Diseño y Desarrollo de un cliente Web Processing Service (WPS) para gvSIG

Estudi dels estàndards definits per l'Open Geospatial Consortium, i més concretament en l'estàndard Web Processing Service (wps). Així mateix, ha tingut una component pràctica que ha consistit en el disseny i desenvolupament d'un client capaç de consumir serveis Web creats segons wps i integrat a la plataforma gvSIG.

Integrated methodologies to study human transcriptional regulation from functional genomics data

Abstract : The human body is composed of a huge number of cells acting together in a concerted manner. The current understanding is that proteins perform most of the necessary activities in keeping a cell alive. The DNA, on the other hand, stores the information on how to produce the different proteins in the genome. Regulating gene transcription is the first important step that can thus affect the life of a cell, modify its functions and its responses to the environment. Regulation is a complex operation that involves specialized proteins, the transcription factors. Transcription factors (TFs) can bind to DNA and activate the processes leading to the expression of genes into new proteins. Errors in this process may lead to diseases. In particular, some transcription factors have been associated with a lethal pathological state, commonly known as cancer, associated with uncontrolled cellular proliferation, invasiveness of healthy tissues and abnormal responses to stimuli. Understanding cancer-related regulatory programs is a difficult task, often involving several TFs interacting together and influencing each other's activity. This Thesis presents new computational methodologies to study gene regulation. In addition we present applications of our methods to the understanding of cancer-related regulatory programs. The understanding of transcriptional regulation is a major challenge. We address this difficult question combining computational approaches with large collections of heterogeneous experimental data. In detail, we design signal processing tools to recover transcription factors binding sites on the DNA from genome-wide surveys like chromatin immunoprecipitation assays on tiling arrays (ChIP-chip). We then use the localization about the binding of TFs to explain expression levels of regulated genes. In this way we identify a regulatory synergy between two TFs, the oncogene C-MYC and SP1. C-MYC and SP1 bind preferentially at promoters and when SP1 binds next to C-NIYC on the DNA, the nearby gene is strongly expressed. The association between the two TFs at promoters is reflected by the binding sites conservation across mammals, by the permissive underlying chromatin states 'it represents an important control mechanism involved in cellular proliferation, thereby involved in cancer. Secondly, we identify the characteristics of TF estrogen receptor alpha (hERa) target genes and we study the influence of hERa in regulating transcription. hERa, upon hormone estrogen signaling, binds to DNA to regulate transcription of its targets in concert with its co-factors. To overcome the scarce experimental data about the binding sites of other TFs that may interact with hERa, we conduct in silico analysis of the sequences underlying the ChIP sites using the collection of position weight matrices (PWMs) of hERa partners, TFs FOXA1 and SP1. We combine ChIP-chip and ChIP-paired-end-diTags (ChIP-pet) data about hERa binding on DNA with the sequence information to explain gene expression levels in a large collection of cancer tissue samples and also on studies about the response of cells to estrogen. We confirm that hERa binding sites are distributed anywhere on the genome. However, we distinguish between binding sites near promoters and binding sites along the transcripts. The first group shows weak binding of hERa and high occurrence of SP1 motifs, in particular near estrogen responsive genes. The second group shows strong binding of hERa and significant correlation between the number of binding sites along a gene and the strength of gene induction in presence of estrogen. Some binding sites of the second group also show presence of FOXA1, but the role of this TF still needs to be investigated. Different mechanisms have been proposed to explain hERa-mediated induction of gene expression. Our work supports the model of hERa activating gene expression from distal binding sites by interacting with promoter bound TFs, like SP1. hERa has been associated with survival rates of breast cancer patients, though explanatory models are still incomplete: this result is important to better understand how hERa can control gene expression. Thirdly, we address the difficult question of regulatory network inference. We tackle this problem analyzing time-series of biological measurements such as quantification of mRNA levels or protein concentrations. Our approach uses the well-established penalized linear regression models where we impose sparseness on the connectivity of the regulatory network. We extend this method enforcing the coherence of the regulatory dependencies: a TF must coherently behave as an activator, or a repressor on all its targets. This requirement is implemented as constraints on the signs of the regressed coefficients in the penalized linear regression model. Our approach is better at reconstructing meaningful biological networks than previous methods based on penalized regression. The method is tested on the DREAM2 challenge of reconstructing a five-genes/TFs regulatory network obtaining the best performance in the "undirected signed excitatory" category. Thus, these bioinformatics methods, which are reliable, interpretable and fast enough to cover large biological dataset, have enabled us to better understand gene regulation in humans.

A Comparison of Mobile Scanning to a Total Station Survey at the I-35 and IA 92 Interchange in Warren County, Iowa, August 15, 2012

The purpose of this project was to investigate the potential for collecting and using data from mobile terrestrial laser scanning (MTLS) technology that would reduce the need for traditional survey methods for the development of highway improvement projects at the Iowa Department of Transportation (Iowa DOT). The primary interest in investigating mobile scanning technology is to minimize the exposure of field surveyors to dangerous high volume traffic situations. Issues investigated were cost, timeframe, accuracy, contracting specifications, data capture extents, data extraction capabilities and data storage issues associated with mobile scanning. The project area selected for evaluation was the I-35/IA 92 interchange in Warren County, Iowa. This project covers approximately one mile of I-35, one mile of IA 92, 4 interchange ramps, and bridges within these limits. Delivered LAS and image files for this project totaled almost 31GB. There is nearly a 6-fold increase in the size of the scan data after post-processing. Camera data, when enabled, produced approximately 900MB of imagery data per mile using a 2- camera, 5 megapixel system. A comparison was done between 1823 points on the pavement that were surveyed by Iowa DOT staff using a total station and the same points generated through the MTLS process. The data acquired through the MTLS and data processing met the Iowa DOT specifications for engineering survey. A list of benefits and challenges is included in the detailed report. With the success of this project, it is anticipate[d] that additional projects will be scanned for the Iowa DOT for use in the development of highway improvement projects.

A design for an advanced architecture of satellite ground segments

This project proposes a preliminary architectural design for a control and data processing center, also known as 'ground segment', for Earth observation satellites.

Design and manufacture of a microdistillation column

Aim of this thesis was to design and manufacture a microdistillation column. The literature review part of this thesis covers stainless steels, material processing and basics about engineering design and distillation. The main focus, however, is on the experimental part. Experimental part is divided into five distinct sections: First part is where the device is introduced and separated into three parts. Secondly the device is designed part by part. It consists mostly of detail problem solving, since the first drawings had already been drawn and the critical dimensions decided. Third part is the manufacture, which was not fully completed since the final assembly was left out of this thesis. Fourth part is the test welding for the device, and its analysis. Finally some ideas for further studies are presented. The main goal of this thesis was accomplished. The device only lacks some final assembly but otherwise it is complete. One thing that became clear during the process was how difficult it is to produce small and precise steel parts with conventional manufacturing methods. Internal stresses within steel plates and thermal distortions can easily ruin small steel structures. Designing appropriate welding jigs is an important task for even simple devices. Laser material processing is a promising tool for this kind of steel processing because of the flexibility, good cutting quality and also precise and low heat input when welding. Next step in this project is the final assembly and the actual distillation tests. The tests will be carried out at Helsinki University of Technology.

Integrated Environment for Launch Vehicle Telemetry Data Management

The telemetry data processing operation intended for a given mission are pre-defined by an onboard telemetry configuration, mission trajectory and overall telemetry methodology have stabilized lately for ISRO vehicles. The given problem on telemetry data processing is reduced through hierarchical problem reduction whereby the sequencing of operations evolves as the control task and operations on data as the function task. The function task Input, Output and execution criteria are captured into tables which are examined by the control task and then schedules when the function task when the criteria is being met.

Design, implementation and application of a generic framework for integrated regional land-use modeling

Land use is a crucial link between human activities and the natural environment and one of the main driving forces of global environmental change. Large parts of the terrestrial land surface are used for agriculture, forestry, settlements and infrastructure. Given the importance of land use, it is essential to understand the multitude of influential factors and resulting land use patterns. An essential methodology to study and quantify such interactions is provided by the adoption of land-use models. By the application of land-use models, it is possible to analyze the complex structure of linkages and feedbacks and to also determine the relevance of driving forces. Modeling land use and land use changes has a long-term tradition. In particular on the regional scale, a variety of models for different regions and research questions has been created. Modeling capabilities grow with steady advances in computer technology, which on the one hand are driven by increasing computing power on the other hand by new methods in software development, e.g. object- and component-oriented architectures. In this thesis, SITE (Simulation of Terrestrial Environments), a novel framework for integrated regional sland-use modeling, will be introduced and discussed. Particular features of SITE are the notably extended capability to integrate models and the strict separation of application and implementation. These features enable efficient development, test and usage of integrated land-use models. On its system side, SITE provides generic data structures (grid, grid cells, attributes etc.) and takes over the responsibility for their administration. By means of a scripting language (Python) that has been extended by language features specific for land-use modeling, these data structures can be utilized and manipulated by modeling applications. The scripting language interpreter is embedded in SITE. The integration of sub models can be achieved via the scripting language or by usage of a generic interface provided by SITE. Furthermore, functionalities important for land-use modeling like model calibration, model tests and analysis support of simulation results have been integrated into the generic framework. During the implementation of SITE, specific emphasis was laid on expandability, maintainability and usability. Along with the modeling framework a land use model for the analysis of the stability of tropical rainforest margins was developed in the context of the collaborative research project STORMA (SFB 552). In a research area in Central Sulawesi, Indonesia, socio-environmental impacts of land-use changes were examined. SITE was used to simulate land-use dynamics in the historical period of 1981 to 2002. Analogous to that, a scenario that did not consider migration in the population dynamics, was analyzed. For the calculation of crop yields and trace gas emissions, the DAYCENT agro-ecosystem model was integrated. In this case study, it could be shown that land-use changes in the Indonesian research area could mainly be characterized by the expansion of agricultural areas at the expense of natural forest. For this reason, the situation had to be interpreted as unsustainable even though increased agricultural use implied economic improvements and higher farmers' incomes. Due to the importance of model calibration, it was explicitly addressed in the SITE architecture through the introduction of a specific component. The calibration functionality can be used by all SITE applications and enables largely automated model calibration. Calibration in SITE is understood as a process that finds an optimal or at least adequate solution for a set of arbitrarily selectable model parameters with respect to an objective function. In SITE, an objective function typically is a map comparison algorithm capable of comparing a simulation result to a reference map. Several map optimization and map comparison methodologies are available and can be combined. The STORMA land-use model was calibrated using a genetic algorithm for optimization and the figure of merit map comparison measure as objective function. The time period for the calibration ranged from 1981 to 2002. For this period, respective reference land-use maps were compiled. It could be shown, that an efficient automated model calibration with SITE is possible. Nevertheless, the selection of the calibration parameters required detailed knowledge about the underlying land-use model and cannot be automated. In another case study decreases in crop yields and resulting losses in income from coffee cultivation were analyzed and quantified under the assumption of four different deforestation scenarios. For this task, an empirical model, describing the dependence of bee pollination and resulting coffee fruit set from the distance to the closest natural forest, was integrated. Land-use simulations showed, that depending on the magnitude and location of ongoing forest conversion, pollination services are expected to decline continuously. This results in a reduction of coffee yields of up to 18% and a loss of net revenues per hectare of up to 14%. However, the study also showed that ecological and economic values can be preserved if patches of natural vegetation are conservated in the agricultural landscape. -----------------------------------------------------------------------

Collaborative design procedures for architects and engineers

This book argues for novel strategies to integrate engineering design procedures and structural analysis data into architectural design. Algorithmic procedures that recently migrated into the architectural practice are utilized to improve the interface of both disciplines. Architectural design is predominately conducted as a negotiation process of various factors but often lacks rigor and data structures to link it to quantitative procedures. Numerical structural design on the other hand could act as a role model for handling data and robust optimization but it often lacks the complexity of architectural design. The goal of this research is to bring together robust methods from structural design and complex dependency networks from architectural design processes. The book presents three case studies of tools and methods that are developed to exemplify, analyze and evaluate a collaborative work flow.

Applicability of Emergence Engineering to Distributed Systems Scenarios

Genetic Programming can be effectively used to create emergent behavior for a group of autonomous agents. In the process we call Offline Emergence Engineering, the behavior is at first bred in a Genetic Programming environment and then deployed to the agents in the real environment. In this article we shortly describe our approach, introduce an extended behavioral rule syntax, and discuss the impact of the expressiveness of the behavioral description to the generation success, using two scenarios in comparison: the election problem and the distributed critical section problem. We evaluate the results, formulating criteria for the applicability of our approach.

Acquiring expert knowledge for the design of conceptual information systems

Conceptual Information Systems unfold the conceptual structure of data stored in relational databases. In the design phase of the system, conceptual hierarchies have to be created which describe different aspects of the data. In this paper, we describe two principal ways of designing such conceptual hierarchies, data driven design and theory driven design and discuss advantages and drawbacks. The central part of the paper shows how Attribute Exploration, a knowledge acquisition tool developped by B. Ganter can be applied for narrowing the gap between both approaches.

Conceptual knowledge processing with formal concept analysis and ontologies

Among many other knowledge representations formalisms, Ontologies and Formal Concept Analysis (FCA) aim at modeling ‘concepts’. We discuss how these two formalisms may complement another from an application point of view. In particular, we will see how FCA can be used to support Ontology Engineering, and how ontologies can be exploited in FCA applications. The interplay of FCA and ontologies is studied along the life cycle of an ontology: (i) FCA can support the building of the ontology as a learning technique. (ii) The established ontology can be analyzed and navigated by using techniques of FCA. (iii) Last but not least, the ontology may be used to improve an FCA application.

Large-Size AlGaN/GaN HEMT Large-Signal Electrothermal Characterization and Modeling for Wireless Digital Communications

The rapid growth in high data rate communication systems has introduced new high spectral efficient modulation techniques and standards such as LTE-A (long term evolution-advanced) for 4G (4th generation) systems. These techniques have provided a broader bandwidth but introduced high peak-to-average power ratio (PAR) problem at the high power amplifier (HPA) level of the communication system base transceiver station (BTS). To avoid spectral spreading due to high PAR, stringent requirement on linearity is needed which brings the HPA to operate at large back-off power at the expense of power efficiency. Consequently, high power devices are fundamental in HPAs for high linearity and efficiency. Recent development in wide bandgap power devices, in particular AlGaN/GaN HEMT, has offered higher power level with superior linearity-efficiency trade-off in microwaves communication. For cost-effective HPA design to production cycle, rigorous computer aided design (CAD) AlGaN/GaN HEMT models are essential to reflect real response with increasing power level and channel temperature. Therefore, large-size AlGaN/GaN HEMT large-signal electrothermal modeling procedure is proposed. The HEMT structure analysis, characterization, data processing, model extraction and model implementation phases have been covered in this thesis including trapping and self-heating dispersion accounting for nonlinear drain current collapse. The small-signal model is extracted using the 22-element modeling procedure developed in our department. The intrinsic large-signal model is deeply investigated in conjunction with linearity prediction. The accuracy of the nonlinear drain current has been enhanced through several issues such as trapping and self-heating characterization. Also, the HEMT structure thermal profile has been investigated and corresponding thermal resistance has been extracted through thermal simulation and chuck-controlled temperature pulsed I(V) and static DC measurements. Higher-order equivalent thermal model is extracted and implemented in the HEMT large-signal model to accurately estimate instantaneous channel temperature. Moreover, trapping and self-heating transients has been characterized through transient measurements. The obtained time constants are represented by equivalent sub-circuits and integrated in the nonlinear drain current implementation to account for complex communication signals dynamic prediction. The obtained verification of this table-based large-size large-signal electrothermal model implementation has illustrated high accuracy in terms of output power, gain, efficiency and nonlinearity prediction with respect to standard large-signal test signals.

Fujaba Days 2011

Fujaba is an Open Source UML CASE tool project started at the software engineering group of Paderborn University in 1997. In 2002 Fujaba has been redesigned and became the Fujaba Tool Suite with a plug-in architecture allowing developers to add functionality easily while retaining full control over their contributions. Multiple Application Domains Fujaba followed the model-driven development philosophy right from its beginning in 1997. At the early days, Fujaba had a special focus on code generation from UML diagrams resulting in a visual programming language with a special emphasis on object structure manipulating rules. Today, at least six rather independent tool versions are under development in Paderborn, Kassel, and Darmstadt for supporting (1) reengineering, (2) embedded real-time systems, (3) education, (4) specification of distributed control systems, (5) integration with the ECLIPSE platform, and (6) MOF-based integration of system (re-) engineering tools. International Community According to our knowledge, quite a number of research groups have also chosen Fujaba as a platform for UML and MDA related research activities. In addition, quite a number of Fujaba users send requests for more functionality and extensions. Therefore, the 8th International Fujaba Days aimed at bringing together Fujaba develop- ers and Fujaba users from all over the world to present their ideas and projects and to discuss them with each other and with the Fujaba core development team.