Just as packet switched networks constituted a major breakthrough in our perception of the information exchange in computer networks so have the decoupling properties of publish/subscribe systems revolutionized the way we look at networking in the context of large scale distributed systems. The decoupling of the components of publish/subscribe systems in time, space and synchronization has created an appealing platform for the asynchronous information exchange among anonymous information producers and consumers. Moreover, the content-based nature of publish/subscribe systems provides a great degree of flexibility and expressiveness as far as construction of data flows is considered. However, a number of challenges and not yet addressed issued still exists in the area of the publish/subscribe systems. One active area of research is directed toward the problem of the efficient content delivery in the content-based publish/subscribe networks. Routing of the information based on the information itself, instead of the explicit source and destination addresses poses challenges as far as efficiency and processing times are concerned. Simultaneously, due to their decoupled nature, publish/subscribe systems introduce new challenges with respect to issues related to dependability and fail-awareness. This thesis seeks to advance the field of research in both directions. First it shows the design and implementation of routing algorithms based on the end-to-end systems design principle. Proposed routing algorithms obsolete the need to perform content-based routing within the publish/subscribe network, pushing this task to the edge of the system. Moreover, this thesis presents a fail-aware approach towards construction of the content-based publish/subscribe system along with its application to the creation of the soft state publish/subscribe system. A soft state publish/subscribe system exposes the self stabilizing behavior as far as transient timing, link and node failures are concerned. The result of this thesis is a family of the XSiena content-based publish/subscribe systems, implementing the proposed concepts and algorithms. The family of the XSiena content-based publish/subscribe systems has been a subject to rigorous evaluation, which confirms the claims made in this thesis.

In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the idea that each variant corresponds to a recognizable pattern, a bubble, in a de Bruijn graph constructed from the RNA-seq reads, we propose a general model for all variants in such graphs. We then introduce an exact method, called KisSplice, to extract alternative splicing events and show that it outperforms general purpose transcriptome assemblers. We put an extra effort to make KisSplice as scalable as possible. In order to improve the running time, we propose a new polynomial delay algorithm to enumerate bubbles. We show that it is several orders of magnitude faster than previous approaches. In order to reduce its memory consumption, we propose a new compact way to build and represent a de Bruijn graph. We show that our approach uses 30% to 40% less memory than the state of the art, with an insignificant impact on the construction time. Additionally, we apply the techniques developed to list bubbles in two classical problems: cycle enumeration and the K-shortest paths problem. We give the first optimal algorithm to list cycles in undirected graphs, improving over Johnson's algorithm. This is the first improvement to this problem in almost 40 years. We then consider a different parameterization of the K-shortest (simple) paths problem: instead of bounding the number of st-paths, we bound the weight of the st-paths. We present new algorithms using exponentially less memory than previous approaches

Just as packet switched networks constituted a major breakthrough in our perception of the information exchange in computer networks so have the decoupling properties of publish/subscribe systems revolutionized the way we look at networking in the context of large scale distributed systems. The decoupling of the components of publish/subscribe systems in time, space and synchronization has created an appealing platform for the asynchronous information exchange among anonymous information producers and consumers. Moreover, the content-based nature of publish/subscribe systems provides a great degree of flexibility and expressiveness as far as construction of data flows is considered. However, a number of challenges and not yet addressed issued still exists in the area of the publish/subscribe systems. One active area of research is directed toward the problem of the efficient content delivery in the content-based publish/subscribe networks. Routing of the information based on the information itself, instead of the explicit source and destination addresses poses challenges as far as efficiency and processing times are concerned. Simultaneously, due to their decoupled nature, publish/subscribe systems introduce new challenges with respect to issues related to dependability and fail-awareness. This thesis seeks to advance the field of research in both directions. First it shows the design and implementation of routing algorithms based on the end-to-end systems design principle. Proposed routing algorithms obsolete the need to perform content-based routing within the publish/subscribe network, pushing this task to the edge of the system. Moreover, this thesis presents a fail-aware approach towards construction of the content-based publish/subscribe system along with its application to the creation of the soft state publish/subscribe system. A soft state publish/subscribe system exposes the self stabilizing behavior as far as transient timing, link and node failures are concerned. The result of this thesis is a family of the XSiena content-based publish/subscribe systems, implementing the proposed concepts and algorithms. The family of the XSiena content-based publish/subscribe systems has been a subject to rigorous evaluation, which confirms the claims made in this thesis.