The Moving Target of Visualization Software for an Ever More Complex World
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Techniques for Visualization and Interaction in Software Architecture Optimization
Institute of Software Technology Reliable Software Systems University of Stuttgart Universitätsstraße 38 D–70569 Stuttgart Masterarbeit Techniques for Visualization and Interaction in Software Architecture Optimization Sebastian Frank Course of Study: Softwaretechnik Examiner: Dr.-Ing. André van Hoorn Supervisor: Dr.-Ing. André van Hoorn Dr. J. Andrés Díaz-Pace, UNICEN, ARG Dr. Santiago Vidal, UNICEN, ARG Commenced: March 25, 2019 Completed: September 25, 2019 CR-Classification: D.2.11, H.5.2, H.1.2 Abstract Software architecture optimization aims at improving the architecture of software systems with regard to a set of quality attributes, e.g., performance, reliability, and modifiability. However, particular tasks in the optimization process are hard to automate. For this reason, architects have to participate in the optimization process, e.g., by making trade-offs and selecting acceptable architectural proposals. The existing software architecture optimization approaches only offer limited support in assisting architects in the necessary tasks by visualizing the architectural proposals. In the best case, these approaches provide very basic visualizations, but often results are only delivered in textual form, which does not allow for an efficient assessment by humans. Hence, this work investigates strategies and techniques to assist architects in specific use cases of software architecture optimization through visualization and interaction. Based on this, an approach to assist architects in these use cases is proposed. A prototype of the proposed approach has been implemented. Domain experts solved tasks based on two case studies. The results show that the approach can assist architects in some of the typical use cases of the domain. Con- ducted time measurements indicate that several hundred architectural proposals can be handled. -
Multi-Touch Table User Interfaces for Co-Located Collaborative Software Visualization
Multi-touch Table User Interfaces for Co-located Collaborative Software Visualization Craig Anslow School of Engineering and Computer Science Victoria University of Wellington, New Zealand [email protected] ABSTRACT Integrated Development Environments (IDE) like Eclipse, Most software visualization systems and tools are designed and the web. These design decisions do not allow users in from a single-user perspective and are bound to the desktop, a co-located environment (within the same room) to easily IDEs, and the web. Few tools are designed with sufficient collaborate, communicate, or be aware of each others activi- support for the social aspects of understanding software such ties to analyse software [19]. Multi-touch user interfaces are as collaboration, communication, and awareness. This re- an interactive technique that allows single or multiple users search aims at supporting co-located collaborative software to collaboratively control graphical displays with more than analysis using software visualization techniques and multi- one finger, mouse pointer, or tangible object on various kinds touch tables. The research will be conducted via qualitative of surfaces and devices. user experiments which will inform the design of collabora- tive software visualization applications and further our un- The goal of this research is to investigate whether multi- derstanding of how software developers work together with touch interaction techniques are more effective for co-located multi-touch user interfaces. collaborative software visualization than existing single user desktop interaction techniques. The research will be con- ACM Classification: H1.2 [User/Machine Systems]: Hu- ducted by user experiments to observe how users interact man Factors; H5.2 [Information interfaces and presentation]: and collaborate with a multi-touch software visualization ap- User Interfaces. -
A Systematic Literature Review of Software Visualization Evaluation T ⁎ L
The Journal of Systems & Software 144 (2018) 165–180 Contents lists available at ScienceDirect The Journal of Systems & Software journal homepage: www.elsevier.com/locate/jss A systematic literature review of software visualization evaluation T ⁎ L. Merino ,a, M. Ghafaria, C. Anslowb, O. Nierstrasza a Software Composition Group, University of Bern, Switzerland b School of Engineering and Computer Science, Victoria University of Wellington, New Zealand ARTICLE INFO ABSTRACT Keywords: Context:Software visualizations can help developers to analyze multiple aspects of complex software systems, but Software visualisation their effectiveness is often uncertain due to the lack of evaluation guidelines. Evaluation Objective: We identify common problems in the evaluation of software visualizations with the goal of for- Literature review mulating guidelines to improve future evaluations. Method:We review the complete literature body of 387 full papers published in the SOFTVIS/VISSOFT con- ferences, and study 181 of those from which we could extract evaluation strategies, data collection methods, and other aspects of the evaluation. Results:Of the proposed software visualization approaches, 62% lack a strong evaluation. We argue that an effective software visualization should not only boost time and correctness but also recollection, usability, en- gagement, and other emotions. Conclusion:We call on researchers proposing new software visualizations to provide evidence of their effec- tiveness by conducting thorough (i) case studies for approaches that must be studied in situ, and when variables can be controlled, (ii) experiments with randomly selected participants of the target audience and real-world open source software systems to promote reproducibility and replicability. We present guidelines to increase the evidence of the effectiveness of software visualization approaches, thus improving their adoption rate. -
Journal of Molecular Graphics and Modelling 73 (2017) 179–190
Journal of Molecular Graphics and Modelling 73 (2017) 179–190 Contents lists available at ScienceDirect Journal of Molecular Graphics and Modelling journa l homepage: www.elsevier.com/locate/JMGM Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates a b c d,1 Weihong Zhang , Steven C. Howell , David W. Wright , Andrew Heindel , e a, b, Xiangyun Qiu , Jianhan Chen ∗, Joseph E. Curtis ∗∗ a Kansas State University, Manhattan, KS, USA b NIST Center for Neutron Research, 100 Bureau Drive, Gaithersburg, MD, USA c Centre for Computational Science, Department of Chemistry, University College London, 10 Gordon St., London, UK d James Madison University, Department of Chemistry & Biochemistry, Harrisonburg, VA, USA e Department of Physics, The George Washington University, Washington, DC, USA a r t i c l e i n f o a b s t r a c t Article history: We describe a general method to use Monte Carlo simulation followed by torsion-angle molecular dynam- Received 13 October 2016 ics simulations to create ensembles of structures to model a wide variety of soft-matter biological systems. Received in revised form 19 January 2017 Our particular emphasis is focused on modeling low-resolution small-angle scattering and reflectivity Accepted 17 February 2017 structural data. We provide examples of this method applied to HIV-1 Gag protein and derived fragment Available online 23 February 2017 proteins, TraI protein, linear B-DNA, a nucleosome core particle, and a glycosylated monoclonal antibody. This procedure will enable a large community of researchers to model low-resolution experimental data MSC: with greater accuracy by using robust physics based simulation and sampling methods which are a 00-01 99-00 significant improvement over traditional methods used to interpret such data. -
Biological Sciences 1
Biological Sciences 1 BIOL UN3208 Introduction to Evolutionary Biology or EEEB UN2001 BIOLOGICAL SCIENCES Environmental Biology I: Elements to Organisms. Departmental Office: 600 Fairchild, 212-854-4581; Interested students should consult listings in other departments for [email protected]; [email protected] courses related to biology. For courses in environmental studies, see listings for Earth and environmental sciences or for ecology, evolution, Director of Undergraduate Studies, Undergraduate Programs and and environmental biology. For courses in human evolution, see listings Laboratories: for anthropology or for ecology, evolution, and environmental biology. Prof. Deborah Mowshowitz, 744D Mudd; 212-854-4497; For courses in the history of evolution, see listings for history and for [email protected] philosophy of science. For a list of courses in computational biology and genomics, visit http://systemsbiology.columbia.edu/courses. Biology Major and Concentration Advisers: For a list of current biology, biochemistry, biophysics, and neuroscience and behavior advisers, please visit http://biology.columbia.edu/ Advanced Placement programs/advisors Transfer Credit A-F: Prof. Alice Heicklen, 744B Mudd; [email protected] Transfer credits granted toward the degree are not automatically counted G-O: Prof. Mary Ann Price, 744A Mudd; [email protected] toward the major. The department determines which transfer credits P-Z: Prof. Tulle Hazelrigg, 753A Mudd, [email protected] can be counted toward the major. For most majors, at least four biology Backup Advisor: Prof. Deborah Mowshowitz, 744D Mudd; 212-854-4497; or biochemistry courses and at least 18 credits of the total (biology, [email protected] biochemistry, math, physics, and chemistry) must be taken at Columbia. -
Visualization of the Static Aspects of Software: a Survey Pierre Caserta, Olivier Zendra
Visualization of the Static aspects of Software: a survey Pierre Caserta, Olivier Zendra To cite this version: Pierre Caserta, Olivier Zendra. Visualization of the Static aspects of Software: a survey. IEEE Trans- actions on Visualization and Computer Graphics, Institute of Electrical and Electronics Engineers, 2011, 17 (7), pp.913-933. 10.1109/TVCG.2010.110. inria-00546158v2 HAL Id: inria-00546158 https://hal.inria.fr/inria-00546158v2 Submitted on 28 Oct 2011 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, VOL. 17, NO. 7, JULY 2011 913 Visualization of the Static Aspects of Software: A Survey Pierre Caserta and Olivier Zendra Abstract—Software is usually complex and always intangible. In practice, the development and maintenance processes are time- consuming activities mainly because software complexity is difficult to manage. Graphical visualization of software has the potential to result in a better and faster understanding of its design and functionality, thus saving time and providing valuable information to improve its quality. However, visualizing software is not an easy task because of the huge amount of information comprised in the software. -
CCP4 Molecular Graphics Documentation Contents Documentation On-Line Documentation Tutorials Ccp4mg Home Contents Quick Reference Print Version Contact References
CCP4 Molecular Graphics file:///E:/ccp4mg-win/help/index.html CCP4 Molecular Graphics Documentation Contents Documentation On-line Documentation Tutorials CCP4mg Home Contents Quick Reference Print version Contact References Documentation Contents General Graphics Window - mouse bindings and short cuts The Tools menu The View menu Projects - data organisation Installation of support programs Molecular models Reading coordinate files and atom typing The Coordinate Model Interface Atom selection Structure Analysis Surfaces and Electrostatic Potentials Symmetry Related Models Animations Other types of data Electron density maps Vectors Electron density in GAUSSIAN cube format Text and imported images Applications Superpose automatic protein superposition and interactive superposition of any structures Presentation Graphics Picture Wizard set up complex pictures quickly Movies Presentations Geometry Run Coot Other utilities Web tools History and Scripting Editing and Saving Files PDF Creator - PDF4Free v2.0 http://www.pdf4free.com 1 of 3 01/11/2007 18:42 CCP4 Molecular Graphics file:///E:/ccp4mg-win/help/index.html Lighting Saving the program status Picture Definition Files (also Object attributes and Introduction to Python) Making presentations Quick Reference See Display Table for general overview of the display table. For information on specific type of data click the appropriate data type in the File list below. File Tools View Applications Coordinate Files General tools General tools Movies Downloading Coordinate .. .. Superpose Files Read electron density Picture Save/restore view Lighting map/MTZ Wizard Read QM maps Save/restore status Transparency Geometry Add vectors/labels Picture definition files View from Rotate,translate,align Add image History and Scripting view Add legend Presentation/Notebook RocknRoll Add crystal List monomer definition Model definition file Preferences Open presentation Tutorials Output screen image Windows Bring a 'lost' window to the front. -
Coot: Model-Building Tools for Molecular Graphics Crystallography ISSN 0907-4449
research papers Acta Crystallographica Section D Biological Coot: model-building tools for molecular graphics Crystallography ISSN 0907-4449 Paul Emsley* and Kevin Cowtan CCP4mg is a project that aims to provide a general-purpose Received 26 February 2004 tool for structural biologists, providing tools for X-ray Accepted 4 August 2004 structure solution, structure comparison and analysis, and York Structural Biology Laboratory, University of York, Heslington, York YO10 5YW, England publication-quality graphics. The map-®tting tools are avail- able as a stand-alone package, distributed as `Coot'. Correspondence e-mail: [email protected] 1. Introduction Molecular graphics still plays an important role in the deter- mination of protein structures using X-ray crystallographic data, despite on-going efforts to automate model building. Functions such as side-chain placement, loop, ligand and fragment ®tting, structure comparison, analysis and validation are routinely performed using molecular graphics. Lower Ê resolution (dmin worse than 2.5 A) data in particular need interactive ®tting. The introduction of FRODO (Jones, 1978) and then O (Jones et al., 1991) to the ®eld of protein crystallography was in each case revolutionary, each in their time breaking new ground in demonstrating what was possible with the current hardware. These tools allowed protein crystallographers to enjoy what is widely held to be the most thrilling part of their work: giving birth (as it were) to a new protein structure. The CCP4 program suite (Collaborative Computational Project, Number 4, 1994) is an integrated collection of software for macromolecular crystallography, with a scope ranging from data processing to structure re®nement and validation. -
Evocells - a Treemap Layout Algorithm for Evolving Tree Data
Initial State EvoCells - A Treemap Layout Algorithm for Evolving Tree Data Willy Scheibel, Christopher Weyand and Jurgen¨ Dollner¨ NextHasso State Plattner Institute Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany Initial | State Keywords: Treemap Layout Algorithm, Time-varying Tree-structured Data, Treemap Layout Metrics. Abstract: We propose the rectangular treemap layout algorithm EvoCells that maps changes in tree-structured data onto an initial treemap layout. Changes in topology and node weights are mapped to insertion, removal, growth, and shrinkage of the layout rectangles. Thereby, rectangles displace their neighbors and stretche their enclosing rectangles with a run-time complexity of O(nlogn). An evaluation using layout stability metrics on the open source ElasticSearch software system suggests EvoCells as a valid alternative for stable treemap layouting. 1 INTRODUCTION regard to algorithmic complexity and layout stability, together with a case-study in the domain of software Tree-structured data is subject to constant change. analytics based on the software system ElasticSearch. In order to manage change, understanding the evo- lution is important. An often used tool to commu- Initial State nicate structure and characteristics of tree-structured data is the treemap (Shneiderman, 1992). Most lay- outs are based on a recursive partition of a given ini- tial 2D rectangular area proportional to the summed weights of the nodes. Besides topology and associ- ated weights, additional visual variables can be used (Carpendale, 2003), including extrusion of the 2D layout to 3D cuboids. The restricted use of the third dimension is reflected by the term 2.5D treemaps (Limberger et al., 2017b). When used over time, treemap layouts are faced Next State by their inherent instability regarding even minor changes to the nodes’ weights used for the spatial layouting, impeding the creation and use of a mental map (Misue et al., 1995). -
Storytelling and Visualization: a Survey
Storytelling and Visualization: A Survey Chao Tong1, Richard Roberts1, Robert S.Laramee1,Kodzo Wegba2, Aidong Lu2, Yun Wang3, Huamin Qu3, Qiong Luo3 and Xiaojuan Ma3 1Visual and Interactive Computing Group, Swansea University 2Department of Computer Science, University of North Carolina at Charlotte 3Department of Computer Science and Engineering, Hong Kong University of Science and Technology Keywords: Storytelling, Narrative, Information visualization, Scientific visualization Abstract: Throughout history, storytelling has been an effective way of conveying information and knowledge. In the field of visualization, storytelling is rapidly gaining momentum and evolving cutting-edge techniques that enhance understanding. Many communities have commented on the importance of storytelling in data visual- ization. Storytellers tend to be integrating complex visualizations into their narratives in growing numbers. In this paper, we present a survey of storytelling literature in visualization and present an overview of the com- mon and important elements in storytelling visualization. We also describe the challenges in this field as well as a novel classification of the literature on storytelling in visualization. Our classification scheme highlights the open and unsolved problems in this field as well as the more mature storytelling sub-fields. The benefits offer a concise overview and a starting point into this rapidly evolving research trend and provide a deeper understanding of this topic. 1 MOTIVATION cation of the literature on storytelling in visualiza- tion. Our classification highlights both mature and “We believe in the power of science, exploration, unsolved problems in this area. The benefit is a con- and storytelling to change the world” - Susan Gold- cise overview and valuable starting point into this berg, Editor in Chief of National Geographic Maga- rapidly growing and evolving research trend. -
Architecture De Dataflow Pour Des Systèmes Modulaires Et Génériques De Simulation De Plante Christophe Pradal
Architecture de dataflow pour des systèmes modulaires et génériques de simulation de plante Christophe Pradal To cite this version: Christophe Pradal. Architecture de dataflow pour des systèmes modulaires et génériques desim- ulation de plante. Modélisation et simulation. Université Montpellier, 2019. Français. NNT : 2019MONTS034. tel-02879776 HAL Id: tel-02879776 https://tel.archives-ouvertes.fr/tel-02879776 Submitted on 24 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THESE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITE DE MONTPELLIER PAR LA VALIDATION DES ACQUIS DE L’EXPERIENCE Année universitaire 2018-2019 En Informatique École doctorale I2S – Information, Structures, Systèmes Unité de recherche UMR AGAP – Université de Montpellier SYNTHÈSE DES TRAVAUX DE RECHERCHE Architecture de Dataflow pour des systèmes modulaires et génériques de simulation de plante Présentée par Christophe PRADAL Le 17 juillet 2019 Référent : Christophe GODIN RAPPORT DE GESTION Devant le jury composé de Christophe GODIN, Directeur de recherche, Inria, Lyon -
Analyzing Feature Implementation by Visual Exploration of Architecturally
Analyzing Feature Implementation by Visual Exploration of Architecturally-Embedded Call-Graphs Johannes Bohnet Jürgen Döllner University of Potsdam University of Potsdam Hasso-Plattner-Institute Hasso-Plattner-Institute Prof.-Dr.-Helmert-Str. 2-3 Prof.-Dr.-Helmert-Str. 2-3 14482 Potsdam, Germany 14482 Potsdam, Germany [email protected] [email protected] ABSTRACT 1. INTRODUCTION Maintenance, reengineering, and refactoring of large and complex As stated in [32] “year after year the lion's share of effort goes software systems are commonly based on modifications and into modifying and extending preexisting systems, about which enhancements related to features. Before developers can modify we know very little”. Requests for software changes are often feature functionality they have to locate the relevant code expressed by end users in terms of features, i.e. an observable components and understand the components’ interaction. In this behavior that is triggered by user interaction. Requesting feature paper, we present a prototype tool for analyzing feature changes concerns bug fixes or enhancements of feature functiona- implementation of large C/C++ software systems by visual lity and is a key concept for maintaining, reengineering, and exploration of dynamically extracted call relations between code refactoring large and complex software systems. To implement components. The component interaction can be analyzed on these new requirements, software developers have to translate the various abstraction levels ranging from function interaction up to feature change requests to changes in code components and their interaction of the system with shared libraries of the operating interaction behavior. The term component is used here in a more system.