A DSL for Defining Instance Templates for the ASMIG System
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Fcastone - FCA file Format Conversion and Interoperability Software
FcaStone - FCA file format conversion and interoperability software Uta Priss Napier University, School of Computing, [email protected] www.upriss.org.uk Abstract. This paper presents FcaStone - a software for FCA file format con- version and interoperability. The paper both describes the features of FcaStone and discusses FCA interoperability issues (such as the specific difficulties en- countered when connecting FCA tools to other tools). The paper ends with a call to the FCA community to develop some sort of standard FCA Interchange For- mat, which could be used for data exchange between stand-alone applications and across the web. 1 Introduction FcaStone1 (named in analogy to ”Rosetta Stone”) is a command-line utility that con- verts between the file formats of commonly-used FCA2 tools (such as ToscanaJ, Con- Exp, Galicia, Colibri3) and between FCA formats and other graph and vector graph- ics formats. The main purpose of FcaStone is to improve the interoperability between FCA, graph editing and vector graphics software. Because it is a command-line tool, FcaStone can easily be incorporated into server-side web applications, which generate concept lattices on demand. FcaStone is open source software and available for down- load from Sourceforge. FcaStone is written in an interpreted language (Perl) and thus platform-independent. Installation on Linux and Apple OS X consists of copying the file to a suitable location. Installation on Windows has also been tested and is also fairly easy. The need for interoperability software was highlighted in discussions among ICCS participants in recent years. Several ICCS authors expressed disappointment with the lack of progress in conceptual structures (CS) research with respect to applications and software (Chein & Genest (2000); Keeler & Pfeiffer (2006)) and with respect to current web developments (Rudolph et al., 2007). -
The Hitchhiker's Guide to Graph Exchange Formats
The Hitchhiker’s Guide to Graph Exchange Formats Prof. Matthew Roughan [email protected] http://www.maths.adelaide.edu.au/matthew.roughan/ Work with Jono Tuke UoA June 4, 2015 M.Roughan (UoA) Hitch Hikers Guide June 4, 2015 1 / 31 Graphs Graph: G(N; E) I N = set of nodes (vertices) I E = set of edges (links) Often we have additional information, e.g., I link distance I node type I graph name M.Roughan (UoA) Hitch Hikers Guide June 4, 2015 2 / 31 Why? To represent data where “connections” are 1st class objects in their own right I storing the data in the right format improves access, processing, ... I it’s natural, elegant, efficient, ... Many, many datasets M.Roughan (UoA) Hitch Hikers Guide June 4, 2015 3 / 31 ISPs: Internode: layer 3 http: //www.internode.on.net/pdf/network/internode-domestic-ip-network.pdf M.Roughan (UoA) Hitch Hikers Guide June 4, 2015 4 / 31 ISPs: Level 3 (NA) http://www.fiberco.org/images/Level3-Metro-Fiber-Map4.jpg M.Roughan (UoA) Hitch Hikers Guide June 4, 2015 5 / 31 Telegraph submarine cables http://en.wikipedia.org/wiki/File:1901_Eastern_Telegraph_cables.png M.Roughan (UoA) Hitch Hikers Guide June 4, 2015 6 / 31 Electricity grid M.Roughan (UoA) Hitch Hikers Guide June 4, 2015 7 / 31 Bus network (Adelaide CBD) M.Roughan (UoA) Hitch Hikers Guide June 4, 2015 8 / 31 French Rail http://www.alleuroperail.com/europe-map-railways.htm M.Roughan (UoA) Hitch Hikers Guide June 4, 2015 9 / 31 Protocol relationships M.Roughan (UoA) Hitch Hikers Guide June 4, 2015 10 / 31 Food web M.Roughan (UoA) Hitch Hikers -
An Exchange Format for Graph Transformation Systems
Electronic Notes in Theoretical Computer Science 127 (2005) 51–63 www.elsevier.com/locate/entcs A New Version of GTXL : An Exchange Format for Graph Transformation Systems Leen Lambers Institut f¨ur Softwaretechnik und Theoretische Informatik Technische Universit¨at Berlin Germany Abstract GTXL (Graph Transformation Exchange Language) is designed to support and stimulate develop- ers to provide their graph transformation-based tools with an exchange functionality regarding the integration with other tools. For this exchange XML was chosen as underlying technology. The exchange of graphs is facilitated by the exchange format GXL which is also XML-based. GTXL uses GXL to describe the graph parts of a graph transformation system. A first version of GTXL arose from the format discussion within the EU Working Group APPLIGRAPH. Trying to restim- ulate the discussion on a common exchange format for graph transformation systems, this paper presents a new version of GTXL. Three important changes have been made. At first, an integrated presentation of rules is introduced, secondly the expression of more general conditions is supported and finally the storage of the underlying semantics of a graph transformation system by means of special attributes is proposed. Keywords: exchange format, graph transformation system, graph transformation-based tools, XML 1 Introduction Graph transformation systems (GTSs) comprise graphs and rules changing these graphs. Comparing them with term rewrite systems, terms correspond to graphs and term rewrite rules to graph rewrite rules. Since graphs are widely used to model various data structures in computer science, graph trans- formation systems can be used to define various modifications of these data 1 Email: [email protected] 1571-0661/$ – see front matter © 2005 Elsevier B.V. -
An XML-Based Description of Structured Networks
Massimo Ancona, Walter Cazzola, Sara Drago, and Francesco Guido. An XML-Based Description of Structured Networks. In Proceedings of Interna- tional Conference Communications 2004, pages 401–406, Bucharest, Romania, June 2004. IEEE Press. An XML-Based Description of Structured Networks Massimo Ancona£ Walter Cazzola† Sara Drago£ Francesco Guido‡ £ DISI University of Genova, e-mail: fancona,[email protected] † DICo University of Milano, e-mail: [email protected] ‡ Marconi Selenia Communication, e-mail: [email protected] Abstract In this paper we present an XML-based formalism to describe hierarchically organized communication networks. After a short overview of existing graph description languages, we discuss the advantages and disadvantages of their application in network optimization. We conclude by extending one of these formalisms with features supporting the description of the relationship between the optimized logical layout of a network and its physical counterpart. Elements for describing traffic parameters are also given. 1 Introduction The problem of network design and optimization has a strategical importance especially for military networks. In this case, design for fault tolerance and security plays a role more and more crucial than the equivalent importance required for commercial and research networks. The reengineering of a large communication network is a complex problem, which consists of different aspects that can be strongly affected by the way of describing data. The plainest way to describe a communication network is to model the relationship among sites and links by means of a weighted undirected graph, but unless some more assumptions are taken, this approach can raise several problems. A first issue is encountered when an analysis and a visualization of the network has to be realized: practical networks include hundreds or often thousands of nodes and links, so that even a simple description and documentation of the network structure is hard to maintain and update. -
Rendering UML Class Diagrams to Support Layout Design
Rendering UML Class Diagrams to Support Layout Design A thesis submitted to the Kent State University Honors College in partial fulfillment of the requirements for University Honors by Paul “P.J.” Leyden December, 2019 Thesis written by Paul “P.J.” Leyden Approved by _______________________________________________________________________, Advisor _____________________________________________, Chair, Department of Computer Science Accepted by ___________________________________________________________, Dean, Honors College ii TABLE OF CONTENTS LIST OF FIGURES ........................................................................................................... iv LIST OF TABLES .............................................................................................................. v Acknowledgements ............................................................................................................ vi CHAPTER 1 Introduction................................................................................................... 1 CHAPTER 2 Related Work ................................................................................................ 4 2.1 UML .......................................................................................................................... 4 2.2 Comprehension and Layout ...................................................................................... 5 2.3 Automatically Reverse Engineering UML Class Diagrams ..................................... 7 2.4 srcUML .................................................................................................................... -
Bioinformatics Methods for the Genetic and Molecular Characterisation Of
BIOINFORMATICS METHODSFORTHE GENETICAND MOLECULAR CHARACTERISATION OFCANCER Dissertation zur Erlangung des Grades des Doktors der Naturwissenschaften der Naturwissenschaftlich-Technischen Fakultäten der Universität des Saarlandes vo n DANIELSTÖCKEL Universität des Saarlandes, MI – Fakultät für Mathematik und Informatik, Informatik b e t r e u e r PROF.DR.HANS-PETERLENHOF 6. dezember 2016 Daten der Verteidigung Datum 25.11.2016, 15 Uhr ct. Vorsitzender Prof. Dr. Volkhard Helms Erstgutachter Prof. Dr. Hans-Peter Lenhof Zweitgutachter Prof. Dr. Andreas Keller Beisitzerin Dr. Christina Backes Dekan Prof. Dr. Frank-Olaf Schreyer This thesis is also available online at: https://somweyr.de/~daniel/ dissertation.zip ii a b s t r ac t Cancer is a class of complex, heterogeneous diseases of which many types have proven to be difficult to treat due to the high ge- netic variability between and within tumours. To improve ther- apy, some cases require a thorough genetic and molecular charac- terisation that allows to identify mutations and pathogenic pro- cesses playing a central role for the development of the disease. Data obtained from modern, biological high-throughput exper- iments can offer valuable insights in this regard. Therefore, we developed a range of interoperable approaches that support the analysis of high-throughput datasets on multiple levels of detail. Mutations are a main driving force behind the development of cancer. To assess their impact on an affected protein, we de- signed BALL-SNP which allows to visualise and analyse single nucleotide variants in a structure context. For modelling the ef- fect of mutations on biological processes we created CausalTrail which is based on causal Bayesian networks and the do-calculus. -
Compiler Support for Operator Overloading and Algorithmic Differentiation in C++
Compiler Support for Operator Overloading and Algorithmic Differentiation in C++ Zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr.rer.nat.) genehmigte Dissertation von Alexander Hück, M.Sc. aus Wiesbaden Tag der Einreichung: 16.01.2020, Tag der Prüfung: 28.02.2020 1. Gutachten: Prof. Dr. Christian Bischof 2. Gutachten: Prof. Dr. Martin Bücker Darmstadt – D 17 Computer Science Department Scientific Computing Compiler Support for Operator Overloading and Algorithmic Differentiation in C++ Doctoral thesis by Alexander Hück, M.Sc. 1. Review: Prof. Dr. Christian Bischof 2. Review: Prof. Dr. Martin Bücker Date of submission: 16.01.2020 Date of thesis defense: 28.02.2020 Darmstadt – D 17 Bitte zitieren Sie dieses Dokument als: URN: urn:nbn:de:tuda-tuprints-115226 URL: http://tuprints.ulb.tu-darmstadt.de/11522 Dieses Dokument wird bereitgestellt von tuprints, E-Publishing-Service der TU Darmstadt http://tuprints.ulb.tu-darmstadt.de [email protected] Die Veröffentlichung steht unter folgender Creative Commons Lizenz: Namensnennung – Keine Bearbeitungen 4.0 International (CC BY–ND 4.0) The publication is under the following Creative Commons license: Attribution – NoDerivatives 4.0 International (CC BY–ND 4.0) Erklärungen laut Promotionsordnung §8 Abs. 1 lit. c PromO Ich versichere hiermit, dass die elektronische Version meiner Dissertation mit der schriftli- chen Version übereinstimmt. §8 Abs. 1 lit. d PromO Ich versichere hiermit, dass zu einem vorherigen Zeitpunkt noch keine Promotion versucht wurde. In diesem Fall sind nähere Angaben über Zeitpunkt, Hochschule, Dissertationsthe- ma und Ergebnis dieses Versuchs mitzuteilen. §9 Abs. 1 PromO Ich versichere hiermit, dass die vorliegende Dissertation selbstständig und nur unter Verwendung der angegebenen Quellen verfasst wurde. -
Drawing Graphs with Graphviz
Drawing graphs with Graphviz Emden R. Gansner June 11, 2012 1 Graphviz Drawing Library Manual, June 11, 2012 2 Contents 1 Introduction 3 1.1 String-based layouts . 3 1.1.1 dot . 4 1.1.2 xdot . 4 1.1.3 plain . 5 1.1.4 plain-ext . 6 1.1.5 GXL and GML . 6 1.2 Graphviz as a library . 6 2 Basic graph drawing 7 2.1 Creating the graph . 7 2.1.1 Attributes . 9 2.2 Laying out the graph . 15 2.3 Rendering the graph . 15 2.3.1 Drawing nodes and edges . 17 2.4 Cleaning up a graph . 18 3 Inside the layouts 19 3.1 dot ............................................... 19 3.2 neato ............................................. 20 3.3 fdp ............................................... 21 3.4 twopi ............................................. 22 3.5 circo .............................................. 22 4 The Graphviz context 22 4.1 Application-specific data . 24 5 Graphics renderers 24 5.1 The GVJ t data structure . 27 5.2 Inside the obj state t data structure . 28 5.3 Color information . 29 6 Adding Plug-ins 30 6.1 Writing a renderer plug-in . 32 6.2 Writing a device plug-in . 33 6.3 Writing an image loading plug-in . 33 7 Unconnected graphs 34 A Compiling and linking 40 B A sample program: simple.c 41 C A sample program: dot.c 42 D A sample program: demo.c 43 E Some basic types and their string representations 44 Graphviz Drawing Library Manual, June 11, 2012 3 1 Introduction The Graphviz package consists of a variety of software for drawing attributed graphs. -
An Open Toolkit for Prototyping Reverse Engineering Visualizations
Joint EUROGRAPHICS - IEEE TCVG Symposium on Visualization (2002) D. Ebert, P. Brunet, I. Navazo (Editors) An Open Toolkit for Prototyping Reverse Engineering Visualizations Alexandru Telea1, Alessandro Maccari2, Claudio Riva2 1 Department of Mathematics and Computer Science Eindhoven University of Technology, The Netherlands [email protected] 2 Software Technology Laboratory Nokia Research Center, Helsinki, Finland alessandro.maccari, [email protected] Abstract Maintenance and evolution of complex software systems (such as mobile telephones) involves activities such as reverse engineering (RE) and software visualization. Although several RE tools exist, we found their architecture hard to adapt to the domain and problem specific requirements posed by our current practice in Nokia. In this paper, we present an open architecture which allows easy prototyping of RE data exploration and visualization scenarios for a large range of domain models. We pay special attention to the visual and interactive requirements of the reverse engineering process. We compare our toolkit with other existing reverse engineering visual tools and outline the differences. 1. Introduction to easily integrate program analysis with visualization facil- ities. Reverse engineering (RE) 15 22 20 is an essential part of To address the above problems, we propose an open soft- maintenance and evolution of complex software systems, ware toolkit for RE tools. Our first aim is easy prototyping of that involves several tasks such as program analysis 15, plan RE data exploration scenarios by combining and customiz- recognition 11, redocumentation 20, and architecture recov- ing existing software components and writing new ones. The ery 20 22. Overall, these tasks can be reduced to two generic presented toolkit accommodates a large range of RE data operations: construction of a layered program representation types, operations, and application scenarios. -
Lesson 8 Graph Visual Analytics: Visualising and Analysing Network Data
ISSS608 Visual Analytics and Applications 10/14/2016 Lesson 8: Visualising and Analysing Network Data Lesson 8 Graph Visual Analytics: Visualising and Analysing Network Data Mentor: Dr. Kam Tin Seong Associate Professor of Information Systems (Practice) School of Information Systems, Singapore Management University Content • Introduction to Graph Visual Analytics • Graph Visualisation in Actions • Basic Principles of Graph – Network data sets – Graph data format • Network Visualisation and Analysis – Network visualisation and analysis process model – Graph layouts and visual attributes – Network metrics • Network visualisation and analysis tools – NodeXL – Gephi 2 8-1 ISSS608 Visual Analytics and Applications 10/14/2016 Lesson 8: Visualising and Analysing Network Data Network in real World • Physical – Transportation (i.e. road, port, rail, etc) – Utility (electricity, water, gas, network cable, etc) – Natural (river, etc) • Abstract – Social media (i.e. e-mail, Facebook, Twitter, Wikipedia, etc) – Organisation (i.e. NGO, politics, customer-company, staff-to-staff, criminal, terrorist, disease, etc) 3 Classical Graph Theory • The Seven Bridges of Königsberg is a historically notable problem in mathematics. Its negative resolution by Leonhard Euler in 1735 laid the foundations of graph theory and prefigured the idea of topology. Source: http://en.wikipedia.org/wiki/Seven_Bridges_of_K%C3%B6nigsberg 4 8-2 ISSS608 Visual Analytics and Applications 10/14/2016 Lesson 8: Visualising and Analysing Network Data Classical Graph Visualisation and -
Hypergraph October 5, 2010
hypergraph October 5, 2010 DirectedHyperedge-class Class DirectedHyperedge Description This class represents directed hyperedges in a Hypergraph-class. A directed hyperedge con- sists of two disjount sets of nodes, those in the tail and those in the head of the hyperedge. Directed hyperedges are sometimes called hyperarcs. Objects from the Class Objects can be created by calls of the form new("DirectedHyperedge", head, tail, label). You can also use the convenience function DirectedHyperedge. Slots tail: Character vector of nodes in the tail of the hyperedge head: Character vector of nodes in the head of the hyperege label: Character string describing the directed hyperedge Extends Class "Hyperedge", directly. Methods head signature(.Object = "DirectedHyperedge"): Return a vector containing the nodes in the head of the hyperedge tail signature(.Object = "DirectedHyperedge"): Return a vector containing the nodes in the tail of the hyperedge initialize signature(.Object = "DirectedHyperedge"): Create a new instance. nodes signature(object = "DirectedHyperedge"): Return a vector containing all nodes present in the hyperedge. show signature(object = "DirectedHyperedge"): Print me toUndirected signature(.Object = "DirectedHyperedge"): Return a Hyperedge- class object that results from coercing to an undirected hyperedge. 1 2 DirectedHyperedge Author(s) Seth Falcon See Also DirectedHyperedge Hyperedge Hyperedge-class Hypergraph-class Examples head <- LETTERS[1:4] tail <- LETTERS[19:21] label <- "Directed hyperedge" dhe <- new("DirectedHyperedge", -
GOLD 3 Un Lenguaje De Programación Imperativo Para La Manipulación De Grafos Y Otras Estructuras De Datos
GOLD 3 Un lenguaje de programación imperativo para la manipulación de grafos y otras estructuras de datos Autor Alejandro Sotelo Arévalo UNIVERSIDAD DE LOS ANDES Asesora Silvia Takahashi Rodríguez, Ph.D. UNIVERSIDAD DE LOS ANDES TESIS DE MAESTRÍA EN INGENIERÍA DEPARTAMENTO DE INGENIERÍA DE SISTEMAS Y COMPUTACIÓN FACULTAD DE INGENIERÍA UNIVERSIDAD DE LOS ANDES BOGOTÁ D.C., COLOMBIA ENERO 27 DE 2012 > > > A las personas que más quiero en este mundo: mi madre Gladys y mi novia Alexandra. > > > Abstract Para disminuir el esfuerzo en la programación de algoritmos sobre grafos y otras estructuras de datos avanzadas es necesario contar con un lenguaje de propósito específico que se preocupe por mejorar la legibilidad de los programas y por acelerar el proceso de desarrollo. Este lenguaje debe mezclar las virtudes del pseudocódigo con las de un lenguaje de alto nivel como Java o C++ para que pueda ser fácilmente entendido por un matemático, por un científico o por un ingeniero. Además, el lenguaje debe ser fácilmente interpretado por las máquinas y debe poder competir con la expresividad de los lenguajes de propósito general. GOLD (Graph Oriented Language Domain) satisface este objetivo, siendo un lenguaje de propósito específico imperativo lo bastante cercano al lenguaje utilizado en el texto Introduction to Algorithms de Thomas Cormen et al. [1] como para ser considerado una especie de pseudocódigo y lo bastante cercano al lenguaje Java como para poder utilizar la potencia de su librería estándar y del entorno de programación Eclipse. Índice general I Preliminares 1 1 Introducción 2 1.1 Resumen ............................................... 2 1.2 Contexto...............................................