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Related papers: Towards a FAIR Documentation of Workflows and Mode…

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This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and…

Biomolecules · Quantitative Biology 2025-04-04 Rommie Amaro , Johan Åqvist , Ivet Bahar , Federica Battistini , Adam Bellaiche , Daniel Beltran , Philip C. Biggin , Massimiliano Bonomi , Gregory R. Bowman , Richard Bryce , Giovanni Bussi , Paolo Carloni , David Case , Andrea Cavalli , Chie-En A. Chang , Thomas E. Cheatham , Margaret S. Cheung , Cris Chipot , Lillian T. Chong , Preeti Choudhary , Gerardo Andres Cisneros , Cecilia Clementi , Rosana Collepardo-Guevara , Peter Coveney , Roberto Covino , T. Daniel Crawford , Matteo Dal Peraro , Bert de Groot , Lucie Delemotte , Marco De Vivo , Jonathan Essex , Franca Fraternali , Jiali Gao , Josep Lluís Gelpí , Francesco Luigi Gervasio , Fernando Danilo Gonzalez-Nilo , Helmut Grubmüller , Marina Guenza , Horacio V. Guzman , Sarah Harris , Teresa Head-Gordon , Rigoberto Hernandez , Adam Hospital , Niu Huang , Xuhui Huang , Gerhard Hummer , Javier Iglesias-Fernández , Jan H. Jensen , Shantenu Jha , Wanting Jiao , William L. Jorgensen , Shina Caroline Lynn Kamerlin , Syma Khalid , Charles Laughton , Michael Levitt , Vittorio Limongelli , Erik Lindahl , Kresten Lindorff-Larsen , Sharon Loverde , Magnus Lundborg , Yun Lyna Luo , Francisco Javier Luque , Charlotte I. Lynch , Alexander MacKerell , Alessandra Magistrato , Siewert J. Marrink , Hugh Martin , J. Andrew McCammon , Kenneth Merz , Vicent Moliner , Adrian Mulholland , Sohail Murad , Athi N. Naganathan , Shikha Nangia , Frank Noe , Agnes Noy , Julianna Oláh , Megan O'Mara , Mary Jo Ondrechen , José N. Onuchic , Alexey Onufriev , Silvia Osuna , Anna R. Panchenko , Sergio Pantano , Carol Parish , Michele Parrinello , Alberto Perez , Tomas Perez-Acle , Juan R. Perilla , B. Montgomery Pettitt , Adriana Pietropalo , Jean-Philip Piquemal , Adolfo Poma , Matej Praprotnik , Maria J. Ramos , Pengyu Ren , Nathalie Reuter , Adrian Roitberg , Edina Rosta , Carme Rovira , Benoit Roux , Ursula Röthlisberger , Karissa Y. Sanbonmatsu , Tamar Schlick , Alexey K. Shaytan , Carlos Simmerling , Jeremy C. Smith , Yuji Sugita , Katarzyna Świderek , Makoto Taiji , Peng Tao , D. Peter Tieleman , Irina G. Tikhonova , Julian Tirado-Rives , Inaki Tunón , Marc W. Van Der Kamp , David Van der Spoel , Sameer Velankar , Gregory A. Voth , Rebecca Wade , Ariel Warshel , Valerie Vaissier Welborn , Stacey Wetmore , Travis J. Wheeler , Chung F. Wong , Lee-Wei Yang , Martin Zacharias , Modesto Orozco

Existing ML benchmarks lack the depth and diversity of annotations needed for evaluating models on business process management (BPM) tasks. BPM is the practice of documenting, measuring, improving, and automating enterprise workflows.…

The rising popularity of computational workflows is driven by the need for repetitive and scalable data processing, sharing of processing know-how, and transparent methods. As both combined records of analysis and descriptions of processing…

The use of approximation is fundamental in computational science. Almost all computational methods adopt approximations in some form in order to obtain a favourable cost/accuracy trade-off and there are usually many approximations that…

Distributed, Parallel, and Cluster Computing · Computer Science 2022-06-14 Michael A. Johnston , Vassilis Vassiliadis

With recent increasing computational and data requirements of scientific applications, the use of large clustered systems as well as distributed resources is inevitable. Although executing large applications in these environments brings…

Distributed, Parallel, and Cluster Computing · Computer Science 2011-06-30 Alexandru Costan , Florin Pop , Corina Stratan , Ciprian Dobre , Catalin Leordeanu , Valentin Cristea

Scientific workflows have become integral tools in broad scientific computing use cases. Science discovery is increasingly dependent on workflows to orchestrate large and complex scientific experiments that range from execution of a…

Distributed, Parallel, and Cluster Computing · Computer Science 2023-04-04 Rafael Ferreira da Silva , Rosa M. Badia , Venkat Bala , Debbie Bard , Peer-Timo Bremer , Ian Buckley , Silvina Caino-Lores , Kyle Chard , Carole Goble , Shantenu Jha , Daniel S. Katz , Daniel Laney , Manish Parashar , Frederic Suter , Nick Tyler , Thomas Uram , Ilkay Altintas , Stefan Andersson , William Arndt , Juan Aznar , Jonathan Bader , Bartosz Balis , Chris Blanton , Kelly Rosa Braghetto , Aharon Brodutch , Paul Brunk , Henri Casanova , Alba Cervera Lierta , Justin Chigu , Taina Coleman , Nick Collier , Iacopo Colonnelli , Frederik Coppens , Michael Crusoe , Will Cunningham , Bruno de Paula Kinoshita , Paolo Di Tommaso , Charles Doutriaux , Matthew Downton , Wael Elwasif , Bjoern Enders , Chris Erdmann , Thomas Fahringer , Ludmilla Figueiredo , Rosa Filgueira , Martin Foltin , Anne Fouilloux , Luiz Gadelha , Andy Gallo , Artur Garcia Saez , Daniel Garijo , Roman Gerlach , Ryan Grant , Samuel Grayson , Patricia Grubel , Johan Gustafsson , Valerie Hayot-Sasson , Oscar Hernandez , Marcus Hilbrich , AnnMary Justine , Ian Laflotte , Fabian Lehmann , Andre Luckow , Jakob Luettgau , Ketan Maheshwari , Motohiko Matsuda , Doriana Medic , Pete Mendygral , Marek Michalewicz , Jorji Nonaka , Maciej Pawlik , Loic Pottier , Line Pouchard , Mathias Putz , Santosh Kumar Radha , Lavanya Ramakrishnan , Sashko Ristov , Paul Romano , Daniel Rosendo , Martin Ruefenacht , Katarzyna Rycerz , Nishant Saurabh , Volodymyr Savchenko , Martin Schulz , Christine Simpson , Raul Sirvent , Tyler Skluzacek , Stian Soiland-Reyes , Renan Souza , Sreenivas Rangan Sukumar , Ziheng Sun , Alan Sussman , Douglas Thain , Mikhail Titov , Benjamin Tovar , Aalap Tripathy , Matteo Turilli , Bartosz Tuznik , Hubertus van Dam , Aurelio Vivas , Logan Ward , Patrick Widener , Sean Wilkinson , Justyna Zawalska , Mahnoor Zulfiqar

Workflow management systems allow the users to develop complex applications at a higher level, by orchestrating functional components without handling the implementation details. Although a wide range of workflow engines are developed in…

Distributed, Parallel, and Cluster Computing · Computer Science 2009-10-06 Alexandru Costan , Corina Stratan , Eliana-Dina Tirsa , Mugurel Ionut Andreica , Valentin Cristea

Large Language Models (LLMs) have recently demonstrated remarkable performance in tasks such as Retrieval-Augmented Generation (RAG) and autonomous AI agent workflows. Yet, when faced with large sets of unstructured documents requiring…

Databases · Computer Science 2025-02-25 Longbin Lai , Changwei Luo , Yunkai Lou , Mingchen Ju , Zhengyi Yang

Since their proposal in 2016, the FAIR principles have been largely discussed by different communities and initiatives involved in the development of infrastructures to enhance support for data findability, accessibility, interoperability,…

This paper introduces the MAESTRO workflow, that enables the coupling of the PORTALS framework [P. Rodriguez-Fernandez et al, Nucl. Fusion 2024] with external solvers for the plasma equilibrium, pedestal physics, divertor constraints and…

From a data perspective, the materials mechanics field is characterized by sparsity of available data, mainly due to the strong microstructure-sensitivity of properties like strength, fracture toughness, and fatigue limit. This requires…

Computational Physics · Physics 2024-11-19 Ronak Shoghi , Alexander Hartmaier

The landscape of workflow systems for scientific applications is notoriously convoluted with hundreds of seemingly equivalent workflow systems, many isolated research claims, and a steep learning curve. To address some of these challenges…

To retrieve and compare scientific data of simulations and experiments in materials science, data needs to be easily accessible and machine readable to qualify and quantify various materials science phenomena. The recent progress in open…

Materials Science · Physics 2025-03-25 Balduin Katzer , Steffen Klinder , Katrin Schulz

In the world of Big Data analytics, there is a series of tools aiming at simplifying programming applications to be executed on clusters. Although each tool claims to provide better programming, data and execution models, for which only…

Distributed, Parallel, and Cluster Computing · Computer Science 2016-06-17 Claudia Misale , Maurizio Drocco , Marco Aldinucci , Guy Tremblay

Markov Logic Networks join probabilistic modeling with first-order logic and have been shown to integrate well with the Semantic Web foundations. While several approaches have been devised to tackle the subproblems of rule mining,…

Databases · Computer Science 2017-11-07 Tommaso Soru , Diego Esteves , Edgard Marx , Axel-Cyrille Ngonga Ngomo

Reproducibility of computational results remains a challenge in materials science, as simulation workflows and parameters are often reported only in unstructured text and tables. While literature data are valuable for validation and reuse,…

The digitalisation of research requires data management systems capable of supporting a broad spectrum of usage scenarios, ranging from document-oriented repositories to fully factographic environments. This paper introduces a…

Digital Libraries · Computer Science 2025-10-22 Victor Dudarev , Alfred Ludwig

Legal practitioners, particularly those early in their careers, face complex, high-stakes tasks that require adaptive, context-sensitive reasoning. While AI holds promise in supporting legal work, current datasets and models are narrowly…

Workflows in biomolecular science are very important as they are intricately intertwined with the scientific outcomes, as well as algorithmic and methodological innovations. The use and effectiveness of workflow tools to meet the needs of…

Software Engineering · Computer Science 2019-05-29 Levi N. Naden , Sam Ellis , Shantenu Jha

Machine learning has been increasingly applied in climate modeling on system emulation acceleration, data-driven parameter inference, forecasting, and knowledge discovery, addressing challenges such as physical consistency, multi-scale…