LEDA-SM: External Memory Algorithms and Data Structures in theory and practice

Data to be processed has dramatically increased during the last years. Nowadays, external memory (mostly hard disks) has to be used to store this massive data. Algorithms and data structures that work on external memory have different properties and specialties that distinguish them from algorithms and data structures, developed for the RAM model. In this thesis, we first explain the functionality of external memory,which is realized by disk drives. We then introduce the most important theoretical I/O models. In the main part, we present the C++ class library LEDA-SM. Library LEDA-SM is an extension of the LEDA library towards external memory computation and consists of a collection of algorithms and data structures that are designed to work efficiently in external memory. In the last two chapters, we present new external memory data structures for external memory priority queues and new external memory construction algorithms for suffix arrays. These new proposals are theoretically analyzed and experimentally tested. All proposals are implemented using the LEDA-SM library. Their efficiency is evaluated by performing a large number of experiments.Die zu verarbeitenden Datenmengen sind in den letzten Jahren dramatisch gestiegen, so daß Externspeicher (in Form von Festplatten) eingesetzt wird, um die Datenmengen zu speichern. Algorithmen und Datenstrukturen, die den Externspeicher benutzen, haben andere algorithmische Anforderungen als eine Vielzahl der bekannten Algorithmen und Datenstrukturen, die für das RAM-Modell entwickelt wurden. Wir geben in dieser Arbeit erst einen Einblick in die Funktionsweise von Externspeicher anhand von Festplatten und erklären die wichtigsten theoretischen Modelle, die zur Analyse von Algorithmen benutzt werden. Weiterhin stellen wir eine neu entwickelte C++ Klassenbibliothek namens LEDA-SM vor. LEDA-SM bietet eine Sammlung von speziellen Externspeicher Algorithmen und Datenstrukturen. Im zweiten Teil entwickeln wir neue Externspeicher-Prioritätswarteschlangen und neue Externspeicher- Konstruktionsalgorithmen für Suffix Arrays. Unsere neuen Verfahren werden theoretisch analysiert, mit Hilfe von LEDA-SM implementiert und anschließend experimentell getestet

A basic analysis toolkit for biological sequences

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at under the GNU GPL

Emerging in the Image of God: From Evolution to Ethics in a Second Naïveté Understanding of Christian Anthropology

Through a careful integration of theological, philosophical, and the natural scientific sources, the biblical concepts of the image of God and the knowledge of good and evil have the potential to remain important and appropriate descriptors of the human condition, including the possibility and necessity of human morality. This study employs French philosopher Paul Ricoeur\u27s notion of second naïveté understanding to demonstrate the hermeneutical significance of contemporary biocultural evolutionary theory for reinterpreting and reappropriating these ancient symbols of Christian anthropology as terms equipped to encapsulate a morally fruitful and intellectually honest conceptual framework for constructing, conducting, and evaluating theological anthropology and ethics today. Forging and polishing this hermeneutical lens for the purpose of recasting a biblically-based picture of humanity involves alloying these ancient concepts with others from the interrelated fields of cognitive linguistics, evolutionary psychology, and emergence. Viewed through this lens, the dissertationing chapters of Genesis describe human beings as creatures wrought of the creation and embedded within it to the same extent as all other creatures. Though ordinary in every other aspect, human creatures are unique in that they have emerged with an ambivalent condition of freedom through which they bear the vocation to re-present the creative beneficence of the God who shares power and does not create through violence. I defend this thesis in seven chapters. In the first chapter, I introduce the research topic, goals, and hermeneutical procedure for this study. Chapters 2 and 3 describe biocultural evolution and evolutionary psychology within a non-reductive emergentist perspective as sources and resources for contemporary theological anthropology. In chapter 4, I propose an articulation of the doctrine of the imago Dei within this evolutionary worldview. Chapter 5 situates the knowledge of good and evil vis-à-vis biocultural evolution and recent biblical studies. I then construct a proposal in chapter 6 for how this second naïveté understanding of the image of God and the knowledge of good and evil dissertations up new frameworks and frontiers for fundamental theological ethics. Finally, chapter 7 offers a summative and prospective conclusion to this study and its likely impact on my future research