Dynamic Graph Queries

Graph databases in many applications - semantic web, transport or biological networks among others - are not only large, but also frequently modified. Evaluating graph queries in this dynamic context is a challenging task, as those queries often combine first-order and navigational features. Motivated by recent results on maintaining dynamic reachability, we study the dynamic evaluation of traditional query languages for graphs in the descriptive complexity framework. Our focus is on maintaining regular path queries, and extensions thereof, by first-order formulas. In particular we are interested in path queries defined by non-regular languages and in extended conjunctive regular path queries (which allow to compare labels of paths based on word relations). Further we study the closely related problems of maintaining distances in graphs and reachability in product graphs. In this preliminary study we obtain upper bounds for those problems in restricted settings, such as undirected and acyclic graphs, or under insertions only, and negative results regarding quantifier-free update formulas. In addition we point out interesting directions for further research

The Complexity of Kings

A king in a directed graph is a node from which each node in the graph can be reached via paths of length at most two. There is a broad literature on tournaments (completely oriented digraphs), and it has been known for more than half a century that all tournaments have at least one king [Lan53]. Recently, kings have proven useful in theoretical computer science, in particular in the study of the complexity of the semifeasible sets [HNP98,HT05] and in the study of the complexity of reachability problems [Tan01,NT02]. In this paper, we study the complexity of recognizing kings. For each succinctly specified family of tournaments, the king problem is known to belong to $\Pi_2^p$ [HOZZ]. We prove that this bound is optimal: We construct a succinctly specified tournament family whose king problem is $\Pi_2^p$-complete. It follows easily from our proof approach that the problem of testing kingship in succinctly specified graphs (which need not be tournaments) is $\Pi_2^p$-complete. We also obtain $\Pi_2^p$-completeness results for k-kings in succinctly specified j-partite tournaments, $k,j \geq 2$, and we generalize our main construction to show that $\Pi_2^p$-completeness holds for testing k-kingship in succinctly specified families of tournaments for all $k \geq 2$

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks