004 Datenverarbeitung; Informatik
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In a recent paper, the Lefschetz number for endomorphisms (modulo trace class operators) of sequences of trace class curvature was introduced. We show that this is a well defined, canonical extension of the classical Lefschetz number and establish the homotopy invariance of this number. Moreover, we apply the results to show that the Lefschetz fixed point formula holds for geometric quasiendomorphisms of elliptic quasicomplexes.
Moderne Kraftfahrzeuge verfügen über eine Vielzahl an Sensoren, welche für einen reibungslosen technischen Betrieb benötigt werden. Hierzu zählen neben fahrzeugspezifischen Sensoren (wie z.B. Motordrehzahl und Fahrzeuggeschwindigkeit) auch umweltspezifische Sensoren (wie z.B. Luftdruck und Umgebungstemperatur). Durch die zunehmende technische Vernetzung wird es möglich, diese Daten der Kraftfahrzeugelektronik aus dem Fahrzeug heraus für die verschiedensten Zwecke zu verwenden.
Die vorliegende Arbeit soll einen Beitrag dazu leisten, diese neue Art an massenhaften Daten im Sinne des Konzepts der „Extended Floating Car Data“ (XFCD) als Geoinformationen nutzbar zu machen und diese für raumzeitliche Visualisierungen (zur visuellen Analyse) anwenden zu können. In diesem Zusammenhang wird speziell die Perspektive des Umwelt- und Verkehrsmonitoring betrachtet, wobei die Anforderungen und Potentiale mit Hilfe von Experteninterviews untersucht werden. Es stellt sich die Frage, welche Daten durch die Kraftfahrzeugelektronik geliefert und wie diese möglichst automatisiert erfasst, verarbeitet, visualisiert und öffentlich bereitgestellt werden können. Neben theoretischen und technischen Grundlagen zur Datenerfassung und -nutzung liegt der Fokus auf den Methoden der kartographischen Visualisierung. Dabei soll der Frage nachgegangenen werden, ob eine technische Implementierung ausschließlich unter Verwendung von Open Source Software möglich ist. Das Ziel der Arbeit bildet ein zweigliedriger Ansatz, welcher zum einen die Visualisierung für ein exemplarisch gewähltes Anwendungsszenario und zum anderen die prototypische Implementierung von der Datenerfassung im Fahrzeug unter Verwendung der gesetzlich vorgeschriebenen „On Board Diagnose“-Schnittstelle und einem Smartphone-gestützten Ablauf bis zur webbasierten Visualisierung umfasst.
Exploratory Data Analysis
(2014)
In bioinformatics the term exploratory data analysis refers to different methods to get an overview of large biological data sets. Hence, it helps to create a framework for further analysis and hypothesis testing. The workflow facilitates this first important step of the data analysis created by high-throughput technologies. The results are different plots showing the structure of the measurements. The goal of the workflow is the automatization of the exploratory data analysis, but also the flexibility should be guaranteed. The basic tool is the free software R.
Deciphering the functioning of biological networks is one of the central tasks in systems biology. In particular, signal transduction networks are crucial for the understanding of the cellular response to external and internal perturbations. Importantly, in order to cope with the complexity of these networks, mathematical and computational modeling is required. We propose a computational modeling framework in order to achieve more robust discoveries in the context of logical signaling networks. More precisely, we focus on modeling the response of logical signaling networks by means of automated reasoning using Answer Set Programming (ASP). ASP provides a declarative language for modeling various knowledge representation and reasoning problems. Moreover, available ASP solvers provide several reasoning modes for assessing the multitude of answer sets. Therefore, leveraging its rich modeling language and its highly efficient solving capacities, we use ASP to address three challenging problems in the context of logical signaling networks: learning of (Boolean) logical networks, experimental design, and identification of intervention strategies. Overall, the contribution of this thesis is three-fold. Firstly, we introduce a mathematical framework for characterizing and reasoning on the response of logical signaling networks. Secondly, we contribute to a growing list of successful applications of ASP in systems biology. Thirdly, we present a software providing a complete pipeline for automated reasoning on the response of logical signaling networks.
Software maintenance encompasses any changes made to a software system after its initial deployment and is thereby one of the key phases in the typical software-engineering lifecycle. In software maintenance, we primarily need to understand structural and behavioral aspects, which are difficult to obtain, e.g., by code reading. Software analysis is therefore a vital tool for maintaining these systems: It provides - the preferably automated - means to extract and evaluate information from their artifacts such as software structure, runtime behavior, and related processes. However, such analysis typically results in massive raw data, so that even experienced engineers face difficulties directly examining, assessing, and understanding these data. Among other things, they require tools with which to explore the data if no clear question can be formulated beforehand. For this, software analysis and visualization provide its users with powerful interactive means. These enable the automation of tasks and, particularly, the acquisition of valuable and actionable insights into the raw data. For instance, one means for exploring runtime behavior is trace visualization. This thesis aims at extending and improving the tool set for visual software analysis by concentrating on several open challenges in the fields of dynamic and static analysis of software systems. This work develops a series of concepts and tools for the exploratory visualization of the respective data to support users in finding and retrieving information on the system artifacts concerned. This is a difficult task, due to the lack of appropriate visualization metaphors; in particular, the visualization of complex runtime behavior poses various questions and challenges of both a technical and conceptual nature. This work focuses on a set of visualization techniques for visually representing control-flow related aspects of software traces from shared-memory software systems: A trace-visualization concept based on icicle plots aids in understanding both single-threaded as well as multi-threaded runtime behavior on the function level. The concept’s extensibility further allows the visualization and analysis of specific aspects of multi-threading such as synchronization, the correlation of such traces with data from static software analysis, and a comparison between traces. Moreover, complementary techniques for simultaneously analyzing system structures and the evolution of related attributes are proposed. These aim at facilitating long-term planning of software architecture and supporting management decisions in software projects by extensions to the circular-bundle-view technique: An extension to 3-dimensional space allows for the use of additional variables simultaneously; interaction techniques allow for the modification of structures in a visual manner. The concepts and techniques presented here are generic and, as such, can be applied beyond software analysis for the visualization of similarly structured data. The techniques' practicability is demonstrated by several qualitative studies using subject data from industry-scale software systems. The studies provide initial evidence that the techniques' application yields useful insights into the subject data and its interrelationships in several scenarios.
In the field of disk-based parallel database management systems exists a great variety of solutions based on a shared-storage or a shared-nothing architecture. In contrast, main memory-based parallel database management systems are dominated solely by the shared-nothing approach as it preserves the in-memory performance advantage by processing data locally on each server. We argue that this unilateral development is going to cease due to the combination of the following three trends: a) Nowadays network technology features remote direct memory access (RDMA) and narrows the performance gap between accessing main memory inside a server and of a remote server to and even below a single order of magnitude. b) Modern storage systems scale gracefully, are elastic, and provide high-availability. c) A modern storage system such as Stanford's RAMCloud even keeps all data resident in main memory. Exploiting these characteristics in the context of a main-memory parallel database management system is desirable. The advent of RDMA-enabled network technology makes the creation of a parallel main memory DBMS based on a shared-storage approach feasible.
This thesis describes building a columnar database on shared main memory-based storage. The thesis discusses the resulting architecture (Part I), the implications on query processing (Part II), and presents an evaluation of the resulting solution in terms of performance, high-availability, and elasticity (Part III).
In our architecture, we use Stanford's RAMCloud as shared-storage, and the self-designed and developed in-memory AnalyticsDB as relational query processor on top. AnalyticsDB encapsulates data access and operator execution via an interface which allows seamless switching between local and remote main memory, while RAMCloud provides not only storage capacity, but also processing power. Combining both aspects allows pushing-down the execution of database operators into the storage system. We describe how the columnar data processed by AnalyticsDB is mapped to RAMCloud's key-value data model and how the performance advantages of columnar data storage can be preserved.
The combination of fast network technology and the possibility to execute database operators in the storage system opens the discussion for site selection. We construct a system model that allows the estimation of operator execution costs in terms of network transfer, data processed in memory, and wall time. This can be used for database operators that work on one relation at a time - such as a scan or materialize operation - to discuss the site selection problem (data pull vs. operator push). Since a database query translates to the execution of several database operators, it is possible that the optimal site selection varies per operator. For the execution of a database operator that works on two (or more) relations at a time, such as a join, the system model is enriched by additional factors such as the chosen algorithm (e.g. Grace- vs. Distributed Block Nested Loop Join vs. Cyclo-Join), the data partitioning of the respective relations, and their overlapping as well as the allowed resource allocation.
We present an evaluation on a cluster with 60 nodes where all nodes are connected via RDMA-enabled network equipment. We show that query processing performance is about 2.4x slower if everything is done via the data pull operator execution strategy (i.e. RAMCloud is being used only for data access) and about 27% slower if operator execution is also supported inside RAMCloud (in comparison to operating only on main memory inside a server without any network communication at all). The fast-crash recovery feature of RAMCloud can be leveraged to provide high-availability, e.g. a server crash during query execution only delays the query response for about one second. Our solution is elastic in a way that it can adapt to changing workloads a) within seconds, b) without interruption of the ongoing query processing, and c) without manual intervention.
Geocoder accuracy ranking
(2014)
Finding an address on a map is sometimes tricky: the chosen map application may be unfamiliar with the enclosed region. There are several geocoders on the market, they have different databases and algorithms to compute the query. Consequently, the geocoding results differ in their quality. Fortunately the geocoders provide a rich set of metadata. The workflow described in this paper compares this metadata with the aim to find out which geocoder is offering the best-fitting coordinate for a given address.
Virtualized cloud data centers provide on-demand resources, enable agile resource provisioning, and host heterogeneous applications with different resource requirements. These data centers consume enormous amounts of energy, increasing operational expenses, inducing high thermal inside data centers, and raising carbon dioxide emissions. The increase in energy consumption can result from ineffective resource management that causes inefficient resource utilization. This dissertation presents detailed models and novel techniques and algorithms for virtual resource management in cloud data centers. The proposed techniques take into account Service Level Agreements (SLAs) and workload heterogeneity in terms of memory access demand and communication patterns of web applications and High Performance Computing (HPC) applications. To evaluate our proposed techniques, we use simulation and real workload traces of web applications and HPC applications and compare our techniques against the other recently proposed techniques using several performance metrics. The major contributions of this dissertation are the following: proactive resource provisioning technique based on robust optimization to increase the hosts' availability for hosting new VMs while minimizing the idle energy consumption. Additionally, this technique mitigates undesirable changes in the power state of the hosts by which the hosts' reliability can be enhanced in avoiding failure during a power state change. The proposed technique exploits the range-based prediction algorithm for implementing robust optimization, taking into consideration the uncertainty of demand. An adaptive range-based prediction for predicting workload with high fluctuations in the short-term. The range prediction is implemented in two ways: standard deviation and median absolute deviation. The range is changed based on an adaptive confidence window to cope with the workload fluctuations. A robust VM consolidation for efficient energy and performance management to achieve equilibrium between energy and performance trade-offs. Our technique reduces the number of VM migrations compared to recently proposed techniques. This also contributes to a reduction in energy consumption by the network infrastructure. Additionally, our technique reduces SLA violations and the number of power state changes. A generic model for the network of a data center to simulate the communication delay and its impact on VM performance, as well as network energy consumption. In addition, a generic model for a memory-bus of a server, including latency and energy consumption models for different memory frequencies. This allows simulating the memory delay and its influence on VM performance, as well as memory energy consumption. Communication-aware and energy-efficient consolidation for parallel applications to enable the dynamic discovery of communication patterns and reschedule VMs using migration based on the determined communication patterns. A novel dynamic pattern discovery technique is implemented, based on signal processing of network utilization of VMs instead of using the information from the hosts' virtual switches or initiation from VMs. The result shows that our proposed approach reduces the network's average utilization, achieves energy savings due to reducing the number of active switches, and provides better VM performance compared to CPU-based placement. Memory-aware VM consolidation for independent VMs, which exploits the diversity of VMs' memory access to balance memory-bus utilization of hosts. The proposed technique, Memory-bus Load Balancing (MLB), reactively redistributes VMs according to their utilization of a memory-bus using VM migration to improve the performance of the overall system. Furthermore, Dynamic Voltage and Frequency Scaling (DVFS) of the memory and the proposed MLB technique are combined to achieve better energy savings.
This work introduces concepts and corresponding tool support to enable a complementary approach in dealing with recovery. Programmers need to recover a development state, or a part thereof, when previously made changes reveal undesired implications. However, when the need arises suddenly and unexpectedly, recovery often involves expensive and tedious work. To avoid tedious work, literature recommends keeping away from unexpected recovery demands by following a structured and disciplined approach, which consists of the application of various best practices including working only on one thing at a time, performing small steps, as well as making proper use of versioning and testing tools. However, the attempt to avoid unexpected recovery is both time-consuming and error-prone. On the one hand, it requires disproportionate effort to minimize the risk of unexpected situations. On the other hand, applying recommended practices selectively, which saves time, can hardly avoid recovery. In addition, the constant need for foresight and self-control has unfavorable implications. It is exhaustive and impedes creative problem solving. This work proposes to make recovery fast and easy and introduces corresponding support called CoExist. Such dedicated support turns situations of unanticipated recovery from tedious experiences into pleasant ones. It makes recovery fast and easy to accomplish, even if explicit commits are unavailable or tests have been ignored for some time. When mistakes and unexpected insights are no longer associated with tedious corrective actions, programmers are encouraged to change source code as a means to reason about it, as opposed to making changes only after structuring and evaluating them mentally. This work further reports on an implementation of the proposed tool support in the Squeak/Smalltalk development environment. The development of the tools has been accompanied by regular performance and usability tests. In addition, this work investigates whether the proposed tools affect programmers’ performance. In a controlled lab study, 22 participants improved the design of two different applications. Using a repeated measurement setup, the study examined the effect of providing CoExist on programming performance. The result of analyzing 88 hours of programming suggests that built-in recovery support as provided with CoExist positively has a positive effect on programming performance in explorative programming tasks.
Geometric generalization is a fundamental concept in the digital mapping process. An increasing amount of spatial data is provided on the web as well as a range of tools to process it. This jABC workflow is used for the automatic testing of web-based generalization services like mapshaper.org by executing its functionality, overlaying both datasets before and after the transformation and displaying them visually in a .tif file. Mostly Web Services and command line tools are used to build an environment where ESRI shapefiles can be uploaded, processed through a chosen generalization service and finally visualized in Irfanview.
With the jABC it is possible to realize workflows for numerous questions in different fields. The goal of this project was to create a workflow for the identification of differentially expressed genes. This is of special interest in biology, for it gives the opportunity to get a better insight in cellular changes due to exogenous stress, diseases and so on. With the knowledge that can be derived from the differentially expressed genes in diseased tissues, it becomes possible to find new targets for treatment.
Analyses of metagenomes in life sciences present new opportunities as well as challenges to the scientific community and call for advanced computational methods and workflows. The large amount of data collected from samples via next-generation sequencing (NGS) technologies render manual approaches to sequence comparison and annotation unsuitable. Rather, fast and efficient computational pipelines are needed to provide comprehensive statistics and summaries and enable the researcher to choose appropriate tools for more specific analyses. The workflow presented here builds upon previous pipelines designed for automated clustering and annotation of raw sequence reads obtained from next-generation sequencing technologies such as 454 and Illumina. Employing specialized algorithms, the sequence reads are processed at three different levels. First, raw reads are clustered at high similarity cutoff to yield clusters which can be exported as multifasta files for further analyses. Independently, open reading frames (ORFs) are predicted from raw reads and clustered at two strictness levels to yield sets of non-redundant sequences and ORF families. Furthermore, single ORFs are annotated by performing searches against the Pfam database
Cloud-RAID
(2014)
Location analyses are among the most common tasks while working with spatial data and geographic information systems. Automating the most frequently used procedures is therefore an important aspect of improving their usability. In this context, this project aims to design and implement a workflow, providing some basic tools for a location analysis. For the implementation with jABC, the workflow was applied to the problem of finding a suitable location for placing an artificial reef. For this analysis three parameters (bathymetry, slope and grain size of the ground material) were taken into account, processed, and visualized with the The Generic Mapping Tools (GMT), which were integrated into the workflow as jETI-SIBs. The implemented workflow thereby showed that the approach to combine jABC with GMT resulted in an user-centric yet user-friendly tool with high-quality cartographic outputs.
This paper describes the implementation of a workflow model for service-oriented computing of potential areas for wind turbines in jABC. By implementing a re-executable model the manual effort of a multi-criteria site analysis can be reduced. The aim is to determine the shift of typical geoprocessing tools of geographic information systems (GIS) from the desktop to the web. The analysis is based on a vector data set and mainly uses web services of the “Center for Spatial Information Science and Systems” (CSISS). This paper discusses effort, benefits and problems associated with the use of the web services.
The protein classification workflow described in this report enables users to get information about a novel protein sequence automatically. The information is derived by different bioinformatic analysis tools which calculate or predict features of a protein sequence. Also, databases are used to compare the novel sequence with known proteins.
In the geoinformatics field, remote sensing data is often used for analyzing the characteristics of the current investigation area. This includes DEMs, which are simple raster grids containing grey scales representing the respective elevation values. The project CREADED that is presented in this paper aims at making these monochrome raster images more significant and more intuitively interpretable. For this purpose, an executable interactive model for creating a colored and relief-shaded Digital Elevation Model (DEM) has been designed using the jABC framework. The process is based on standard jABC-SIBs and SIBs that provide specific GIS functions, which are available as Web services, command line tools and scripts.
Process models specify behavioral execution constraints between activities as well as between activities and data objects. A data object is characterized by its states and state transitions represented as object life cycle. For process execution, all behavioral execution constraints must be correct. Correctness can be verified via soundness checking which currently only considers control flow information. For data correctness, conformance between a process model and its object life cycles is checked. Current approaches abstract from dependencies between multiple data objects and require fully specified process models although, in real-world process repositories, often underspecified models are found. Coping with these issues, we introduce the concept of synchronized object life cycles and we define a mapping of data constraints of a process model to Petri nets extending an existing mapping. Further, we apply the notion of weak conformance to process models to tell whether each time an activity needs to access a data object in a particular state, it is guaranteed that the data object is in or can reach the expected state. Then, we introduce an algorithm for an integrated verification of control flow correctness and weak data conformance using soundness checking.
摘要。哈索•普拉特纳研究院 (HPI) 的新型互动在线教育平台 openHPI (https://openHPI.de) 可以为从事信息技术和信息学领域内容的工作和感兴趣的学员提供可自由访问的、免费的在线课程。与斯坦福大学于 2011 年首推,之后也在美国其他精英大学提供的“网络公开群众课”(简称 MOOC)一样,openHPI 同样在互联网中提供学习视频和阅读材料,其中综合了支持学习的自我测试、家庭作业和社交讨论论坛,并刺激对促进学习的虚拟学习团队的培训。与“传统的”讲座平台,比如 tele-TASK 平台 (http://www.tele-task.de) 不同(在该平台中,可调用以多媒体方式记录的和已准备好的讲座),openHPI 提供的是按教学法准备的在线课程。这些课程的开始时间固定,之后在连续六个课程周稳定的提供以多媒体方式准备的、尽可能可以互动的学习材料。每周讲解课程主题的一章。为此在该周开始前会准备一系列学习视频、文字、自我测试和家庭作业材料,课程学员在该周将精力用于处理这些内容。这些计划与一个社交讨论平台相结合,学员在该平台上可以与课程导师和其他学员交换意见、解答问题和讨论更多主题。当然,学员可以自己决定学习活动的类型和范围。他们可以为课程作出自己的贡献,比如在论坛中引用博文或推文。之后其他学员可以评论、讨论或自己扩展这些博文或推文。这样学员、教师和提供的学习内容就在一个虚拟的团体中与社交学习网络相互结合起来。