eXamine: a Cytoscape app for exploring annotated modules in networks

Background. Biological networks have growing importance for the interpretation of high-throughput "omics" data. Statistical and combinatorial methods allow to obtain mechanistic insights through the extraction of smaller subnetwork modules. Further enrichment analyses provide set-based annotations of these modules. Results. We present eXamine, a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. Our approach extends upon Self Organizing Maps to simultaneously lay out nodes, links, and set contours. Conclusions. We implemented eXamine as a freely available Cytoscape app. Using eXamine we study a module that is activated by the virally-encoded G-protein coupled receptor US28 and formulate a novel hypothesis about its functioning

3GPP Long Term Evolution: Architecture, Protocols and Interfaces

The evolution of wireless networks is a continuous phenomenon. Some key trends in this changing process include: reduced latency, increased performance with substantial reduction in costs, and seamless mobility. Long Term Evolution (LTE) is based on an evolved architecture that makes it a candidate of choice for next generation wireless mobile networks. This paper provides an overview of both the core and access networks of LTE. Functional details of the associated protocols and interfaces are also presented

Options for Securing RTP Sessions

The Real-time Transport Protocol (RTP) is used in a large number of different application domains and environments. This heterogeneity implies that different security mechanisms are needed to provide services such as confidentiality, integrity, and source authentication of RTP and RTP Control Protocol (RTCP) packets suitable for the various environments. The range of solutions makes it difficult for RTP-based application developers to pick the most suitable mechanism. This document provides an overview of a number of security solutions for RTP and gives guidance for developers on how to choose the appropriate security mechanism

Logic Integer Programming Models for Signaling Networks

We propose a static and a dynamic approach to model biological signaling networks, and show how each can be used to answer relevant biological questions. For this we use the two different mathematical tools of Propositional Logic and Integer Programming. The power of discrete mathematics for handling qualitative as well as quantitative data has so far not been exploited in Molecular Biology, which is mostly driven by experimental research, relying on first-order or statistical models. The arising logic statements and integer programs are analyzed and can be solved with standard software. For a restricted class of problems the logic models reduce to a polynomial-time solvable satisfiability algorithm. Additionally, a more dynamic model enables enumeration of possible time resolutions in poly-logarithmic time. Computational experiments are included