Abstract. In the context of protein engineering, we consider the problem of computing an mRNA sequence of maximal codon-wise similarity to a given mRNA (and consequently, to a given protein) that additionally satisfies some secondary structure constraints, the so-called mRNA Structure Optimization (MRSO) problem. Since MRSO is known to be APX-hard, Bongartz [10] suggested to attack the problem using the approach of parameterized complexity. In this paper we propose three fixed-parameter algorithms that apply for several interesting parameters of MRSO. We believe these algorithms to be relevant for practical applications today, as well as for possible future applications. Furthermore, our results extend the known tractability borderline of MRSO, and provide new research horizons for further improvements of this sort.

We consider the problem of drawing a graph with a given symmetry such that the number of edge crossings is minimal. We show that this problem is NP-hard, even if the order of orbits around the rotation center or along the reection axis is fixed. Nevertheless, there is a linear time algorithm to test planarity and to construct a planar embedding if possible. Finally, we devise an O(m log m) algorithm for computing a crossing minimal drawing if inter-orbit edges may not cross orbits, showing in particular that intra-orbit edges do not contribute to the NP-hardness of the crossing minimization problem for symmetries.

We consider the problem of drawing a set of simple paths along the edges of an embedded underlying graph G = (V,E), so that the total number of crossings among pairs of paths is minimized. This problem arises when drawing metro maps, where the embedding of G depicts the structure of the underlying network, the nodes of G correspond to train stations, an edge connecting two nodes implies that there exists a railway line which connects them, whereas the paths illustrate the lines connecting terminal stations. We call this the metro-line crossing minimization problem (MLCM). In contrast to the problem of drawing the underlying graph nicely, MLCM has received fewer attention. It was recently introduced by Benkert et. al in [2]. In this paper, as a first step towards solving MLCM in arbitrary graphs, we study path and tree networks. We examine several variations of the problem for which we develop algorithms for obtaining optimal solutions.

Abstract. Many real-life scheduling, routing and location problems can be formulated as combinatorial optimization problems whose goal is to find a linear layout of an input graph in such a way that the number of edge crossings is minimized. In this paper, we study a restricted version of the linear layout problem where the order of vertices on the line is fixed, the so-called fixed linear crossing number problem (FLCNP). We show that this N P-hard problem can be reduced to the well-known maximum cut problem. The latter problem was intensively studied in the literature; efficient exact algorithms based on the branch-and-cut technique have been developed. By an experimental evaluation on a variety of graphs, we show that using this reduction for solving FLCNP compares favorably to earlier branch-and-bound algorithms. 1

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We consider the problem of drawing a set of simple paths along the edges of an embedded underlying graph G = (V, E) so that the total number of crossings among pairs of paths is minimized. This problem arises when drawing metro maps, where the embedding of G depicts the structure of the underlying network, the nodes of G correspond to train stations, an edge connecting two nodes implies that there exists a railway track connecting them, whereas the paths illustrate the metro lines connecting terminal stations. We call this the metro-line crossing minimization problem (MLCM). We examine several variations of the problem for which we develop algorithms that yield optimal solutions.

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We present a novel paradigm to visualize the evolution of the service provided by one of the most popular root name servers, called K-root, operated by the RIPE Network Coordination Centre (RIPE NCC) and distributed in several locations (instances) worldwide. Our approach can be usedtoeither monitor what happenedduringaprescribed time interval or observe the status of the service in near real-time. We visualize how and when the clients of K-root migrate from one instance to another, how the workload associated with each instance changes over time, and what are the instances that contribute to offer the service to a selected Internet Service Provider. In addition, the visualization aims at distinguishing usual from unusual operational patterns. This helps not only to improve the quality of the service but also to spot security-related issues and to investigate unexpected routing changes. Submitted:

We present a novel paradigm to visualize the evolution of the service provided by one of the most popular root name servers, called K-root, operated by the RIPE Network Coordination Centre (RIPE NCC) and distributed in several locations (instances) worldwide. Our approach can be usedtoeither monitor what happenedduringaprescribed time interval or observe the status of the service in near real-time. We visualize how and when the clients of K-root migrate from one instance to another, how the workload associated with each instance changes over time, and what are the instances that contribute to offer the service to a selected Internet Service Provider. In addition, the visualization aims at distinguishing usual from unusual operational patterns. This helps not only to improve the quality of the service but also to spot security-related issues and to investigate unexpected routing changes. Submitted: