pathways
We have improved our framework to design and analyze biological networks. This framework focused on protein-protein interaction networks described as graph rewriting systems. Such networks can be used to model some signaling pathways that control the cell cycle. The task is made difficult due to the combinatorial blow up in the number of reachable species (i.e., non-isomorphic connected components of proteins).
Participants : Jonathan Hayman, Tobias Heindel [CEA-List] .
Domain-specific rule-based languages can be understood intuitively as transforming graph-like structures, but due to their expressivity these are difficult to model in `traditional' graph rewriting frameworks.
In  , we introduce pattern graphs and closed morphisms as a more abstract graph-like model and show how Kappa can be encoded in them by connecting its single-pushout semantics to that for Kappa. This level of abstraction elucidates the earlier single-pushout result for Kappa, teasing apart the proof and guiding the way to richer languages, for example the introduction of compartments within cells.
Semantics and causality
Participants : Vincent Danos [University of Edinburgh] , Jérôme Feret, Walter Fontana [Harvard Medical School] , Russ Harmer [Paris VII] , Jonathan Hayman, Jean Krivine [Paris VII] , Chris Thompson-Walsh [University of Cambridge] , Glynn Winskel [University of Cambridge] .
In  , we introduce a novel way of constructing concise causal histories (pathways) to represent how specified structures are formed during simulation of systems represented by rulebased models. This is founded on a new, clean, graph-based semantics introduced in the first part of this paper for Kappa, a rule-based modelling language that has emerged as a natural description of protein-protein interactions in molecular biology. The semantics is capable of capturing the whole of Kappa, including subtle side-effects on deletion of structure, and its structured presentation provides the basis for the translation of techniques to other models. In particular, we give a notion of trajectory compression, which restricts a trace culminating in the production of a given structure to the actions necessary for the structure to occur. This is central to the reconstruction of biochemical pathways due to the failure of traditional techniques to provide adequately concise causal histories, and we expect it to be applicable in a range of other modelling situations.
Case study: Combinatorial drift in yeast model
Participants : Vincent Danos [University of Edinburgh] , Eric Deeds [University of Kansas] , Jérôme Feret, Walter Fontana [Harvard Medical School] , Russ Harmer [Paris VII] , Jean Krivine [Paris VII] .
The assembly of molecular machines and transient signaling complexes does not typically occur under circumstances in which the appropriate proteins are isolated from all others present in the cell. Rather, assembly must proceed in the context of large-scale protein-protein interaction (PPI) networks that are characterized both by conflict and combinatorial complexity. Conflict refers to the fact that protein interfaces can often bind many different partners in a mutually exclusive way, while combinatorial complexity refers to the explosion in the number of distinct complexes that can be formed by a network of binding possibilities.
In  , we use computational models so as to explore the consequences of these characteristics for the global dynamics of a PPI network based on highly curated yeast two-hybrid data. The limited molecular context represented in this data-type translates formally into an assumption of independent binding sites for each protein. The challenge of avoiding the explicit enumeration of the astronomically many possibilities for complex formation is met by a rule-based approach to kinetic modeling. Despite imposing global biophysical constraints, we find that initially identical simulations rapidly diverge in the space of molecular possibilities, eventually sampling disjoint sets of large complexes. We refer to this phenomenon as “compositional drift". Since interaction data in PPI networks lack detailed information about geometric and biological constraints, our study does not represent a quantitative description of cellular dynamics. Rather, our work brings to light a fundamental problem (the control of compositional drift) that must be solved by mechanisms of assembly in the context of large networks. In cases where drift is not (or cannot be) completely controlled by the cell, this phenomenon could constitute a novel source of phenotypic heterogeneity in cell populations.
Automatic Reduction of Stochastic Semantics
Participants : Ferdinanda Camporesi, Jérôme Feret, Norman Ferns, Thomas Henzinger [Institute of Science and Technology, Austria] , Heinz Koeppl [ETH Zürich] , Tatjana Petrov [ETH Zürich] .
Biology, Protein-protein interaction networks, Stochastic semantics, Verification.
We have proposed an abstract interpretation-based framework for reducing the state-space of stochastic semantics for protein-protein interaction networks. Our framework ensures that the trace distribution of the reduced system is the exact projection of the trace distribution of the concrete system. Moreover, when the abstraction is complete, if each state with the same abstraction is equiprobable at initial state, each state with the same abstraction is equiprobable at any time .
In  , we have formalized the model reduction framework for the stochastic semantics and we have established the relationships with the notions of lumpability, and bisimulation.
In  , we have showed that the reduced models can be expressed in Kappa, and we have provided a procedure to do it.