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arXiv 2019年

作者： Dargaville, S. Buchan, A.G. Smedley-Stevenson, R.P. Smith, P.N. Pain, C.C. Applied Modelling and Computation Group Imperial College LondonSW7 2AZ United Kingdom School of Engineering and Material Sciences Queen Mary University of London E14 NS United Kingdom AWE Aldermaston ReadingRG7 4PR United Kingdom ANSWERS Software Service Wood PLC Kimmeridge House Dorset Green Technology Park DorchesterDT2 8ZB United Kingdom

This paper describes an angular adaptivity algorithm for Boltzmann transport applications which for the first time shows evidence of O(n) scaling in both runtime and memory usage, where n is the number of adapted angles. This adaptivity uses Haar wavelets, which perform structured h-adaptivity built on top of a hierarchical P0 FEM discretisation of a 2D angular domain, allowing different anisotropic angular resolution to be applied across space/energy. Fixed angular refinement, along with regular and goal-based error metrics are shown in three example problems taken from neutronics/radiative transfer applications. We use a spatial discretisation designed to use less memory than competing alternatives in general applications and gives us the flexibility to use a matrix-free multgrid method as our iterative method. This relies on scalable matrix-vector products using Fast Wavelet Transforms and allows the use of traditional sweep algorithms if desired. Copyright © 2019, The Authors. All rights reserved.

关键词： Iterative methods

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Approaches to model transformation reuse (Invited talk): From concepts to a-posteriori typing 9th

Approaches to model transformation reuse (Invited talk): Fro...

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9th International Conference on Theory and Practice of Model Transformations, ICMT 2016 Held as Part of Conference on software Technologies: Applications and Foundations, STAF 2016

作者： De Lara, Juan Modelling and Software Engineering Group Universidad Autónoma de Madrid Spain

ISBN: (纸本)9783319420639

Models are the main assets of Model-Driven engineering (MDE), and hence model transformations are essential to automate the model manipulations required by MDE. Different kinds of transformations are common in MDE, like in-place, model-to-model, or model-to-text. In all cases, their definition is based on the meta-models of the models to be manipulated. However, the proliferation of meta-models in MDE (e.g., in connection with Domain-Specific Languages, DSLs) complicates transformation reuse. This is so as transformations are defined for particular meta-models and are not applicable to other meta-models, even if they have some commonalities. Therefore, in order to facilitate the creation of DSL-based MDE solutions, flexible means to reuse transformations across heterogeneous meta-models are required. © Springer International Publishing Switzerland 2016.

关键词： Problem oriented languages

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The need to implement FAIR principles in biomolecular simulations

arXiv

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arXiv 2024年

作者： Amaro, R. Åqvist, J. Bahar, I. Battistini, F. Bellaiche, A. Beltran, D. Biggin, P.C. Bonomi, M. Bowman, G.R. Bryce, R. Bussi, G. Carloni, P. Case, D. Cavalli, A. Chang, C.A. Cheatham, T.E. Cheung, M.S. Chipot, C. Chong, L.T. Choudhary, P. Cisneros, G.A. Clementi, C. Collepardo-Guevara, R. Coveney, P. Covino, R. Crawford, T.D. Dal Peraro, M. de Groot, B. Delemotte, L. De Vivo, M. Essex, J. Fraternali, F. Gao, J. Gelpí, J.L. Gervasio, F.L. Gonzalez-Nilo, F.D. Grubmüller, H. Guenza, M.G. Guzman, H.V. Harris, S. Head-Gordon, T. Hernandez, R. Hospital, A. Huang, N. Huang, X. Hummer, G. Iglesias-Fernández, J. Jensen, J.H. Jha, S. Jiao, W. Jorgensen, W.L. Kamerlin, S.C.L. Khalid, S. Laughton, C. Levitt, M. Limongelli, V. Lindahl, E. Lindorff-Larsen, K. Loverde, S. Lundborg, M. Luo, Y.L. Luque, F.J. Lynch, C.I. MacKerell, A. Magistrato, A. Marrink, S.J. Martin, H. McCammon, J.A. Merz, K. Moliner, V. Mulholland, A. Murad, S. Naganathan, A.N. Nangia, S. Noe, F. Noy, A. Oláh, J. O'Mara, M. Ondrechen, M.J. Onuchic, J.N. Onufriev, A. Osuna, S. Palermo, G. Panchenko, A.R. Pantano, S. Parish, C. Parrinello, M. Perez, A. Perez-Acle, T. Perilla, J.R. Pettitt, B.M. Pietropaolo, A. Piquemal, J.-P. Poma, A. Praprotnik, M. Ramos, M.J. Ren, P. Reuter, N. Roitberg, A. Rosta, E. Rovira, C. Roux, B. Röthlisberger, U. Sanbonmatsu, K. Schlick, T. Shaytan, A.K. Simmerling, C. Smith, J.C. Sugita, Y. Świderek, K. Taiji, M. Tao, P. Tikhonova, I.G. Tirado-Rives, J. Tuñón, I. Van Der Kamp, M.W. Van der Spoel, D. Velankar, S. Voth, G.A. Wade, R. Warshel, A. Welborn, V.V. Wetmore, S. Wong, C.F. Yang, L.-W. Zacharias, M. Orozco, M. Department of Molecular Biology University of California San DiegoCA United States Department of Cell and Molecular Biology Uppsala University Uppsala Sweden Laufer Center for Physical and Quantitative Biology Renaissance School of Medicine Stony Brook University Stony BrookNY United States Department of Biochemistry and Cell Biology Renaissance School of Medicine Stony Brook University Stony BrookNY United States Barcelona Spain European Molecular Biology Laboratory European Bioinformatics Institute Hinxton United Kingdom Structural Bioinformatics and Computational Biochemistry Department of Biochemistry University of Oxford Oxford United Kingdom Institut Pasteur Université Paris Cité CNRS UMR 3528 Computational Structural Biology Unit Paris France Department of Biochemistry and Biophysics University of Pennsylvania PhiladelphiaPA United States Division of Pharmacy and Optometry University of Manchester Manchester United Kingdom Scuola Internazionale Superiore di Studi Avanzati-SISSA Trieste Italy Computational Biomedicine Institute of Advanced Simulations IAS-5 Institute for Neuroscience and Medicine INM-9 Forschungszentrum Jülich GmbH Jülich Germany Department of Physics and Universitätsklinikum RWTH Aachen University Aachen Germany Department of Chemistry & Chemical Biology Rutgers University PiscatawayNJ United States Istituto Italiano di Tecnologia Drug Discovery and Development Bologna Italy Lausanne Switzerland Department of Chemistry University of California RiversideCA United States Department of Medicinal Chemistry College of Pharmacy University of Utah Salt Lake CityUT United States Department of Physics University of Washington SeattleWA United States Pacific Northwest National Laboratory RichlandWA United States LIA CNRS-UIUC UMR n°7019 Université de Lorraine Vandœuvre-lès-Nancy France Department of Physics University of Illinois at Urbana-Champaign UrbanaIL United States Department of Biochemistry and Molecular Biol

The communities that embraced data archiving efforts decades ago are now, in the era of data-driven biology, those gaining the most from the AI revolution. The structural biology community was a pioneer in this regard by establishing the Protein Data Bank (PDB) in 1971 and making data accessible using the FAIR (Findable, Accessible, Interoperable and Reusable) principles even before these were articulated [1, 2]. The genomics/bioinformatics community has followed the example, establishing many widely used databases [3, 4]. By contrast, molecular simulation has been anchored in usage paradigms dating back to the seventies, when molecular dynamics (MD) simulation was first applied to study biomacromolecules [5]. At that time, MD was used by theoretical physicists and chemists in "proof of concept" simulations. Still, fifty years later, MD has evolved into a cornerstone molecular biology technique that can provide accurate quantitative analysis and property prediction. MD is now employed by tens of thousands of researchers worldwide, accounting for roughly 15% of global supercomputer usage. Unfortunately, these rich and costly data are not systematically maintained, and when further analyses are required, simulations have to be rerun-an unacceptable situation from scientific, environmental and sustainability standpoints. In this letter, we argue for a collaborative endeavor to archive MD simulation data and describe ongoing efforts to establish cost-effective and sustainable data archiving strategies. © 2024, CC BY-NC-SA.

关键词： Biotic

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An Extensible Meta-modelling Assistant

An Extensible Meta-Modelling Assistant

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International Conference on Enterprise Distributed Object Computing (EDOC)

作者： Angel Mora Segura Ana Pescador Juan de Lara Manuel Wimmer Modelling and Software Engineering Research Group Universidad Autónoma de Madrid Spain Business Informatics Group TU Wien Austria

ISBN: (纸本)9781467398862

Meta-models play a pivotal role in Model-Driven engineering (MDE). They are used to create domain-specific models, and to type model management operations like model transformations or code generators. However, even though creating meta-models is a common activity, it is currently mostly a manual activity, which does not profit from existing knowledge. In order to facilitate the meta-modelling task, we propose an extensible meta-modelling assistant. While primarily focussed on helping in the creation of meta- models, it can also help in creating models. The assistant permits the provision of heterogeneous data description sources (like ontologies, RDF data, XML schemas, database schemas and meta-models), and enables their uniform querying. Different kinds of queries are supported, and improved through synonym search. Query results are prioritized through sense disambiguation, can be graphically visualized, and incorporated into the (meta-)model being built. The assistant has been realized within Eclipse, and its architecture has been designed to be independent of the meta-modelling technology used. As a proof- of-concept, we show its integration within DSL-tao, a pattern-based meta-modelling tool built by our group, and two other tools developed by third-parties. The usefulness of the system is illustrated with a running example in the process modelling domain.

关键词： Unified modeling language Biological system modeling DSL Data models Ontologies Resource description framework Organizations

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Recursion and Iteration support in USE validator with AnATLyzer 15

Recursion and Iteration support in USE validator with AnATLy...

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15th International Workshop on OCL and Textual Modeling, OCL 2015

作者： Cuadrado, Jesús Sánchez Modelling and Software Engineering Research Group Universidad Autónoma de Madrid Spain

Model finders enable numerous verification approaches based on searching the existence of models satisfying certain properties of interest. One of such approaches is AnATLyzer, a static analysis tool for ATL transformations, which relies on USE Validator to provide fine grained analysis based on finding witness models that satisfy the OCL path conditions associated to particular errors. However it is limited by the fact that USE Validator does not include built-in support for analysing recursive operations and the iterate collection operator. This paper reports our approach to allow USE Validator to analyse OCL path conditions containing recursive operations and iterate, with the aim of widening the amount of actual transformations that can be processed by AnATLyzer. We present our approach, based on unfolding recursion into a finite number of steps, and we discuss how to take into account practical aspects such as inheritance and details about the implementation.

关键词： Static analysis

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Reusable model transformation components with bentō 8th

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8th International Conference on Theory and Practice of Model Transformations, ICMT 2015

作者： Cuadrado, Jesús Sánchez Guerra, Esther de Lara, Juan Modelling and Software Engineering Research Group Universidad Autónoma de Madrid Madrid Spain

ISBN: (纸本)9783319211541

Building high-quality transformations that can be used in real projects is complex and time-consuming. For this reason, the ability to reuse existing transformations in different, unforeseen scenarios is very valuable. However, there is scarce tool support for this task. This paper presents bentō, a tool which supports the development and execution of reusable transformation components. In bentō, a reusable transformation is written as a regular ATL transformation, but it uses concepts as meta-models. Reuse is achieved by binding such concepts to meta-models, which induces the transformation adaptation. Moreover, composite components enable chaining transformations, and it is possible to convert an existing transformation into a reusable component. Bentō is implemented as an Eclipse plug-in, available as free software. © Springer International Publishing Switzerland 2015.

关键词： Computers

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Building MDE cloud services with DISTIL 3

Building MDE cloud services with DISTIL

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3rd International Workshop on Model-Driven engineering on and for the Cloud, CloudMDE 2015

作者： Manzanares, Carlos Carrascal Cuadrado, Jesús Sánchez De Lara, Juan Modelling and Software Engineering Research Group Computer Science Department Universidad Autónoma de Madrid Spain

Model-Driven engineering (MDE) techniques, like transformations, queries, and code generators, were devised for local, single-CPU architectures. However, the increasing complexity of the systems to be built and their high demands in terms of computation, memory and storage, requires more scalable and flexible MDE techniques, likely using services and the cloud. Nonetheless, the cost of developing MDE solutions on the cloud is high without proper automation mechanisms. In order to alleviate this situation, we present DISTIL, a domain-specific language to describe MDE services, which is able to generate (NoSQL-based) respositories for the artefacts of interest, and skeletons for (single or composite) services, ready to be deployed in Heroku. We illustrate the approach through the construction of a repository and a set of cloud-based services for bentō reusable transformation components.

关键词： Problem oriented languages

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Scalable model exploration through abstraction and fragmentation strategies 3

Scalable model exploration through abstraction and fragmenta...

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3rd Workshop on Scalable Model Driven engineering, BigMDE 2015

作者： Garmendia, Antonio Jiménez-Pastor, Antonio De Lara, Juan Modelling and Software Engineering Research Group Computer Science Department Universidad Autónoma de Madrid Spain

Model-Driven engineering (MDE) promotes the use of models to conduct all phases of software development in an automated way. However, for complex systems, these models may become large and unwieldy, and hence difficult to process and comprehend. In order to alleviate this situation, we explore the combination of model fragmentation strategies, to split models into more manageable chunks;and model abstraction and visualization mechanisms, able to provide simpler views of the models. The feasibility of this combination is confirmed based on an evaluation over a synthetic models, and the model sets of the GraBaTs'09 contest.

关键词： software design

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Rapid development of interactive applications based on online social networks

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2014年 8787卷 505-520页

作者： Segura, Ángel Mora De Lara, Juan Cuadrado, Jesús Sánchez Modelling and Software Engineering Group Department of Computer Science Universidad Autónoma de Madrid Spain

Online social networks, like Twitter or Google+, are widely used for all kind of purposes, and the proliferation of smartphones enables their use anywhere, anytime. The instant messaging capabilities of these services are used in an ad-hoc way for social activities, like organizing meetings or gathering preferences among a group of friends, or as a means to contact community managers of companies or *** with automation mechanisms, posts (messages in social networks) can be used as a dialogue mechanism between users and computer applications. In this paper we propose the concept of post-based application, an application that uses short messages as a medium to obtain input commands from users and produce outputs, describing several scenarios where these applications are of interest. In addition, we provide an automated, Model-Driven engineering approach (currently targeting Twitter) for their rapid construction, including dedicated Domain-Specific Languages to express the interesting parts to be detected in posts;and query matched posts, aggregate information or synthesize posts. © Springer International Publishing Switzerland 2014.

关键词： Social networking (online)

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Reverse engineering of model transformations for reusability

Reverse engineering of model transformations for reusability

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7th International Conference on Model Transformation, ICMT 2014, Part of the software Technology: Applications and Foundations, STAF 2014

作者： Cuadrado, Jesús Sánchez Guerra, Esther De Lara, Juan Modelling and Software Engineering Research Group Universidad Autónoma de Madrid Spain

ISBN: (纸本)9783319087887

Reuse techniques are key for the industrial adoption of Model-Driven engineering (MDE). However, while reusability has been successfully applied to programming languages, its use is scarce in MDE and, in particular, in model transformations. In previous works, we developed an approach that enables the reuse of model transformations for different meta-models. This is achieved by defining reusable components that encapsulate a generic transformation template and expose an interface called concept declaring the structural requirements that any meta-model using the component should fulfil. Binding the concept to one of such meta-models induces an adaptation of the template, which becomes applicable to the meta-model. To facilitate reuse, concepts need to be concise, reflecting only the minimal set of requirements demanded by the transformation. In this paper, we automate the reverse engineering of existing transformations into reusable transformation components. To make a transformation reusable, we use the information obtained from its static analysis to derive a concept that is minimal with respect to the transformation and maximizes its reuse opportunities, and then evolve the transformation accordingly. The paper describes a prototype implementation and an evaluation using transformations from the ATL zoo. © 2014 Springer International Publishing Switzerland.

关键词： Reusability

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