Delta-oriented Architectural Variability Using MontiCore

Modeling of software architectures is a fundamental part of software development processes. Reuse of software components and early analysis of software topologies allow the reduction of development costs and increases software quality. Integrating variability modeling concepts into architecture description languages (ADLs) is essential for the development of diverse software systems with high demands on software quality. In this paper, we present the integration of delta modeling into the existing ADL MontiArc. Delta modeling is a language-independent variability modeling approach supporting proactive, reactive and extractive product line development. We show how ?-MontiArc, a language for explicit modeling of architectural variability based on delta modeling, is implemented as domain-specific language (DSL) using the DSL development framework MontiCore. We also demonstrate how MontiCore's language reuse mechanisms provide efficient means to derive an implementation of ?-MontiArc tool implementation. We evaluate ?-Monti-Arc by comparing it with annotative variability modeling.Comment: 10 pages, 9 figures. ECSA '11 5th European Conference on Software Architecture: Companion Volume, ACM New York, NY, USA, Article No. 6, September 201

Considerations about quality in model-driven engineering

The final publication is available at Springer via http://dx.doi.org/10.1007/s11219-016-9350-6The virtue of quality is not itself a subject; it depends on a subject. In the software engineering field, quality means good software products that meet customer expectations, constraints, and requirements. Despite the numerous approaches, methods, descriptive models, and tools, that have been developed, a level of consensus has been reached by software practitioners. However, in the model-driven engineering (MDE) field, which has emerged from software engineering paradigms, quality continues to be a great challenge since the subject is not fully defined. The use of models alone is not enough to manage all of the quality issues at the modeling language level. In this work, we present the current state and some relevant considerations regarding quality in MDE, by identifying current categories in quality conception and by highlighting quality issues in real applications of the model-driven initiatives. We identified 16 categories in the definition of quality in MDE. From this identification, by applying an adaptive sampling approach, we discovered the five most influential authors for the works that propose definitions of quality. These include (in order): the OMG standards (e.g., MDA, UML, MOF, OCL, SysML), the ISO standards for software quality models (e.g., 9126 and 25,000), Krogstie, Lindland, and Moody. We also discovered families of works about quality, i.e., works that belong to the same author or topic. Seventy-three works were found with evidence of the mismatch between the academic/research field of quality evaluation of modeling languages and actual MDE practice in industry. We demonstrate that this field does not currently solve quality issues reported in industrial scenarios. The evidence of the mismatch was grouped in eight categories, four for academic/research evidence and four for industrial reports. These categories were detected based on the scope proposed in each one of the academic/research works and from the questions and issues raised by real practitioners. We then proposed a scenario to illustrate quality issues in a real information system project in which multiple modeling languages were used. For the evaluation of the quality of this MDE scenario, we chose one of the most cited and influential quality frameworks; it was detected from the information obtained in the identification of the categories about quality definition for MDE. We demonstrated that the selected framework falls short in addressing the quality issues. Finally, based on the findings, we derive eight challenges for quality evaluation in MDE projects that current quality initiatives do not address sufficiently.F.G, would like to thank COLCIENCIAS (Colombia) for funding this work through the Colciencias Grant call 512-2010. This work has been supported by the Gene-ralitat Valenciana Project IDEO (PROMETEOII/2014/039), the European Commission FP7 Project CaaS (611351), and ERDF structural funds.Giraldo-Velásquez, FD.; España Cubillo, S.; Pastor López, O.; Giraldo, WJ. (2016). Considerations about quality in model-driven engineering. Software Quality Journal. 1-66. https://doi.org/10.1007/s11219-016-9350-6S166(1985). Iso information processing—documentation symbols and conventions for data, program and system flowcharts, program network charts and system resources charts. ISO 5807:1985(E) (pp. 1–25).(2011). Iso/iec/ieee systems and software engineering – architecture description. ISO/IEC/IEEE 42010:2011(E) (Revision of ISO/IEC 42010:2007 and IEEE Std 1471-2000) (pp. 1–46).Abran, A., Moore, J.W., Bourque, P., Dupuis, R., & Tripp, L.L. (2013). Guide to the Software Engineering Body of Knowledge (SWEBOK) version 3 public review. IEEE. ISO Technical Report ISO/IEC TR 19759.Agner, L.T.W., Soares, I.W., Stadzisz, P.C., & Simão, J.M. (2013). A brazilian survey on {UML} and model-driven practices for embedded software development. Journal of Systems and Software, 86(4), 997–1005. {SI} : Software Engineering in Brazil: Retrospective and Prospective Views.Amstel, M.F.V. (2010). The right tool for the right job: assessing model transformation quality. pages 69–74. Affiliation: Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, Netherlands. Cited By (since 1996):1.Aranda, J., Damian, D., & Borici, A. (2012). Transition to model-driven engineering: what is revolutionary, what remains the same?. In Proceedings of the 15th international conference on model driven engineering languages and systems, MODELS’12 (pp. 692–708). Berlin, Heidelberg: Springer.Arendt, T., & Taentzer, G. (2013). A tool environment for quality assurance based on the eclipse modeling framework. Automated Software Engineering, 20(2), 141–184.Atkinson, C., Bunse, C., & Wüst, J. (2003). Driving component-based software development through quality modelling, volume 2693. Cited By (since 1996):3.Baker, P., Loh, S., & Weil, F. (2005). Model-driven engineering in a large industrial context—motorola case study. In Briand, L., & Williams, C. (Eds.) Model Driven Engineering Languages and Systems, volume 3713 of Lecture Notes in Computer Science (pp. 476–491). Berlin, Heidelberg: Springer.Barišić, A., Amaral, V., Goulão, M., & Barroca, B. (2011). Quality in use of domain-specific languages: a case study. In Proceedings of the 3rd ACM SIGPLAN workshop on evaluation and usability of programming languages and tools, PLATEAU ’11 (pp. 65–72). New York: ACM.Becker, J., Bergener, P., Breuker, D., & Rackers, M. (2010). Evaluating the expressiveness of domain specific modeling languages using the bunge-wand-weber ontology. In 2010 43rd Hawaii international conference on system sciences (HICSS) (pp. 1–10).Bertrand Portier, L.A. (2009). Model driven development misperceptions and challenges.Bézivin, J., & Kurtev, I. (2005). Model-based technology integration with the technical space concept. In Proceedings of the Metainformatics Symposium: Springer.Brambilla, M. (2016). How mature is of model-driven engineering as an engineering discipline @ONLINE.Brambilla, M., & Fraternali, P. (2014). Large-scale model-driven engineering of web user interaction: The webml and webratio experience. Science of Computer Programming, 89 Part B(0), 71 – 87. Special issue on Success Stories in Model Driven Engineering.Brown, A. (2009). Simple and practical model driven architecture (mda) @ONLINE.Bruel, J.-M., Combemale, B., Ober, I., & Raynal, H. (2015). Mde in practice for computational science. Procedia Computer Science, 51, 660–669.Budgen, D., Burn, A.J., Brereton, O.P., Kitchenham, B.A., & Pretorius, R. (2011). Empirical evidence about the uml: a systematic literature review. Software: Practice and Experience, 41(4), 363–392.Burden, H., Heldal, R., & Whittle, J. (2014). Comparing and contrasting model-driven engineering at three large companies. In Proceedings of the 8th ACM/IEEE International Symposium on Empirical Software Engineering and Measurement, ESEM ’14 (pp. 14:1–14:10). New York: ACM.Cabot, J. Has mda been abandoned (by the omg)?Cabot, J. (2009). Modeling will be commonplace in three years time @ONLINE.Cachero, C., Poels, G., Calero, C., & Marhuenda, Y. (2007). Towards a Quality-Aware Engineering Process for the Development of Web Applications. Working Papers of Faculty of Economics and Business Administration, Ghent University, Belgium 07/462, Ghent University, Faculty of Economics and Business Administration.Challenger, M., Kardas, G., & Tekinerdogan, B. (2015). A systematic approach to evaluating domain-specific modeling language environments for multi-agent systems. Software Quality Journal, 1–41.Chaudron, M.V., Heijstek, W., & Nugroho, A. (2012). How effective is uml modeling? Software & Systems Modeling, 11(4), 571–580. J2: Softw Syst Model.Chenouard, R., Granvilliers, L., & Soto, R. (2008). Model-driven constraint programming. pages 236–246. Affiliation: CNRS, LINA, Universit de Nantes, France; Affiliation: Pontificia Universidad Catlica de, Valparaiso, Chile. Cited By (since 1996):8.Clark, T., & Muller, P.-A. (2012). Exploiting model driven technology: a tale of two startups. Software and Systems Modeling, 11(4), 481–493.Corneliussen, L. (2008). What do you think of model-driven software development?Costal, D., Gómez, C., & Guizzardi, G. (2011). Formal semantics and ontological analysis for understanding subsetting, specialization and redefinition of associations in uml. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 6998 LNCS:189–203. cited By (since 1996)3.Cruz-Lemus, J.A., Maes, A., Género, M., Poels, G., & Piattini, M. (2010). The impact of structural complexity on the understandability of uml statechart diagrams. Information Sciences, 180(11), 2209–2220. Cited By (since 1996):14.Cuadrado, J.S., Izquierdo, J.L.C., & Molina, J.G. (2014). Applying model-driven engineering in small software enterprises. Science of Computer Programming, 89 Part B(0), 176 – 198. Special issue on Success Stories in Model Driven Engineering.Da Silva, A.R. (2015). Model-driven engineering: a survey supported by the unified conceptual model. Computer Languages Systems and Structures, 43, 139–155.Da Silva Teixeira, D.G.M., Quirino, G.K., Gailly, F., De Almeida Falbo, R., Guizzardi, G., & Perini Barcellos, M. (2016). PoN-S: a Systematic Approach for Applying the Physics of Notation (PoN), (pp. 432–447). Cham: Springer International Publishing.Davies, I., Green, P., Rosemann, M., Indulska, M., & Gallo, S. (2006). How do practitioners use conceptual modeling in practice? Data and Knowledge Engineering, 58(3), 358 – 380. Including the special issue : {ER} 2004ER 2004.Davies, J., Milward, D., Wang, C.-W., & Welch, J. (2015). Formal model-driven engineering of critical information systems. Science of Computer Programming, 103(0), 88 – 113. Selected papers from the First International Workshop on Formal Techniques for Safety-Critical Systems (FTSCS 2012).De Oca, I.M.-M., Snoeck, M., Reijers, H.A., & Rodríguez-Morffi, A. (2015). A systematic literature review of studies on business process modeling quality. Information and Software Technology, 58, 187–205.DenHaan, J. (2009). 8 reasons why model driven development is dangerous @ONLINE.DenHaan, J. (2010). Model driven engineering vs the commando pattern @ONLINE.DenHaan, J. (2011a). Why aren’t we all doing model driven development yet @ONLINE.DenHaan, J. (2011b). Why there is no future model driven development @ONLINE.Di Ruscio, D., Iovino, L., & Pierantonio, A. (2013). Managing the coupled evolution of metamodels and textual concrete syntax specifications. cited By (since 1996)0.Dijkman, R.M., Dumas, M., & Ouyang, C. (2008). Semantics and analysis of business process models in {BPMN}. Information and Software Technology, 50(12), 1281–1294.Domínguez-Mayo, F.J., Escalona, M.J., Mejías, M., Ramos, I., & Fernández, L. (2011). A framework for the quality evaluation of mdwe methodologies and information technology infrastructures. International Journal of Human Capital and Information Technology Professionals, 2(4), 11–22.Domínguez-Mayo, F.J., Escalona, M.J., Mejías, M., & Torres, A.H. (2010). A quality model in a quality evaluation framework for mdwe methodologies. pages 495–506. Affiliation: Departamento de Lenguajes y Sistemas Informíticos, University of Seville, Seville, Spain., Cited By (since 1996):1.Dubray, J.-J. (2011). Why did mde miss the boat?.Escalona, M.J., Gutiérrez, J.J., Pérez-Pérez, M., Molina, A., Domínguez-Mayo, E., & Domínguez-Mayo, F.J. (2011). Measuring the Quality of Model-Driven Projects with NDT-Quality, (pp. 307–317). New York: Springer.Espinilla, M., Domínguez-Mayo, F.J., Escalona, M.J., Mejías, M., Ross, M., & Staples, G. (2011). A Method Based on AHP to Define the Quality Model of QuEF (Vol. 123, pp. 685–694). Berlin, Heidelberg: Springer.Fabra, J., Castro, V.D., Álvarez, P., & Marcos, E. (2012). Automatic execution of business process models: exploiting the benefits of model-driven engineering approaches. Journal of Systems and Software, 85(3), 607–625. Novel approaches in the design and implementation of systems/software architecture.Falkenberg, E.D., Hesse, W., Lindgreen, P., Nilsson, B.E., Oei, J.L.H., Rolland, C., Stamper, R.K., Assche, F.J.M.V., Verrijn-Stuart, A.A., & Voss, K. (1996). Frisco: a framework of information system concepts. Technical report, The IFIP WG 8. 1 Task Group FRISCO.Fettke, P., Houy, C., Vella, A.-L., & Loos, P. (2012). Towards the Reconstruction and Evaluation of Conceptual Model Quality Discourses – Methodical Framework and Application in the Context of Model Understandability, volume 113 of Lecture Notes in Business Information Processing, chapter 28, pages 406–421, Springer, Berlin, Heidelberg.Finnie, S. (2015). Modeling community: Are we missing something?Fournier, C. (2008). Is uml [email protected], R., & Rumpe, B. (2007). Model-driven development of complex software: a research roadmap. In Future of Software Engineering, 2007, FOSE ’07 (pp. 37–54).Gallego, M., Giraldo, F.D., & Hitpass, B. (2015). Adapting the pbec-otss software selection approach for bpm suites: an application case. In 2015 34th International Conference of the Chilean Computer Science Society (SCCC) (pp. 1–10).Galvão, I., & Goknil, A. (2007). Survey of traceability approaches in model-driven engineering. cited By (since 1996)22.Giraldo, F., España, S., Giraldo, W., & Pastor, O. (2015). Modelling language quality evaluation in model-driven information systems engineering: a roadmap. In 2015 IEEE 9th International Conference on Research Challenges in Information Science (RCIS) (pp. 64–69).Giraldo, F., España, S., & Pastor, O. (2014). Analysing the concept of quality in model-driven engineering literature: a systematic review. In 2014 IEEE Eighth International Conference on Research Challenges in Information Science (RCIS) (pp. 1–12).Giraldo, F.D., España, S., & Pastor, O. (2016). Evidences of the mismatch between industry and academy on modelling language quality evaluation. arXiv: 1606.02025 .González, C., & Cabot, J. (2014). Formal verification of static software models in mde: a systematic review. Information and Software Technology, 56(8), 821–838. cited By (since 1996)0.González, C.A., Büttner, F., Clarisó, R., & Cabot, J. (2012). Emftocsp: a tool for the lightweight verification of emf models. pages 44–50. Affiliation: cole des Mines de Nantes, INRIA, LINA, Nantes, France; Affiliation: Universitat Oberta de Catalunya, Barcelona, Spain. Cited By (since 1996):1.Gorschek, T., Tempero, E., & Angelis, L. (2014). On the use of software design models in software development practice: an empirical investigation. Journal of Systems and Software, 95(0), 176– 193.Goulão, M., Amaral, V., & Mernik, M. (2016). Quality in model-driven engineering: a tertiary study. Software Quality Journal, 1–33.Grobshtein, Y., & Dori, D. (2011). Generating sysml views from an opm model: design and evaluation. Systems Engineering, 14(3), 327–340.Haan, J.d. (2008). 8 reasons why model-driven approaches (will) fail.Harel, D., & Rumpe, B. (2000). Modeling languages: Syntax, semantics and all that stuff, part i: The basic stuff, Israel. Technical report Jerusalem Israel.Harel, D., & Rumpe, B. (2004). Meaningful modeling: what’s the semantics of semantics? Computer, 37(10), 64–72.Hebig, R., & Bendraou, R. (2014). On the need to study the impact of model driven engineering on software processes. In Proceedings of the 2014 International Conference on Software and System Process, ICSSP 2014 (pp. 164–168). New York: ACM.Heidari, F., & Loucopoulos, P. (2014). Quality evaluation framework (qef): modeling and evaluating quality of business processes. International Journal of Accounting Information Systems, 15(3), 193–223. Business Process Modeling.Heymans, P., Schobbens, P.Y., Trigaux, J.C., Bontemps, Y., Matulevicius, R., & Classen, A. (2008). Evaluating formal properties of feature diagram languages. Software, IET, 2(3), 281–302. ID 2.Hindawi, M., Morel, L., Aubry, R., & Sourrouille, J.-L. (2009). Description and Implementation of a UML Style Guide (Vol. 5421, pp. 291–302). Berlin: Springer.Hoang, D. (2012). Current limitations of mdd and its implications @ONLINE.Hodges, W. (2013). Model theory Zalta, E.N. (Ed.) The Stanford Encyclopedia of Philosophy. Fall 2013 edition.Hutchinson, J., Rouncefield, M., & Whittle, J. (2011a). Model-driven engineering practices in industry. In Proceedings of the 33rd International Conference on Software Engineering, ICSE’11 (pp. 633–642). New York: ACM.Hutchinson, J., Whittle, J., & Rouncefield, M. (2014). Model-driven engineering practices in industry: social, organizational and managerial factors that lead to success or failure. Science of Computer Programming, 89 Part B(0), 144–161. Special issue on Success Stories in Model Driven Engineering.Hutchinson, J., Whittle, J., Rouncefield, M., & Kristoffersen, S. (2011b). Empirical assessment of mde in industry. In Proceedings of the 33rd International Conference on Software Engineering, ICSE’11 (pp. 471–480). New York: ACM.Igarza, I.M.H., Boada, D.H.G., & Valdés, A.P. (2012). Una introducción al desarrollo de software dirigido por modelos. Serie Científica, 5(3).ISO/IEC (2001). ISO/IEC 9126. Software engineering—Product quality. ISO/IEC.Izurieta, C., Rojas, G., & Griffith, I. (2015). Preemptive management of model driven technical debt for improving software quality. In Proceedings of the 11th International ACM SIGSOFT Conference on Quality of Software Architectures, QoSA’15 (pp. 31–36). New York: ACM.Jalali, S., & Wohlin, C. (2012). Systematic literature studies: Database searches vs. backward snowballing. In Proceedings of the ACM-IEEE International Symposium on Empirical Software Engineering and Measurement, ESEM’12 (pp. 29–38). New York: ACM.Kahraman, G., & Bilgen, S. (2013). A framework for qualitative assessment of domain-specific languages. Software & Systems Modeling, 1–22.Kessentini, M., Langer, P., & Wimmer, M. (2013). Searching models, modeling search: On the synergies of sbse and mde (pp. 51–54).Kitchenham, B., & Charters, S. (2007). Guidelines for performing Systematic Literature Reviews in Software Engineering. Technical Report EBSE 2007-001, Keele University and Durham University Joint Report.Kitchenham, B., Pfleeger, S., Pickard, L., Jones, P., Hoaglin, D., El Emam, K., & Rosenberg, J. (2002). Preliminary guidelines for empirical research in software engineering. IEEE Transactions on Software Engineering, 28(8), 721–734.Klinke, M. (2008). Do you use mda/mdd/mdsd, any kind of model-driven approach? Will it be the future?Köhnlein, J. (2013). Eclipse diagram editors from a user’s perspective.Kolovos, D.S., Paige, R.F., & Polack, F.A. (2008). The grand challenge of scalability for model driven engineering. In Models in Software Engineering (pp. 48–53): Springer.Kolovos, D.S., Rose, L.M., Matragkas, N., Paige, R.F., Guerra, E., Cuadrado, J.S., De Lara, J., Ráth, I., Varró, D., Tisi, M., & Cabot, J. (2013). A research roadmap towards achieving scalability in model driven engineering. In Proceedings of the Workshop on Scalability in Model Driven Engineering, BigMDE’13 (pp. 2:1–2:10). New York: ACM.Krill, P. (2016). Uml to be ejected from microsoft visual studio (infoworld).Krogstie, J. (2012a). Model-based development and evolution of information systems: a quality approach, Springer Publishing Company, Incorporated.Krogstie, J. (2012b). Quality of modelling languages, (pp. 249–280). London: Springer.Krogstie, J. (2012c). Quality of models, (pp. 205–247). London: Springer.Krogstie, J. (2012d). Specialisations of SEQUAL, (pp. 281–326). London: Springer.Krogstie, J., Lindland, O.I., & Sindre, G. (1995). Defining quality aspects for conceptual models. In Proceedings of the IFIP International Working Conference on Information System Concepts: Towards a Consolidation of Views (pp. 216–231). London: Chapman & Hall, Ltd.Kruchten, P. (2000). The rational unified process: an introduction, 2nd edn. Boston: Addison-Wesley Longman Publishing Co., Inc.Kruchten, P., Nord, R., & Ozkaya, I. (2012). Technical debt: from metaphor to theory and practice. Software, IEEE, 29(6), 18–21.Kulkarni, V., Reddy, S., & Rajbhoj, A. (2010). Scaling up model driven engineering – experience and lessons learnt. In Petriu, D., Rouquette, N., & Haugen, y. (Eds.) Model Driven Engineering Languages and Systems, volume 6395 of Lecture Notes in Computer Science (pp. 331–345). Berlin, Heidelberg: Springer.Laguna, M.A., & Marqués, J.M. (2010). Uml support for designing software product lines: the package merge mechanism, 16(17), 2313–2332.Lange, C. (2007a). Model size matters. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 4364 LNCS:211–216. cited By (since 1996)1.Lange, C., & Chaudron, M. (2005). Managing Model Quality in UML-Based Software Development. In 13th IEEE International Workshop on Technology and Engineering Practice, 2005 (pp. 7–16).Lange, C., Chaudron, M.R.V., Muskens, J., Somers, L.J., & Dortmans, H.M. (2003). An empirical investigation in quantifying inconsistency and incompleteness of uml designs. In Incompleteness of UML Designs, Proceedings Workshop on Consistency Problems in UML-based Software Development, 6th International Conference on Unified Modeling Language, UML, 2003.Lange, C., DuBois, B., Chaudron, M., & Demeyer, S. (2006). An experimental investigation of uml modeling conventions. In Nierstrasz, O., Whittle, J., Harel, D., & Reggio, G. (Eds.) Model Driven Engineering Languages and Systems, volume 4199 of Lecture Notes in Computer Science (pp. 27–41). Berlin, Heidelberg: Springer.Lange, C.F.J., & Chaudron, M.R.V. (2006). Effe

Model-Driven Development of High-Assurance Active Medical Devices

Advanced medical devices exploit the advantages of embedded software whose development is subject to compliance with stringent requirements of standardization and certification regimes due to the critical nature of such systems. This paper presents initial results and lessons learned from an ongoing project focusing on the development of a formal model of a subsystem of a software-controlled safety-critical Active Medical Device (AMD) responsible for renal replacement therapy. The use of formal approaches for the development of AMDs is highly recommended by standards and regulations, and motivates the recent advancement of the state of the art of related methods and tools including Event-B and Rodin applied in this paper. It is expected that the presented model development approach and the specification of a high-confidence medical system will contribute to the still sparse experience base available at the disposal of the scientific and practitioner community of formal methods and software engineering

A Road Map to Bio-inspired Software Engineering

Software production research is quickly evolving on two parallel approaches: conventional and bio-inspired. The bio-inspired approaches are generally developed and presented as enhancements of the conventional ones. However the conventional approaches benefit from their integration with their global context, through software engineering methodologies, for being advantageous.The integration of bio-inspired approaches with bio-inspired software engineering methodologies will enrich them and let them be irrefutably be the best. This paper identify the motivations to the emergence of such bio-inspired software engineering, presents a first approach to it, with a road map, and some of its challenges.The application of this first approach on different software systems categories is presented with its summary evaluation. However, the evaluation on industrial scale remains a challenge.Comment: 08 page

Latent Dirichlet Allocation (LDA) and Topic modeling: models, applications, a survey

Topic modeling is one of the most powerful techniques in text mining for data mining, latent data discovery, and finding relationships among data, text documents. Researchers have published many articles in the field of topic modeling and applied in various fields such as software engineering, political science, medical and linguistic science, etc. There are various methods for topic modeling, which Latent Dirichlet allocation (LDA) is one of the most popular methods in this field. Researchers have proposed various models based on the LDA in topic modeling. According to previous work, this paper can be very useful and valuable for introducing LDA approaches in topic modeling. In this paper, we investigated scholarly articles highly (between 2003 to 2016) related to Topic Modeling based on LDA to discover the research development, current trends and intellectual structure of topic modeling. Also, we summarize challenges and introduce famous tools and datasets in topic modeling based on LDA.Comment: arXiv admin note: text overlap with arXiv:1505.07302 by other author

Spatial Stochastic Modeling with MCell and CellBlender

This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations. Spatial stochastic modeling approaches are indicated when diffusion is relatively slow and spatial inhomogeneities involve relatively small numbers of particles. The popular software package MCell allows particle-based stochastic simulations of biochemical systems in complex three dimensional (3D) geometries, which are important for many cell biology applications. Here, we provide an overview of the simulation algorithms used by MCell and the underlying theory. We then give a tutorial on building and simulating MCell models using the CellBlender graphical user interface, that is built as a plug-in to Blender, a widely-used and freely available software platform for 3D modeling. The tutorial starts with simple models that demonstrate basic MCell functionality and then advances to a number of more complex examples that demonstrate a range of features and provide examples of important biophysical effects that require spatially-resolved stochastic dynamics to capture.Comment: Munsky et al., Quantitative Biology: Theory, Computational Methods, and Models, MIT Press, 201

Shape: A 3D Modeling Tool for Astrophysics

We present a flexible interactive 3D morpho-kinematical modeling application for astrophysics. Compared to other systems, our application reduces the restrictions on the physical assumptions, data type and amount that is required for a reconstruction of an object's morphology. It is one of the first publicly available tools to apply interactive graphics to astrophysical modeling. The tool allows astrophysicists to provide a-priori knowledge about the object by interactively defining 3D structural elements. By direct comparison of model prediction with observational data, model parameters can then be automatically optimized to fit the observation. The tool has already been successfully used in a number of astrophysical research projects.Comment: 13 pages, 11 figures, accepted for publication in the "IEEE Transactions on Visualization and Computer Graphics

A Framework for the Implementation of Industrial Automation Systems Based on PLCs

Industrial automation systems (IASs) are traditionally developed using a sequential approach where the automation software, which is commonly based on the IEC 61131 languages, is developed when the design and in many cases the implementation of mechanical parts have been completed. However, it is claimed that this approach does not lead to the optimal system design and that the IEC 61131 does not meet new challenges in this domain. In this paper, a system engineering process based on the new version of IEC 61131, which supports Object Orientation, is presented. SysML and UML are utilized to introduce a higher layer of abstraction in the design space of IAS and Internet of Things (IoT) is considered as an enabling technology for the integration of Cyber and Cyber-physical components of the system, bringing into the industrial automation domain the benefits of these technologies.Comment: 13 pages, 9 figures Corrected typos. Corrections to Fig. 5a and 9. results unchange

Requirements variability specification for data intensive software

Nowadays, the use of feature modeling technique, in software requirements specification, increased the variation support in Data Intensive Software Product Lines (DISPLs) requirements modeling. It is considered the easiest and the most efficient way to express commonalities and variability among different products requirements. Several recent works, in DISPLs requirements, handled data variability by different models which are far from real world concepts. This,leaded to difficulties in analyzing, designing, implementing, and maintaining this variability. However, this work proposes a software requirements specification methodology based on concepts more close to the nature and which are inspired from genetics. This bio-inspiration has carried out important results in DISPLs requirements variability specification with feature modeling, which were not approached by the conventional approaches.The feature model was enriched with features and relations, facilitating the requirements variation management, not yet considered in the current relevant works.The use of genetics-based methodology seems to be promising in data intensive software requirements variability specification.Comment: 12 page

BeSpaceD: Towards a Tool Framework and Methodology for the Specification and Verification of Spatial Behavior of Distributed Software Component Systems

In this report, we present work towards a framework for modeling and checking behavior of spatially distributed component systems. Design goals of our framework are the ability to model spatial behavior in a component oriented, simple and intuitive way, the possibility to automatically analyse and verify systems and integration possibilities with other modeling and verification tools. We present examples and the verification steps necessary to prove properties such as range coverage or the absence of collisions between components and technical details