Mario Pickavet

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks

SUMMARYnNetwork motifs in integrated molecular networks represent functional relationships between distinct data types. They aggregate to form dense topological structures corresponding to functional modules which cannot be detected by traditional graph clustering algorithms. We developed CyClus3D, a Cytoscape plugin for clustering composite three-node network motifs using a 3D spectral clustering algorithm.nnnAVAILABILITYnVia the Cytoscape plugin manager or http://bioinformatics.psb.ugent.be/software/details/CyClus3D.

Overspill routing in optical networks: a new architecture for future-proof IP-over-WDM networks

Packet switched based network architectures exhibit a high degree of resource sharing and consequently make very efficient use of the available bandwidth. On the other hand, they experience a great amount of transit traffic in IP routers, increasing costs. Wavelength switched based concepts can reduce this transit traffic, but have limited resource sharing and consequently need more resources (wavelengths) to avoid losses. We present a new hybrid network architecture, Overspill Routing In Optical Networks (ORION), which combines the benefits of wavelength switched networks and packet switched networks. An example node hardware design and corresponding control architecture is presented. A case study quantifying the benefits of ORION when compared to three other network architectures is also discussed.

SONET/SDH Networks

This chapter focuses on the Synchronous Digital Hierarchy (SDH)/ Synchronous Optical NETwork (SONET) technology. The chapter discusses the fault, performance, and configuration management aspects of the network recovery in the SONET/SDH transmission networks. The SDH/SONET technology is widely accepted as a network technology that has already proven to be capable of providing very fast protection switching. A transmission network can be decomposed in one or more layers. Each network layer can be modeled as a set of atomic functions interconnecting the reference points in the network layer. One of the major progresses in SDH is that the clocks used for processing the received signals and generating signals to be transmitted in all nodes are synchronized with each other through a synchronization network. This allows byte interleaved instead of bit-interleaved multiplexing and prevents stuffing to compensate for the frequency mismatch between the different clocks. Accessing each individual multiplexed signal is possible by using a pointer to the appropriate byte in a repetitive frame structure, thereby avoiding the need to demultiplex (and re-multiplex) the high bandwidth aggregate signal, significantly reducing the complexity of the network equipment.

Chapter 4 – IP Routing

Publisher Summary nThis chapter focuses on the fundamental aspects of the link state protocols, which include the reliable network topology discovery mechanism, the distributed shortest path computation, and the routing table calculation. The chapter reviews the dynamic aspects of the distributed routing and delineates the various steps occurring during the network convergence. Running a routing protocol is done for each node to build a routing table that contains the shortest path to each reachable Internet protocol (IP) prefix. The entire path does not have to be stored to route the packet, instead, the router maintains a data structure called the forwarding information base (FIB) that contains the next hop for each reachable IP prefix along with other protocol information. There are several routing protocols, which can be divided into two categories—the distance vector routing protocols and the link state routing protocols. Different failure profiles can occur in an IP/Multi-Protocol Label Switching (MPLS) network. There are two families of failure detection mechanisms that can be used to detect such failures and their respective performance and scalability—the lower layers failure notification and the hello-based mechanisms.

Chapter 6 – Multilayer Networks

Publisher Summary nThis chapter discusses the recovery mechanisms and the strategies used for multilayer networks. It reviews some examples and case studies of recovery in such networks. These include the optical restoration and the MPLS traffic engineering (TE) fast reroute (FRR), the Synchronous Optical NETwork (SONET)/Synchronous Digital Hierarchy (SDH) protection and Internet protocol (IP) routing, the MPLS TE Fast Reroute and the IP routing. It describes three categories for providing the recovery in multilayer networks—the single-layer recovery schemes in multilayer networks, the static multilayer recovery schemes, and the dynamic multilayer recovery strategies. The labels in regular MPLS are represented as integers attached to an IP packet. The concept of the generalized MPLS (G-MPLS) allows a label to be represented as an integer, a time slot in a time division multiplexing (TDM) frame, a wavelength or waveband on a fiber, or as a fiber in a cable. The generalized label request consists of a label switch path (LSP) encoding type, a switching type, and a generalized payload identifier (G-PID). The encoding of the generalized label object depends on the link on which the label is used.