State diagram design application for EDAG Production Solutions

En este trabajo de fin de grado se presenta el desarrollo realizado de una aplicación de escritorio para la empresa EDAG Production Solutions GmbH & Co. KG, dedicada a implementar soluciones de producción para sus clientes. Dentro de la empresa, los desarrolladores de software del departamento de producción IT emplean distintas herramientas software al trabajar en las diferentes fases que un proyecto requiere, y, como le ocurre a otras empresas, para ciertos casos el mercado no ofrece soluciones accesibles cuando se trata de resolver problemas concretos. En concreto, EDAG Production Solutions GmbH & Co. KG necesita para el departamento de producción IT una aplicación de escritorio para diseñar diagramas que representan el comportamiento de un sistema y que, a partir de este diseño, genere automáticamente una plantilla del diagrama escrito en Java, ya que esta tarea se realiza manualmente y el tiempo de desarrollo de un proyecto se reducirá notablemente con esta herramienta. Actualmente, la empresa no ve adecuadas las soluciones existentes ya que o no son software libre o no permiten generar código a partir de un diagrama de la forma que necesitan. Además, estas herramientas no son intuitivas y demasiado complejas para lo que realmente necesita la empresa, por ello buscan una solución más adecuada a sus necesidades. La aplicación desarrollada como trabajo final de grado permite esta funcionalidad que EDAG Production Solutions GmbH & Co. KG necesita. Además de la importación y exportación de diagramas en formato GraphML. Esta aplicación se ha desarrollado utilizando Angular, un framework para desarrollar aplicaciones web, sobre Electron, un framework de código abierto que permite ejecutar componentes para aplicaciones web en una aplicación de escritorio compatible con los sistemas operativos para ordenador más utilizados

GraphML-SBGN bidirectional converter for metabolic networks.

peer reviewedSystems biology researchers need feasible solutions for editing and visualisation of large biological diagrams. Here, we present the ySBGN bidirectional converter that translates metabolic pathways, developed in the general-purpose yEd Graph Editor (using the GraphML format) into the Systems Biology Graphical Notation Markup Language (SBGN-ML) standard format and vice versa. We illustrate the functionality of this converter by applying it to the translation of the ReconMap resource (available in the SBGN-ML format) to the yEd-specific GraphML and back. The ySBGN tool makes possible to draw extensive metabolic diagrams in a powerful general-purpose graph editor while providing results in the standard SBGN format

Specification and implementation of mapping rule visualization and editing : MapVOWL and the RMLEditor

Visual tools are implemented to help users in defining how to generate Linked Data from raw data. This is possible thanks to mapping languages which enable detaching mapping rules from the implementation that executes them. However, no thorough research has been conducted so far on how to visualize such mapping rules, especially if they become large and require considering multiple heterogeneous raw data sources and transformed data values. In the past, we proposed the RMLEditor, a visual graph-based user interface, which allows users to easily create mapping rules for generating Linked Data from raw data. In this paper, we build on top of our existing work: we (i) specify a visual notation for graph visualizations used to represent mapping rules, (ii) introduce an approach for manipulating rules when large visualizations emerge, and (iii) propose an approach to uniformly visualize data fraction of raw data sources combined with an interactive interface for uniform data fraction transformations. We perform two additional comparative user studies. The first one compares the use of the visual notation to present mapping rules to the use of a mapping language directly, which reveals that the visual notation is preferred. The second one compares the use of the graph-based RMLEditor for creating mapping rules to the form-based RMLx Visual Editor, which reveals that graph-based visualizations are preferred to create mapping rules through the use of our proposed visual notation and uniform representation of heterogeneous data sources and data values. (C) 2018 Elsevier B.V. All rights reserved

gViz, a novel tool for the visualization of co-expression networks

<p>Abstract</p> <p>Background</p> <p>The quantity of microarray data available on the Internet has grown dramatically over the past years and now represents millions of Euros worth of underused information. One way to use this data is through co-expression analysis. To avoid a certain amount of bias, such data must often be analyzed at the genome scale, for example by network representation. The identification of co-expression networks is an important means to unravel gene to gene interactions and the underlying functional relationship between them. However, it is very difficult to explore and analyze a network of such dimensions. Several programs (Cytoscape, yEd) have already been developed for network analysis; however, to our knowledge, there are no available GraphML compatible programs.</p> <p>Findings</p> <p>We designed and developed gViz, a GraphML network visualization and exploration tool. gViz is built on clustering coefficient-based algorithms and is a novel tool to visualize and manipulate networks of co-expression interactions among a selection of probesets (each representing a single gene or transcript), based on a set of microarray co-expression data stored as an adjacency matrix.</p> <p>Conclusions</p> <p>We present here gViz, a software tool designed to visualize and explore large GraphML networks, combining network theory, biological annotation data, microarray data analysis and advanced graphical features.</p

On semantic annotation of decision models

The growth of service sector in recent years has led to renewed research interests in the design and management of service systems. Decision support systems (DSS) play an important role in supporting this endeavor, through management of organizational resources such as models and data, thus forming the “back stage” of service systems. In this article, we identify the requirements for semantically annotating decision models and propose a model representation scheme, termed Semantically Annotated Structure Modeling Markup Language (SA-SMML) that extends Structure Modeling Markup Language (SMML) by incorporating mechanisms for linking semantic models such as ontologies that represent problem domain knowledge concepts. This model representation format is also amenable to a scalable Service-Oriented Architecture (SOA) for managing models in distributed environments. The proposed model representation technique leverages recent advances in the areas of semantic web, and semantic web services. Along with design considerations, we demonstrate the utility of this representation format with an illustrative usage scenarios with a particular emphasis on model discovery and composition in a distributed environment

An XML-based schema definition for model sharing and reuse in a distributed environment

This research leverages the inherent synergy between structured modeling and the eXtensible Markup Language (XML) to facilitate model sharing and reuse in a distributed environment. This is accomplished by providing an XML-based schema definition and two alternative supporting architectures. The XML schema defines a new markup language referred to as the Structured Modeling Markup Language (SMML) for representing models. The schema is based on the structured modeling paradigm as a formalism for conceiving, representing and manipulating a wide variety of models. Overall, SMML and supporting architectures allow different types of models, developed in a variety of modeling platforms to be represented in a standardized format and shared in a distributed environment. The paper demonstrates the proposed SMML through two case studies