Intermediate function analysis for improving constructability

Ph.DDOCTOR OF PHILOSOPH

Learning condition-specific networks

Condition-specific cellular networks are networks of genes and proteins that describe functional interactions among genes occurring under different environmental conditions. These networks provide a systems-level view of how the parts-list (genes and proteins) interact within the cell as it functions under changing environmental conditions and can provide insight into mechanisms of stress response, cellular differentiation and disease susceptibility. The principle challenge, however, is that cellular networks remain unknown for most conditions and must be inferred from activity levels of genes (mRNA levels) under different conditions. This dissertation aims to develop computational approaches for inferring, analyzing and validating cellular networks of genes from expression data. This dissertation first describes an unsupervised machine learning framework for inferring cellular networks using expression data from a single condition. Here cellular networks are represented as undirected probabilistic graphical models and are learned using a novel, data-driven algorithm. Then several approaches are described that can learn networks using data from multiple conditions. These approaches apply to cases where the condition may or may not be known and, therefore, must be inferred as part of the learning problem. For the latter, the condition variable is allowed to influence expression of genes at different levels of granularity: condition variable per gene to a single condition variable for all genes. Results on simulated data suggest that the algorithm performance depends greatly on the size and number of connected components of the union network of all conditions. These algorithms are also applied to microarray data from two yeast populations, quiescent and non-quiescent, isolated from glucose starved cultures. Our results suggest that by sharing information across multiple conditions, better networks can be learned for both conditions, with many more biologically meaningful dependencies, than if networks were learned for these conditions independently. In particular, processes that were shared among both cell populations were involved in response to glucose starvation, whereas the processes specific to individual populations captured characteristics unique to each population. These algorithms were also applied for learning networks across multiple species: yeast (S. cerevisiae) and fly (D. melanogaster). Preliminary analysis suggests that sharing patterns across species is much more complex than across different populations of the same species and basic metabolic processes are shared across the two species. Finally, this dissertation focuses on validation of cellular networks. This validation framework describes scores for measuring how well network learning algorithms capture higher-order dependencies. This framework also introduces a measure for evaluating the entire inferred network structure based on the extent to which similarly functioning genes are close together on the network

A Language-centered Approach to support environmental modeling with Cellular Automata

Die Anwendung von Methodiken und Technologien aus dem Bereich der Softwaretechnik auf den Bereich der Umweltmodellierung ist eine gemeinhin akzeptierte Vorgehensweise. Im Rahmen der "modellgetriebenen Entwicklung"(MDE, model-driven engineering) werden Technologien entwickelt, die darauf abzielen, Softwaresysteme vorwiegend auf Basis von im Vergleich zu Programmquelltexten relativ abstrakten Modellen zu entwickeln. Ein wesentlicher Bestandteil von MDE sind Techniken zur effizienten Entwicklung von "domänenspezifischen Sprachen"( DSL, domain-specific language), die auf Sprachmetamodellen beruhen. Die vorliegende Arbeit zeigt, wie modellgetriebene Entwicklung, und insbesondere die metamodellbasierte Beschreibung von DSLs, darüber hinaus Aspekte der Pragmatik unterstützen kann, deren Relevanz im erkenntnistheoretischen und kognitiven Hintergrund wissenschaftlichen Forschens begründet wird. Hierzu wird vor dem Hintergrund der Erkenntnisse des "modellbasierten Forschens"(model-based science und model-based reasoning) gezeigt, wie insbesondere durch Metamodelle beschriebene DSLs Möglichkeiten bieten, entsprechende pragmatische Aspekte besonders zu berücksichtigen, indem sie als Werkzeug zur Erkenntnisgewinnung aufgefasst werden. Dies ist v.a. im Kontext großer Unsicherheiten, wie sie für weite Teile der Umweltmodellierung charakterisierend sind, von grundsätzlicher Bedeutung. Die Formulierung eines sprachzentrierten Ansatzes (LCA, language-centered approach) für die Werkzeugunterstützung konkretisiert die genannten Aspekte und bildet die Basis für eine beispielhafte Implementierung eines Werkzeuges mit einer DSL für die Beschreibung von Zellulären Automaten (ZA) für die Umweltmodellierung. Anwendungsfälle belegen die Verwendbarkeit von ECAL und der entsprechenden metamodellbasierten Werkzeugimplementierung.The application of methods and technologies of software engineering to environmental modeling and simulation (EMS) is common, since both areas share basic issues of software development and digital simulation. Recent developments within the context of "Model-driven Engineering" (MDE) aim at supporting the development of software systems at the base of relatively abstract models as opposed to programming language code. A basic ingredient of MDE is the development of methods that allow the efficient development of "domain-specific languages" (DSL), in particular at the base of language metamodels. This thesis shows how MDE and language metamodeling in particular, may support pragmatic aspects that reflect epistemic and cognitive aspects of scientific investigations. For this, DSLs and language metamodeling in particular are set into the context of "model-based science" and "model-based reasoning". It is shown that the specific properties of metamodel-based DSLs may be used to support those properties, in particular transparency, which are of particular relevance against the background of uncertainty, that is a characterizing property of EMS. The findings are the base for the formulation of an corresponding specific metamodel- based approach for the provision of modeling tools for EMS (Language-centered Approach, LCA), which has been implemented (modeling tool ECA-EMS), including a new DSL for CA modeling for EMS (ECAL). At the base of this implementation, the applicability of this approach is shown

Architecture, Services and Protocols for CRUTIAL

This document describes the complete specification of the architecture, services and protocols of the project CRUTIAL. The CRUTIAL Architecture intends to reply to a grand challenge of computer science and control engineering: how to achieve resilience of critical information infrastructures (CII), in particular in the electrical sector. In general lines, the document starts by presenting the main architectural options and components of the architecture, with a special emphasis on a protection device called the CRUTIAL Information Switch (CIS). Given the various criticality levels of the equipments that have to be protected, and the cost of using a replicated device, we define a hierarchy of CIS designs incrementally more resilient. The different CIS designs offer various trade offs in terms of capabilities to prevent and tolerate intrusions, both in the device itself and in the information infrastructure. The Middleware Services, APIs and Protocols chapter describes our approach to intrusion tolerant middleware. The CRUTIAL middleware comprises several building blocks that are organized on a set of layers. The Multipoint Network layer is the lowest layer of the middleware, and features an abstraction of basic communication services, such as provided by standard protocols, like IP, IPsec, UDP, TCP and SSL/TLS. The Communication Support layer features three important building blocks: the Randomized Intrusion-Tolerant Services (RITAS), the CIS Communication service and the Fosel service for mitigating DoS attacks. The Activity Support layer comprises the CIS Protection service, and the Access Control and Authorization service. The Access Control and Authorization service is implemented through PolyOrBAC, which defines the rules for information exchange and collaboration between sub-modules of the architecture, corresponding in fact to different facilities of the CII’s organizations. The Monitoring and Failure Detection layer contains a definition of the services devoted to monitoring and failure detection activities. The Runtime Support Services, APIs, and Protocols chapter features as a main component the Proactive-Reactive Recovery service, whose aim is to guarantee perpetual correct execution of any components it protects.Project co-funded by the European Commission within the Sixth Frame-work Programme (2002-2006

Combining SOA and BPM Technologies for Cross-System Process Automation

This paper summarizes the results of an industry case study that introduced a cross-system business process automation solution based on a combination of SOA and BPM standard technologies (i.e., BPMN, BPEL, WSDL). Besides discussing major weaknesses of the existing, custom-built, solution and comparing them against experiences with the developed prototype, the paper presents a course of action for transforming the current solution into the proposed solution. This includes a general approach, consisting of four distinct steps, as well as specific action items that are to be performed for every step. The discussion also covers language and tool support and challenges arising from the transformation

Modeling complex cellular systems: from differential equations to constraint-based models

In the beginning of the 20th century, scientists realized the necessity of purifying enzymes to unravel their mechanistic nature. A century and tremendous progresses in the natural sciences later, molecular and systems biology became fundamental pillars of modern biology. Moreover, natural scientists developed an increasing interest in theoretical models. In the first part of my thesis, I present my contribution to the field of studying the dynamics of biological phenomena. I present fundamental issues arising, when neglecting substrate inhibition in kinetic modeling. Furthermore, I describe a model that considers experimental data to simulate the transition of normal proliferating into cellular senescent cells. Since large-scaled models are more comprehensive, they commonly prohibit a mechanistic modeling approach. In order to analyze such models, nevertheless, constraint-based methods proved to be suitable tools. In the second part of my thesis, I contribute three studies to constraint-based modeling. I describe the established concept of elementary flux modes, which resemble non-decomposable and theoretically feasible pathways of metabolic networks. Subsequently, I present the analysis of the nitrogen metabolism network of Chlamydomonas reinhardtii with respect to circadian regulation, which gives rise to about three million elementary flux modes. In the last study, I present a comprehensive work on metabolic costs of amino acid and protein production in Escherichia coli. These costs were manually calculated as well as based on a flux balance analysis of an E. coli genome-scale metabolic model. Both approaches, either dynamic or constraint-based modeling, proved to be suitable strategies to describe biological processes at different levels. Whereas dynamic modeling allowed for a precise description of the temporal behavior of biological species, constraint-based modeling enabled studies, where the complexity of the investigated phenomena prohibits kinetic modeling

Manipulation of global chromatin architecture in the human cell nucleus and critical assessment of current model views

In spite of strong evidence that the mammalian cell nucleus is a highly organized organelle, a consensus on basic principles of global nuclear architecture has not so far been achieved. The existence of major architectural features such as an organized interchromatin compartment and higher order organization of chromatin postulated by some of the models is questioned or even refused by the others. This study was set up to test predictions of the various model views after manipulating nuclear architecture by applying the induced formation of hypercondensed chromatin (HCC). This method leads to massive but completely reversible conformational changes of chromatin arrangements in living cell nuclei, but does not affect the cells survivability. Nuclear functions like transcription, replication and cell cycling were immediately stalled when HCC formation was induced, but were rapidly recovered upon recovery of normal chromatin configurations. The emerging pattern of HCC revealed a 3D network of interconnected chromosome territories. The surface of the emerging HCC bundles was the site of preceding activity like RNA transcription or DNA replication, which confirmed the existence of a distinct topological arrangement of functional processes with respect to the architecture of chromatin. This arrangement could further be demonstrated by analyzing the topography of defined chromatin modifications, showing that active chromatin is preferentially located at the HCC bundle surfaces, whereas inactive chromatin regions are preferentially found in the HCC bundle interior. The emerging patterns of HCC were further strikingly similar in consecutively repeated cycles of HCC formation and recovery, demonstrating a non-random but pre-existing and defined chromatin and interchromatin topography. All results of this study were obtained using confocal laser scanning microscopy. A protocol for deconvolution of confocal images was established to enhance confocal image quality to an extent sufficient for subsequent image analysis. In contribution to the present model views this study demonstrates: [1] That most chromatin exists in the form of higher-order sub-compartments ('~1 Mb chromatin domains') above the level of extended 30 nm fibers and [2] That an interchromatin compartment exists as a dynamic, structurally distinct nuclear compartment, which is functionally linked with the chromatin compartment. An updated chromosome territory-interchromatin compartment model on the basis of the gained results is presented at the end of this thesis together with an attempt to provide a comprehensive view linking ultrastructural with light microscopic insights

Gene and Protein Networks in Understanding Cellular Function

Over the past decades, networks have emerged as a useful way of representing complex large-scale systems in a variety of fields. In cellular and molecular biology, gene and protein networks have attracted considerable interest as tools for making sense of increasingly large volumes of data. Despite this interest, there is still substantial debate over how to best exploit network models in cellular biology. This thesis explores the use of gene and protein networks in various biological contexts. The first part of the thesis (Chapter 2) examines protein function prediction using network-based ‘guilt-by-association’ approaches. Given the falling costs of genome sequencing and the availability of large volumes of biological data, automated annotation of gene and protein function is becoming increasingly useful. Chapter 2 describes the development of a new network-based protein function prediction method and compares it to a leading algorithm on a number of benchmarks. Biases in benchmarking methods are also explicitly explored. The second part (Chapters 3 and 4) explores network approaches in understanding loss of function variation in the human genome. For a number of genes, homozygous loss of function appears to have no detrimental effect. A possible explanation is that these genes are only necessary in specific genetic backgrounds. Chapter 3 develops methods for identifying these types of relationships between apparently loss of function tolerant genes. Chapter 4 describes the use of networks in predicting the functional effects of loss of function mutations. The third part of the thesis (Chapters 5 and 6) uses network representations to model the effects of cellular stress on yeast cells. Chapter 5 examines stress induced changes in co-expression and protein interaction networks, finding evidence of increased modularisation in both types of network. Chapter 6 explores the effect of stress on resilience to node removal in the co-expression networks

Sonic interactions in virtual environments

This book tackles the design of 3D spatial interactions in an audio-centered and audio-first perspective, providing the fundamental notions related to the creation and evaluation of immersive sonic experiences. The key elements that enhance the sensation of place in a virtual environment (VE) are: Immersive audio: the computational aspects of the acoustical-space properties of Virutal Reality (VR) technologies Sonic interaction: the human-computer interplay through auditory feedback in VE VR systems: naturally support multimodal integration, impacting different application domains Sonic Interactions in Virtual Environments will feature state-of-the-art research on real-time auralization, sonic interaction design in VR, quality of the experience in multimodal scenarios, and applications. Contributors and editors include interdisciplinary experts from the fields of computer science, engineering, acoustics, psychology, design, humanities, and beyond. Their mission is to shape an emerging new field of study at the intersection of sonic interaction design and immersive media, embracing an archipelago of existing research spread in different audio communities and to increase among the VR communities, researchers, and practitioners, the awareness of the importance of sonic elements when designing immersive environments