World lines

In this paper we present World Lines as a novel interactive visualization that provides complete control over multiple heterogeneous simulation runs. In many application areas, decisions can only be made by exploring alternative scenarios. The goal of the suggested approach is to support users in this decision making process. In this setting, the data domain is extended to a set of alternative worlds where only one outcome will actually happen. World Lines integrate simulation, visualization and computational steering into a single unified system that is capable of dealing with the extended solution space. World Lines represent simulation runs as causally connected tracks that share a common time axis. This setup enables users to interfere and add new information quickly. A World Line is introduced as a visual combination of user events and their effects in order to present a possible future. To quickly find the most attractive outcome, we suggest World Lines as the governing component in a system of multiple linked views and a simulation component. World Lines employ linking and brushing to enable comparative visual analysis of multiple simulations in linked views. Analysis results can be mapped to various visual variables that World Lines provide in order to highlight the most compelling solutions. To demonstrate this technique we present a flooding scenario and show the usefulness of the integrated approach to support informed decision making.     

Gremlin: an interactive visualization model for analyzing genomic rearrangements

In this work we present, apply, and evaluate a novel, interactive visualization model for comparative analysis of structural variants and rearrangements in human and cancer genomes, with emphasis on data integration and uncertainty visualization. To support both global trend analysis and local feature detection, this model enables explorations continuously scaled from the high-level, complete genome perspective, down to the low-level, structural rearrangement view, while preserving global context at all times. We have implemented these techniques in Gremlin, a genomic rearrangement explorer with multi-scale, linked interactions, which we apply to four human cancer genome data sets for evaluation. Using an insight-based evaluation methodology, we compare Gremlin to Circos, the state-of-the-art in genomic rearrangement visualization, through a small user study with computational biologists working in rearrangement analysis. Results from user study evaluations demonstrate that this visualization model enables more total insights, more insights per minute, and more complex insights than the current state-of-the-art for visual analysis and exploration of genome rearrangements.     

Cryptanalysis of the application secure alternative to SNMP (APSSNMP)

The APSSNMP network management protocol was proposed as a secure alternative to the Simple Network Management Protocol (SNMP) used in the TCP/IP suite. The designers claimed that it resists meet-in-the-middle (MITM) attacks. In this paper, we present an advanced MITM attack on the APSSNMP and hence show that it fails to achieve its design objective of providing better security against MITM attacks. Since the APSSNMP has been presented in several journals, and IEEE and IASTED conferences, our result is important to highlight to network implementers and users of distributed systems that the APSSNMP is not secure for practical deployment.     

Fast computation of minimal elementary decompositions of metabolic flux vectors

The concept of elementary flux vector is valuable in a number of applications of metabolic engineering. For instance, in metabolic flux analysis, each admissible flux vector can be expressed as a non-negative linear combination of a small number of elementary flux vectors. However a critical issue concerns the total number of elementary flux vectors which may be huge because it combinatorially increases with the size of the metabolic network. In this paper we present a fast algorithm that randomly computes a decomposition of admissible flux vectors in a minimal number of elementary flux vectors without explicitly enumerating all of them.     

The State of the Art in Topology‐Based Visualization of Unsteady Flow

Vector fields are a common concept for the representation of many different kinds of flow phenomena in science and engineering. Methods based on vector field topology are known for their convenience for visualizing and analysing steady flows, but a counterpart for unsteady flows is still missing. However, a lot of good and relevant work aiming at such a solution is available. We give an overview of previous research leading towards topology‐based and topology‐inspired visualization of unsteady flow, pointing out the different approaches and methodologies involved as well as their relation to each other, taking classical (i.e. steady) vector field topology as our starting point. Particularly, we focus on Lagrangian methods, space–time domain approaches, local methods and stochastic and multifield approaches. Furthermore, we illustrate our review with practical examples for the different approaches.     

Distributed data clustering in sensor networks

Low overhead analysis of large distributed data sets is necessary for current data centers and for future sensor networks. In such systems, each node holds some data value, e.g., a local sensor read, and a concise picture of the global system state needs to be obtained. In resource-constrained environments like sensor networks, this needs to be done without collecting all the data at any location, i.e., in a distributed manner. To this end, we address the distributed clustering problem, in which numerous interconnected nodes compute a clustering of their data, i.e., partition these values into multiple clusters, and describe each cluster concisely. We present a generic algorithm that solves the distributed clustering problem and may be implemented in various topologies, using different clustering types. For example, the generic algorithm can be instantiated to cluster values according to distance, targeting the same problem as the famous k-means clustering algorithm. However, the distance criterion is often not sufficient to provide good clustering results. We present an instantiation of the generic algorithm that describes the values as a Gaussian Mixture (a set of weighted normal distributions), and uses machine learning tools for clustering decisions. Simulations show the robustness, speed and scalability of this algorithm. We prove that any implementation of the generic algorithm converges over any connected topology, clustering criterion and cluster representation, in fully asynchronous settings.     

Good programming in transactional memory : Game theory meets multicore architecture

In a multicore transactional memory (TM) system, concurrent execution threads interact and interfere with each other through shared memory. The less interference a thread provokes the better for the system. However, as a programmer is primarily interested in optimizing her individual code’s performance rather than the system’s overall performance, she does not have a natural incentive to provoke as little interference as possible. Hence, a TM system must be designed compatible with good programming incentives (GPI), i.e., writing efficient code for the overall system should coincide with writing code that optimizes an individual thread’s performance. We show that with most contention managers (CM) proposed in the literature so far, TM systems are not GPI compatible. We provide a generic framework for CMs that base their decisions on priorities and explain how to modify Timestamp-like CMs so as to feature GPI compatibility. In general, however, priority-based conflict resolution policies are prone to be exploited by selfish programmers. In contrast, a simple non-priority-based manager that resolves conflicts at random is GPI compatible.     

The Koala component model for consumer electronics software

Most consumer electronics today contain embedded software. In the early days, developing CE software presented relatively minor challenges, but in the past several years three significant problems have arisen: size and complexity of the software in individual products; the increasing diversity of products and their software; and the need for decreased development time. The question of handling diversity and complexity in embedded software at an increasing production speed becomes an urgent one. The authors present their belief that the answer lies not in hiring more software engineers. They are not readily available, and even if they were, experience shows that larger projects induce larger lead times and often result in greater complexity. Instead, they believe that the answer lies in the use and reuse of software components that work within an explicit software architecture. The Koala model, a component-oriented approach detailed in this article, is their way of handling the diversity of software in consumer electronics. Used for embedded software in TV sets, it allows late binding of reusable components with no additional overhead