AccuSyn: Using Simulated Annealing to Declutter Genome Visualizations

We apply Simulated Annealing, a well-known metaheuristic for obtaining near-optimal solutions to optimization problems, to discover conserved synteny relations (similar features) in genomes. The analysis of synteny gives biologists insights into the evolutionary history of species and the functional relationships between genes. However, as even simple organisms have huge numbers of genomic features, syntenic plots initially present an enormous clutter of connections, making the structure difficult to understand. We address this problem by using Simulated Annealing to minimize link crossings. Our interactive web-based synteny browser, AccuSyn, visualizes syntenic relations with circular plots of chromosomes and draws links between similar blocks of genes. It also brings together a huge amount of genomic data by integrating an adjacent view and additional tracks, to visualize the details of the blocks and accompanying genomic data, respectively. Our work shows multiple ways to manually declutter a synteny plot and then thoroughly explains how we integrated Simulated Annealing, along with human interventions as a human-in-the-loop approach, to achieve an accurate representation of conserved synteny relations for any genome. The goal of AccuSyn was to make a fairly complete tool combining ideas from four major areas: genetics, information visualization, heuristic search, and human-in-the-loop. Our results contribute to a better understanding of synteny plots and show the potential that decluttering algorithms have for syntenic analysis, adding more clues for evolutionary development. At this writing, AccuSyn is already actively used in the research being done at the University of Saskatchewan and has already produced a visualization of the recently-sequenced Wheat genome

Automatic generation of software interfaces for supporting decisionmaking processes. An application of domain engineering & machine learning

[EN] Data analysis is a key process to foster knowledge generation in particular domains or fields of study. With a strong informative foundation derived from the analysis of collected data, decision-makers can make strategic choices with the aim of obtaining valuable benefits in their specific areas of action. However, given the steady growth of data volumes, data analysis needs to rely on powerful tools to enable knowledge extraction. Information dashboards offer a software solution to analyze large volumes of data visually to identify patterns and relations and make decisions according to the presented information. But decision-makers may have different goals and, consequently, different necessities regarding their dashboards. Moreover, the variety of data sources, structures, and domains can hamper the design and implementation of these tools. This Ph.D. Thesis tackles the challenge of improving the development process of information dashboards and data visualizations while enhancing their quality and features in terms of personalization, usability, and flexibility, among others. Several research activities have been carried out to support this thesis. First, a systematic literature mapping and review was performed to analyze different methodologies and solutions related to the automatic generation of tailored information dashboards. The outcomes of the review led to the selection of a modeldriven approach in combination with the software product line paradigm to deal with the automatic generation of information dashboards. In this context, a meta-model was developed following a domain engineering approach. This meta-model represents the skeleton of information dashboards and data visualizations through the abstraction of their components and features and has been the backbone of the subsequent generative pipeline of these tools. The meta-model and generative pipeline have been tested through their integration in different scenarios, both theoretical and practical. Regarding the theoretical dimension of the research, the meta-model has been successfully integrated with other meta-model to support knowledge generation in learning ecosystems, and as a framework to conceptualize and instantiate information dashboards in different domains. In terms of the practical applications, the focus has been put on how to transform the meta-model into an instance adapted to a specific context, and how to finally transform this later model into code, i.e., the final, functional product. These practical scenarios involved the automatic generation of dashboards in the context of a Ph.D. Programme, the application of Artificial Intelligence algorithms in the process, and the development of a graphical instantiation platform that combines the meta-model and the generative pipeline into a visual generation system. Finally, different case studies have been conducted in the employment and employability, health, and education domains. The number of applications of the meta-model in theoretical and practical dimensions and domains is also a result itself. Every outcome associated to this thesis is driven by the dashboard meta-model, which also proves its versatility and flexibility when it comes to conceptualize, generate, and capture knowledge related to dashboards and data visualizations

Illustrating the Benefits of Openness: A Large-Scale Spatial Economic Dispatch Model Using the Julia Language

In this paper we introduce a five-fold approach to open science comprised of open data, open-source software (that is, programming and modeling tools, model code, and numerical solvers), as well as open-access dissemination. The advantages of open energy models are being discussed. A fully open-source bottom-up electricity sector model with high spatial resolution using the Julia programming environment is then being developed, describing source code and a data set for Germany. This large-scale model of the electricity market includes both generation dispatch from thermal and renewable sources in the spot market as well as the physical transmission network, minimizing total system costs in a linear approach. It calculates the economic dispatch on an hourly basis for a full year, taking into account demand, infeed from renewables, storage, and exchanges with neighboring countries. Following the open approach, the model code and used data set are fully publicly accessible and we use open-source solvers like ECOS and CLP. The model is then being benchmarked regarding runtime of building and solving against a representation in GAMS as a commercial algebraic modeling language and against Gurobi, CPLEX, and Mosek as commercial solvers. With this paper we demonstrate in a proof-of-concept the power and abilities, as well as the beauty of open-source modeling systems. This openness has the potential to increase the transparency of policy advice and to empower stakeholders with fewer financial possibilities.BMWi, 03ET4028A, Verbundvorhaben: Langfristige Planung und kurzfristige Optimierung des Elektrizitätssystems in Deutschland im europäischen Kontext, Teilvorhaben: Langfristige Planung des Übertragungsnetzes in Deutschland unter Berücksichtigung der Interpendenzen zur Erzeugungsplanung, sowie zum Wärme- und Gassektor

Methods and Tools for Management of Distributed Event Processing Applications

Die Erfassung und Verarbeitung von Ereignissen aus cyber-physischen Systemen bietet Anwendern die Möglichkeit, kontinuierlich über Leistungsdaten und aufkommende Probleme unterrichtet zu werden (Situational Awareness) oder Wartungsprozesse zustandsabhängig zu optimieren (Condition-based Maintenance). Derartige Szenarien verlangen aufgrund der Vielzahl und Frequenz der Daten sowie der Anforderung einer echtzeitnahen Auswertung den Einsatz geeigneter Technologien. Unter dem Namen Event Processing haben sich dabei Technologien etabliert, die in der Lage sind, Datenströme in Echtzeit zu verarbeiten und komplexe Ereignismuster auf Basis räumlicher, zeitlicher oder kausaler Zusammenhänge zu erkennen. Gleichzeitig sind heute in diesem Bereich verfügbare Systeme jedoch noch durch eine hohe technische Komplexität der zugrunde liegenden deklarativen Sprachen gekennzeichnet, die bei der Entwicklung echtzeitfähiger Anwendungen zu langsamen Entwicklungszyklen aufgrund notwendiger technischer Expertise führt. Gerade diese Anwendungen weisen allerdings häufig eine hohe Dynamik in Bezug auf Veränderungen von Anforderungen der zu erkennenden Situationen, aber auch der zugrunde liegenden Sensordaten hinsichtlich ihrer Syntax und Semantik auf. Der primäre Beitrag dieser Arbeit ermöglicht Fachanwendern durch die Abstraktion von technischen Details, selbständig verteilte echtzeitfähige Anwendungen in Form von sogenannten Echtzeit-Verarbeitungspipelines zu erstellen, zu bearbeiten und auszuführen. Die Beiträge der Arbeit lassen sich wie folgt zusammenfassen: 1. Eine Methodik zur Entwicklung echtzeitfähiger Anwendungen unter Berücksichtigung von Erweiterbarkeit sowie der Zugänglichkeit für Fachanwender. 2. Modelle zur semantischen Beschreibung der Charakteristika von Ereignisproduzenten, Ereignisverarbeitungseinheiten und Ereigniskonsumenten. 3. Ein System zur Ausführung von Verarbeitungspipelines bestehend aus geographisch verteilten Ereignisverarbeitungseinheiten. 4. Ein Software-Artefakt zur graphischen Modellierung von Verarbeitungspipelines sowie deren automatisierter Ausführung. Die Beiträge werden in verschiedenen Szenarien aus den Bereichen Produktion und Logistik vorgestellt, angewendet und evaluiert

The Strucplot Framework: Visualizing Multi-way

This paper describes the “strucplot” framework for the visualization of multi-way contingency tables. Strucplot displays include hierarchical conditional plots such as mosaic, association, and sieve plots, and can be combined into more complex, specialized plots for visualizing conditional independence, GLMs, and the results of independence tests. The framework’s modular design allows flexible customization of the plots’ graphical appearance, including shading, labeling, spacing, and legend, by means of “graphical appearance control” functions. The framework is provided by the R package vcd

Epiviz: Integrative Visual Analysis Software for Genomics

Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling of a small number of moderately sized datasets. Workflows that involve the integration and exploration of multiple heterogeneous data sources, small and large, public and user specific have been poorly addressed by these tools. Commonly, the data visualized in these tools is the output of analyses performed in powerful computing environments like R/Bioconductor or Python. Two essential aspects of data analysis are usually treated as distinct, in spite of being part of the same exploratory process: algorithmic analysis and interactive visualization. In current technologies these are not integrated within one tool, but rather, one precedes the other. Recent technological advances in web-based data visualization have made it possible for interactive visualization tools to tightly integrate with powerful algorithmic tools, without being restricted to one such tool in particular. We introduce Epiviz (http://epiviz.cbcb.umd.edu), an integrative visualization tool that bridges the gap between the two types of tools, simplifying genomic data analysis workflows. Epiviz is the first genomics interactive visualization tool to provide tight-knit integration with computational and statistical modeling and data analysis. We discuss three ways in which Epiviz advances the field of genomic data analysis: 1) it brings code to interactive visualizations at various different levels; 2) takes the first steps in the direction of collaborative data analysis by incorporating user plugins from source control providers, as well as by allowing analysis states to be shared among the scientific community; 3) combines established analysis features that have never before been available simultaneously in a visualization tool for genomics. Epiviz can be used in multiple branches of genomics data analysis for various types of datasets, of which we detail two: functional genomics data, aligned to a continuous coordinate such as the genome, and metagenomics, organized according to volatile hierarchical coordinate spaces. We also present security implications of the current design, performance benchmarks, a series of limitations and future research steps

Digital Humanities and Libraries and Archives in Religious Studies

How are digital humanists drawing on libraries and archives to advance research in the field of religious studies and theology? How can librarians and archivists make their collections accessible in return? This volume showcases the perspectives of faculty, librarians, archivists, and allied cultural heritage professionals who are drawing on primary and secondary sources in innovative ways to create digital humanities projects in the field