The Open Graph Drawing Framework (OGDF)
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Network Monitoring & Management Using Cacti
Network Monitoring & Management Using Cacti Network Startup Resource Center www.nsrc.org These materials are licensed under the Creative Commons Attribution-NonCommercial 4.0 International license (http://creativecommons.org/licenses/by-nc/4.0/) Introduction Network Monitoring Tools Availability Reliability Performance Cact monitors the performance and usage of devices. Introduction Cacti: Uses RRDtool, PHP and stores data in MySQL. It supports the use of SNMP and graphics with RRDtool. “Cacti is a complete frontend to RRDTool, it stores all of the necessary information to create graphs and populate them with data in a MySQL database. The frontend is completely PHP driven. Along with being able to maintain Graphs, Data Sources, and Round Robin Archives in a database, cacti handles the data gathering. There is also SNMP support for those used to creating traffic graphs with MRTG.” Introduction • A tool to monitor, store and present network and system/server statistics • Designed around RRDTool with a special emphasis on the graphical interface • Almost all of Cacti's functionality can be configured via the Web. • You can find Cacti here: http://www.cacti.net/ Getting RRDtool • Round Robin Database for time series data storage • Command line based • From the author of MRTG • Made to be faster and more flexible • Includes CGI and Graphing tools, plus APIs • Solves the Historical Trends and Simple Interface problems as well as storage issues Find RRDtool here:http://oss.oetiker.ch/rrdtool/ RRDtool Database Format General Description 1. Cacti is written as a group of PHP scripts. 2. The key script is “poller.php”, which runs every 5 minutes (by default). -
Munin Documentation Release 2.0.44
Munin Documentation Release 2.0.44 Stig Sandbeck Mathisen <[email protected]> Dec 20, 2018 Contents 1 Munin installation 3 1.1 Prerequisites.............................................3 1.2 Installing Munin...........................................4 1.3 Initial configuration.........................................7 1.4 Getting help.............................................8 1.5 Upgrading Munin from 1.x to 2.x..................................8 2 The Munin master 9 2.1 Role..................................................9 2.2 Components.............................................9 2.3 Configuration.............................................9 2.4 Other documentation.........................................9 3 The Munin node 13 3.1 Role.................................................. 13 3.2 Configuration............................................. 13 3.3 Other documentation......................................... 13 4 The Munin plugin 15 4.1 Role.................................................. 15 4.2 Other documentation......................................... 15 5 Documenting Munin 21 5.1 Nomenclature............................................ 21 6 Reference 25 6.1 Man pages.............................................. 25 6.2 Other reference material....................................... 40 7 Examples 43 7.1 Apache virtualhost configuration.................................. 43 7.2 lighttpd configuration........................................ 44 7.3 nginx configuration.......................................... 45 7.4 Graph aggregation -
Automatic Placement of Authorization Hooks in the Linux Security Modules Framework
Automatic Placement of Authorization Hooks in the Linux Security Modules Framework Vinod Ganapathy [email protected] University of Wisconsin, Madison Joint work with Trent Jaeger Somesh Jha [email protected] [email protected] Pennsylvania State University University of Wisconsin, Madison Context of this talk Authorization policies and their enforcement Three concepts: Subjects (e.g., users, processes) Objects (e.g., system resources) Security-sensitive operations on objects. Authorization policy: A set of triples: (Subject, Object, Operation) Key question: How to ensure that the authorization policy is enforced? CCS 2005 Automatic Placement of Authorization Hooks in the Linux Security Modules Framework 2 Enforcing authorization policies Reference monitor consults the policy. Application queries monitor at appropriate locations. Can I perform operation OP? Reference Monitor Application to Policy be secured Yes/No (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) CCS 2005 Automatic Placement of Authorization Hooks in the Linux Security Modules Framework 3 Linux security modules framework Framework for authorization policy enforcement. Uses a reference monitor-based architecture. Integrated into Linux-2.6 Linux Kernel Reference Monitor Policy (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) CCS 2005 Automatic Placement of Authorization Hooks in the Linux Security Modules Framework 4 Linux security modules framework Reference monitor calls (hooks) placed appropriately in the Linux kernel. Each hook is an authorization query. Linux Kernel Reference Monitor Policy (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) Hooks CCS 2005 Automatic Placement of Authorization Hooks in the Linux Security Modules Framework 5 Linux security modules framework Authorization query of the form: (subj., obj., oper.)? Kernel performs operation only if query succeeds. -
Masked Graph Modeling for Molecule Generation ✉ Omar Mahmood 1, Elman Mansimov2, Richard Bonneau 3 & Kyunghyun Cho 2
ARTICLE https://doi.org/10.1038/s41467-021-23415-2 OPEN Masked graph modeling for molecule generation ✉ Omar Mahmood 1, Elman Mansimov2, Richard Bonneau 3 & Kyunghyun Cho 2 De novo, in-silico design of molecules is a challenging problem with applications in drug discovery and material design. We introduce a masked graph model, which learns a dis- tribution over graphs by capturing conditional distributions over unobserved nodes (atoms) and edges (bonds) given observed ones. We train and then sample from our model by iteratively masking and replacing different parts of initialized graphs. We evaluate our 1234567890():,; approach on the QM9 and ChEMBL datasets using the GuacaMol distribution-learning benchmark. We find that validity, KL-divergence and Fréchet ChemNet Distance scores are anti-correlated with novelty, and that we can trade off between these metrics more effec- tively than existing models. On distributional metrics, our model outperforms previously proposed graph-based approaches and is competitive with SMILES-based approaches. Finally, we show our model generates molecules with desired values of specified properties while maintaining physiochemical similarity to the training distribution. 1 Center for Data Science, New York University, New York, NY, USA. 2 Department of Computer Science, Courant Institute of Mathematical Sciences, New ✉ York, NY, USA. 3 Center for Genomics and Systems Biology, New York University, New York, NY, USA. email: [email protected] NATURE COMMUNICATIONS | (2021) 12:3156 | https://doi.org/10.1038/s41467-021-23415-2 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-021-23415-2 he design of de novo molecules in-silico with desired prop- enable more informative comparisons between models that use Terties is an essential part of drug discovery and materials different molecular representations. -
Algorithms for Graph Visualization Flow Methods: Orthogonal Layout
Algorithms for Graph Visualization Flow Methods: Orthogonal Layout INSTITUT FUR¨ THEORETISCHE INFORMATIK · FAKULTAT¨ FUR¨ INFORMATIK Tamara Mchedlidze 18.01.2018 1 Dr. Tamara Mchedlidze · Algorithmen zur Visualisierung von Graphen Flussmethoden: orthogonales Graphenzeichnen Orthogonal Layout • Edges consist of vertical and horizontal segments • Applied in many areas ER diagram in OGDF UML diagram by Oracle Organigram of HS Limburg Circuit diagram by Jeff Atwood 2 - 1 Dr. Tamara Mchedlidze · Algorithmen zur Visualisierung von Graphen Flussmethoden: orthogonales Graphenzeichnen Orthogonal Layout • Edges consist of vertical and horizontal segments • Applied in many areas Aesthetic functions? ER diagram in OGDF UML diagram by Oracle Organigram of HS Limburg Circuit diagram by Jeff Atwood 2 - 2 Dr. Tamara Mchedlidze · Algorithmen zur Visualisierung von Graphen Flussmethoden: orthogonales Graphenzeichnen Orthogonal Layout • Edges consist of vertical and horizontal segments • Applied in many areas Aesthetic functions: • number of bends • length of edges • ER diagram in OGDF width, height, area • monotonicity of edges UML diagram by Oracle • ... Organigram of HS Limburg Circuit diagram by Jeff Atwood 2 - 3 Dr. Tamara Mchedlidze · Algorithmen zur Visualisierung von Graphen Flussmethoden: orthogonales Graphenzeichnen (Planar) Orthogonal Drawings Three-step approach: Topology { Shape { Metrics [Tamassia SIAM J. Comput. 1987] V = fv1; v2; v3; v4g E = fv1v2; v1v3; v1v4; v2v3; v2v4g 3 - 1 Dr. Tamara Mchedlidze · Algorithmen zur Visualisierung von Graphen Flussmethoden: orthogonales Graphenzeichnen (Planar) Orthogonal Drawings Three-step approach: Topology { Shape { Metrics [Tamassia SIAM J. Comput. 1987] V = fv1; v2; v3; v4g E = fv1v2; v1v3; v1v4; v2v3; v2v4g combinatorial embedding/ planarization 4 3 Reduce Crossings 2 1 3 - 2 Dr. Tamara Mchedlidze · Algorithmen zur Visualisierung von Graphen Flussmethoden: orthogonales Graphenzeichnen (Planar) Orthogonal Drawings Three-step approach: Topology { Shape { Metrics [Tamassia SIAM J. -
Graph Drawing Dagstuhl Seminar
05191 Abstracts Collection Graph Drawing Dagstuhl Seminar Michael Jünger1, Stephen Kobourov2 and Petra Mutzel3 1 Univ. of Köln, DE 2 Univ. of Arizona, US [email protected] 3 Univ. of Dortmund, DE [email protected] Abstract. From 08.05. to 13.05.05, the Dagstuhl Seminar 05191 Graph Drawing was held in the International Conference and Research Cen- ter (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The rst section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available. Keywords. Graph Drawing, Visualization, Layout Algorithms, Inter- active Visualization 05191 Executive Summary Graph Drawing This paper summarizes the topics, aims, and achievements of the Dagstuhl Sem- inar 05191 on Graph Drawing. Keywords: Graph drawing Joint work of: Jünger, Michael; Kobourov, Stephen; Mutzel, Petra Full Paper: http://drops.dagstuhl.de/opus/volltexte/2006/342 05191 Open Problem Session Report This is a report on an informal session intended to stimulate communication and sharing of problems. Hence the attributions and citations may contain inaccu- racies, and are certainly not complete. Keywords: Open problems, graph drawing Joint work of: Whitesides, Sue Full Paper: http://drops.dagstuhl.de/opus/volltexte/2006/338 Dagstuhl Seminar Proceedings 05191 Graph Drawing http://drops.dagstuhl.de/opus/volltexte/2006/348 2 M. Jünger, S. Kobourov and P. Mutzel Matrix Zoom: A Visual Interface to Semi-external Graphs James Abello (Rutgers Univ. -
Operational Semantics with Hierarchical Abstract Syntax Graphs*
Operational Semantics with Hierarchical Abstract Syntax Graphs* Dan R. Ghica Huawei Research, Edinburgh University of Birmingham, UK This is a motivating tutorial introduction to a semantic analysis of programming languages using a graphical language as the representation of terms, and graph rewriting as a representation of reduc- tion rules. We show how the graphical language automatically incorporates desirable features, such as a-equivalence and how it can describe pure computation, imperative store, and control features in a uniform framework. The graph semantics combines some of the best features of structural oper- ational semantics and abstract machines, while offering powerful new methods for reasoning about contextual equivalence. All technical details are available in an extended technical report by Muroya and the author [11] and in Muroya’s doctoral dissertation [21]. 1 Hierarchical abstract syntax graphs Before proceeding with the business of analysing and transforming the source code of a program, a com- piler first parses the input text into a sequence of atoms, the lexemes, and then assembles them into a tree, the Abstract Syntax Tree (AST), which corresponds to its grammatical structure. The reason for preferring the AST to raw text or a sequence of lexemes is quite obvious. The structure of the AST incor- porates most of the information needed for the following stage of compilation, in particular identifying operations as nodes in the tree and operands as their branches. This makes the AST algorithmically well suited for its purpose. Conversely, the AST excludes irrelevant lexemes, such as separators (white-space, commas, semicolons) and aggregators (brackets, braces), by making them implicit in the tree-like struc- ture. -
The Open Graph Drawing Framework (OGDF)
17 The Open Graph Drawing Framework (OGDF) Markus Chimani Friedrich-Schiller-Universit¨at Jena 17.1 Introduction::::::::::::::::::::::::::::::::::::::::::::::::: 543 • Carsten Gutwenger The History of the OGDF Outline TU Dortmund 17.2 Major Design Concepts:::::::::::::::::::::::::::::::::::: 544 Modularization • Self-Contained and Portable Source Code Michael J¨unger 17.3 General Algorithms and Data Structures ::::::::::::::: 546 • University of Cologne Augmentation and Subgraph Algorithms Graph Decomposition • Planarity and Planarization Gunnar W. Klau 17.4 Graph Drawing Algorithms ::::::::::::::::::::::::::::::: 550 • Centrum Wiskunde & Planar Drawing Algorithms Hierarchical Drawing • • Informatica Algorithms Energy-Based Drawing Algorithms Drawing Clustered Graphs Karsten Klein 17.5 Success Stories :::::::::::::::::::::::::::::::::::::::::::::: 562 • • TU Dortmund SPQR-Trees Exact Crossing Minimization Upward Graph Drawing Petra Mutzel Acknowledgments :::::::::::::::::::::::::::::::::::::::::::::::::: 564 TU Dortmund References :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 565 17.1 Introduction We present the Open Graph Drawing Framework (OGDF), a C++ library of algorithms and data structures for graph drawing. The ultimate goal of the OGDF is to help bridge the gap between theory and practice in the field of automatic graph drawing. The library offers a wide variety of algorithms and data structures, some of them requiring complex and involved implementations, e.g., algorithms for planarity testing and planarization, or data structures for graph decomposition. A substantial part of these algorithms and data structures are building blocks of graph drawing algorithms, and the OGDF aims at pro- viding such functionality in a reusable form, thus also providing a powerful platform for implementing new algorithms. The OGDF can be obtained from its website at: http://www.ogdf.net This website also provides further information like tutorials, examples, contact information, and links to related projects. -
The Graph Crossing Number and Its Variants: a Survey
The Graph Crossing Number and its Variants: A Survey Marcus Schaefer School of Computing DePaul University Chicago, Illinois 60604, USA [email protected] Submitted: Dec 20, 2011; Accepted: Apr 4, 2013; Published: April 17, 2013 Third edition, Dec 22, 2017 Mathematics Subject Classifications: 05C62, 68R10 Abstract The crossing number is a popular tool in graph drawing and visualization, but there is not really just one crossing number; there is a large family of crossing number notions of which the crossing number is the best known. We survey the rich variety of crossing number variants that have been introduced in the literature for purposes that range from studying the theoretical underpinnings of the crossing number to crossing minimization for visualization problems. 1 So, Which Crossing Number is it? The crossing number, cr(G), of a graph G is the smallest number of crossings required in any drawing of G. Or is it? According to a popular introductory textbook on combi- natorics [460, page 40] the crossing number of a graph is “the minimum number of pairs of crossing edges in a depiction of G”. So, which one is it? Is there even a difference? To start with the second question, the easy answer is: yes, obviously there is a differ- ence, the difference between counting all crossings and counting pairs of edges that cross. But maybe these different ways of counting don’t make a difference and always come out the same? That is a harder question to answer. Pach and Tóth in their paper “Which Crossing Number is it Anyway?” [369] coined the term pair crossing number, pcr, for the crossing number in the second definition. -
A New Approximation Algorithm for Bend Minimization in the Kandinsky Model
A New Approximation Algorithm for Bend Minimization in the Kandinsky Model Wilhelm Barth1, Petra Mutzel2, and Canan Yıldız1 1 Institute of Computer Graphics and Algorithms, Vienna University of Technology Favoritenstraße 9-11, 1040 Wien, Austria {barth,yildizca}@ads.tuwien.ac.at http://www.ads.tuwien.ac.at/ 2 Department of Computer Science, University of Dortmund Otto-Hahn-Str. 14, D-44227 Dortmund, Germany [email protected] http://ls11-www.cs.uni-dortmund.de/ Abstract. The Kandinsky model has been introduced by F¨oßmeier and Kaufmann in order to deal with planar orthogonal drawings of planar graphs with maximal vertex degree higher than four [7]. No polynomial- time algorithm is known for computing a (region preserving) bend mini- mal Kandinsky drawing. In this paper we suggest a new 2-approximation algorithm for this problem. Our extensive computational experiments [13] show that the quality of the computed solutions is better than those of its predecessors [6]. E.g., for all instances in the Rome graph bench- mark library [4] it computed the optimal solution, and for randomly generated triangulated graphs with up to 800 vertices, the absolute error was less than 2 on average. 1 Introduction Given a planar graph G =(V,E,F) with a fixed embedding F ,weconsider the problem of finding a region-preserving planar orthogonal drawing with the minimum number of bends. For graphs with maximal degree 4 this problem can be solved in polynomial time [12] if no parallel edge segments leaving a vertex at the same side are allowed. The idea is to set up a network in which each flow corresponds to an orthogonal drawing and vice versa. -
Algorithms for Incremental Planar Graph Drawing and Two-Page Book Embeddings
Algorithms for Incremental Planar Graph Drawing and Two-page Book Embeddings Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakult¨at der Universit¨at zu Koln¨ vorgelegt von Martin Gronemann aus Unna Koln¨ 2015 Berichterstatter (Gutachter): Prof. Dr. Michael Junger¨ Prof. Dr. Markus Chimani Prof. Dr. Bettina Speckmann Tag der m¨undlichenPr¨ufung: 23. Juni 2015 Zusammenfassung Diese Arbeit besch¨aftigt sich mit zwei Problemen bei denen es um Knoten- ordnungen in planaren Graphen geht. Hierbei werden als erstes Ordnungen betrachtet, die als Grundlage fur¨ inkrementelle Zeichenalgorithmen dienen. Solche Algorithmen erweitern in der Regel eine vorhandene Zeichnung durch schrittweises Hinzufugen¨ von Knoten in der durch die Ordnung gegebene Rei- henfolge. Zu diesem Zweck kommen im Gebiet des Graphenzeichnens verschie- dene Ordnungstypen zum Einsatz. Einigen dieser Ordnungen fehlen allerdings gewunschte¨ oder sogar fur¨ einige Algorithmen notwendige Eigenschaften. Diese Eigenschaften werden genauer untersucht und dabei ein neuer Typ von Ord- nung entwickelt, die sogenannte bitonische st-Ordnung, eine Ordnung, welche Eigenschaften kanonischer Ordnungen mit der Flexibilit¨at herk¨ommlicher st- Ordnungen kombiniert. Die zus¨atzliche Eigenschaft bitonisch zu sein erm¨oglicht es, eine st-Ordnung wie eine kanonische Ordnung zu verwenden. Es wird gezeigt, dass fur¨ jeden zwei-zusammenh¨angenden planaren Graphen eine bitonische st-Ordnung in linearer Zeit berechnet werden kann. Im Ge- gensatz zu kanonischen Ordnungen, k¨onnen st-Ordnungen naturgem¨aß auch fur¨ gerichtete Graphen verwendet werden. Diese F¨ahigkeit ist fur¨ das Zeichnen von aufw¨artsplanaren Graphen von besonderem Interesse, da eine bitonische st-Ordnung unter Umst¨anden es erlauben wurde,¨ vorhandene ungerichtete Zei- chenverfahren fur¨ den gerichteten Fall anzupassen. -
New Approaches on Octilinear Graph Drawing
New Approaches on Octilinear Graph Drawing Dissertation der Mathematisch-Naturwissenschaftlichen Fakult¨at der Eberhard Karls Universit¨atT¨ubingen zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) vorgelegt von Dipl.-Inform. (Bioinf.) Robert Krug aus Ulm T¨ubingen 2015 abc Gedruckt mit Genehmigung der Mathematisch-Naturwissenschaftlichen Fakult¨at der Eberhard Karls Universit¨atT¨ubingen. Tag der m¨undlichen Qualifikation 28.04.2015 Dekan: Prof. Dr. Wolfgang Rosenstiel 1. Berichterstatter: Prof. Dr. Michael Kaufmann 2. Berichterstatter: Prof. Dr. Peter Hauck Acknowledgements First and foremost I thank my advisor Prof. Dr. Michael Kaufmann, for giving me the opportunity to be part of his great group and write this thesis, for supporting me this whole time and enabling me to visit several international workshops and conferences. I am deeply grateful to my colleague Dr. Michael Bekos who not only par- ticipated in every research project that made it into this thesis but also gave me great support during the writing of this thesis and was a very pleasant officemate. My thanks also go to my current and former colleagues Till Bruckdorfer, Philip Effinger, Andreas Gerasch, Niklas Heinsohn, Markus Geyer, Stephan Kottler, Martin Siebenhaller and Christian Zielke who provided a very nice working atmosphere and valuable input in many scientific and non-scientific discussions during our coffee-breaks. I thank all my coauthors, namely Michael Bekos, Markus Geyer, Martin Gronemann, Michael Kaufmann, Thorsten Ludwig, Stefan N¨aherand Vin- cenzo Roselli for the pleasant and productive collaborations. I am most thankful to my friends Chrissi and Klaus who, together with Ju- lian and Laura, always offered me delicious meals and delightful company which I especially appreciated in stressful times of approaching deadlines.