28 papers · ranked by Valyu relevance
Ove Johan Ragnar Gustafsson, Sean R. Wilkinson, Finn Bacall, Stian Soiland-Reyes + 11 more
'Stian Soiland-Reyes' 'Simone Leo' 'Luca Pireddu' 'Stuart Owen' 'Nick Juty' 'José M. Fernández' 'Tom Brown' 'Hervé Ménager' 'Björn Grüning' 'Salvador Capella-Gutierrez' 'Frederik Coppens' 'Carole Goble'] The rising popularity of computational workflows is driven by the need for repetitive and scalable data processing…
Jason P. Kurs, Manuele Simi, Fabien Campagne
Computational workflows and pipelines are often created to automate series of processing steps. For instance, workflows enable one to standardize analysis for large projects or core facilities, but are also useful for individual biologists who need to perform repetitive data processing. Some workflow systems, designed…
Ask Hjorth Larsen, Mikael J. Kuisma, Tara M. Boland, Fredrik A. Nilsson + 1 more
'Fredrik A. Nilsson' 'Kristian S. Thygesen'] We introduce Taskblaster, a generic and lightweight Python framework for composing, executing, and managing computational workflows with automated error handling. Taskblaster supports dynamic workflows including flow control using branches and iteration, making the system…
Gaurav Kaushik, Sinisa Ivkovic, Janko Simonovic, Nebojsa Tijanic + 2 more
As biomedical data becomes increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. However, for the insights gained from these analyses to be meaningful, the analysis methods themselves must be transparent and reproducible. To address this issue, numerous groups have…
Mahnoor Zulfiqar, Michael R. Crusoe, Birgitta König-Ries, Christoph Steinbeck + 2 more
Scientific workflows facilitate the automation of data analysis tasks by integrating various software and tools executed in a particular order. To enable transparency and reusability in workflows, it is essential to implement the FAIR principles. Here, we describe our experiences implementing the FAIR principles for…
Pau Andrio, Adam Hospital, Cristian Ramon-Cortes, Javier Conejero + 4 more
The usage of workflows has led to progress in many fields of science, where the need to process large amounts of data is coupled with difficulty in accessing and efficiently using High Performance Computing platforms. On the one hand, scientists are focused on their problem and concerned with how to process their data.…
Stephen R. Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang + 1 more
Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution…
Levi N. Naden, Sam Ellis, Shantenu Jha
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 the biomolecular science community is varied. MolSSI co-organized a biomolecular…
Tibor Šimko, Lukas Alexander Heinrich, Clemens Lange, Adelina Eleonora Lintuluoto + 5 more
'Adelina Eleonora Lintuluoto' 'Danika Marina MacDonell' 'Audrius Mečionis' 'Diego Rodríguez Rodríguez' 'Parth Shandilya' 'Marco Vidal García'] We describe a novel approach for experimental High-Energy Physics (HEP) data analyses that is centred around the declarative rather than imperative paradigm when describing…
Jan Janssen, Janine George, Julian Geiger, Marnik Bercx + 7 more
Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this challenge, we introduce here the Python Workflow Definition (PWD) as a workflow…
Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines and assist with job automation and aids reproducibility of analyses. Many contemporary workflow tools are specialized and not designed…
Thomas Löhr, Michele Assante, Michael Dodds, Lili Cao + 4 more
'Mikhail A. Kabeshov' 'Jon Paul Janet' 'Marco Klähn' 'Ola Engkvist'] Many computational chemistry and molecular simulation workflows can be expressed as graphs. This abstraction is useful to modularize and potentially reuse existing components, as well as provide parallelization and ease reproducibility. Existing tools…
Raphaël Robidas, Claude Legault
Computational chemistry is an increasingly active field due to the improvement of computing resources and theoretical tools. However, its use remains usually limited to technically-inclined users due to the technical challenges of preparing, launching and analyzing calculations. In this context, we have developed…
Junaid Arshad, Alexander Hoffmann, Sandra Gesing, Richard Grunzke + 4 more
'Jens Krüger' 'Tamas Kiss' 'Sonja Herres-Pawlis' 'Gabor Terstyanszky'] Background In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on…
J. Harry Moore, Matthias R. Bauer, Jeff Guo, Atanas Patronov + 2 more
We present Icolos, a workflow manager written in Python as a tool for automating complex structure-based workflows. Icolos can be used as a standalone tool, for example in virtual screening campaigns, or can be used in conjunction with deep learning-based molecular generation facilitated for example by REINVENT, a…
Philipp Diercks, Dennis Gläser, Ontje Lünsdorf, Michael Selzer + 2 more
'Bernd Flemisch' 'Jörg F. Unger'] - 12205 Berlin, Germany - 2Lehrstuhl für Wasser- und - Umweltsystemmodellierung, Institut für Hydromechanik und Hydrosystemmodellierung, Universität - Stuttgart, Pfaffenwaldring 61, 70569 Stuttgart, Germany 3 Institut für Angewandte Materialien-MMS, - Karlsruher Institut für…
Simon Boothroyd, Lee-Ping Wang, David Mobley, John Chodera + 1 more
Developing accurate classical force field representations of molecules is key to realizing the full potential of molecular simulations, both as a powerful route to gaining fundamental insight into a broad spectrum of chemical and biological phenomena, and for predicting physicochemical and mechanical properties of…
Frédéric Suter, Tainã Coleman, İlkay Altintaş, Rosa M. Badía + 22 more
Fred´ eric Suter ´ a,∗ , Taina Coleman ˜ b,∗ , ˙Ilkay Altintas¸ b , Rosa M. Badia c , Bartosz Balis d , Kyle Chard e , Iacopo Colonnelli f , Ewa Deelman g , Paolo Di Tommaso h , Thomas Fahringer i , Carole Goble j , Shantenu Jha k , Daniel S. Katz l , Johannes Koster ¨ m, Ulf Leser n , Kshitij Mehta a , Hilary Oliver o…
Gordon Gibb, Nick Brown, W Rupert, Nash + 6 more
'Santiago Monedero' 'Humberto Díaz Fidalgo' 'Joaquín Ramirez' 'Adrián Cardíl' 'Max Kontak'] Abstract—In this paper we present a workflow management system which permits the kinds of data-driven workflows required by urgent computing, namely where new data is integrated into the workflow as a disaster progresses in…
Daniel Garijo, Sarah Kinnings, Li Xie, Lei Xie + 4 more
'Philip E. Bourne' 'Yolanda Gil' 'Christos A. Ouzounis'] How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by…
Victor Cuevas-Vicenttín, Saumen Dey, Sven Köhler, Sean Riddle + 1 more
Scientific workflows are becoming increasingly popular for compute-intensive and data-intensive scientific applications. The vision and promise of scientific workflows includes rapid, easy workflow design, reuse, scalable execution, and other advantages, e.g., to facilitate "reproducible science" through provenance…
Peter Kraus, Edan Bainglass, Francisco F. Ramirez, Enea Svaluto-Ferro + 7 more
Compliance with good research data management practices means trust in the integrity of the data, and it is achievable by a full control of the data gathering process. In this work, we demonstrate tooling which bridges these two aspects, and illustrate its use in a case study of automated battery cycling. We…
Pei-Chi Yang, Shweta Purawat, Pek U. Ieong, Mao-Tsuen Jeng + 7 more
Multi-scale computational modeling is a major branch of computational biology as evidenced by the US federal interagency Multi-Scale Modeling Consortium and major international projects. It invariably involves specific and detailed sequences of data analysis and simulation, often with multiple tools and datasets, and…
Jay Jay Billings, Andrew Bennett, Jordan H. Deyton, Kasper Gammeltoft + 9 more
'Kasper Gammeltoft' 'Jonah Graham' 'Dasha Gorin' 'Hari B. Krishnan' 'Menghan Li' 'Alexander McCaskey' 'Taylor Patterson' 'Robert Smith' 'Gregory R. Watson' 'Anna Wójtowicz'] Jay Jay Billings 1 , 2 , Andrew R. Bennett 1 , 3 , Jordan Deyton 1 , 4 , Kasper Gammeltoft 1 , 5 , Jonah Graham 6 , Dasha Gorin 1 , 7 , Hari…
Eftychia Eva Kontou, Axel Walter, Oliver Alka, Julianus Pfeuffer + 5 more
Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for…
Mark P Waller, Thomas Dresselhaus, Jack Yang
Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code.…
Samantha Durdy, Cameron J. Hargreaves, Mark Dennison, Benjamin Wagg + 5 more
The discovery of new materials often requires collaboration between experimental and computational chemists. Web based platforms allow more flexibility in this collaboration by giving access to computational tools without the need for access to computational researchers. We present Liverpool Materials Discovery Server…
Jay Jay Billings, Shantenu Jha
The role of scalable high-performance workflows and flexible workflow management systems that can support multiple simulations will continue to increase in importance. For example, with the end of Dennard scaling, there is a need to substitute a single long running simulation with multiple repeats of shorter…