22 papers · ranked by Valyu relevance
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…
Jan Janssen, Janine George, Julian Geiger, Marnik Bercx + 7 more
'Christina Ertural' 'Joerg Schaarschmidt' 'Alex M. Ganose' 'Giovanni Pizzi' 'Tilmann Hickel' 'Joerg Neugebauer'] 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…
Martin Uhrin, Sebastiaan P. Huber, Ju‐Song Yu, Nicola Marzari + 1 more
'Giovanni Pizzi'] Over the last two decades, the field of computational science has seen a dramatic shift towards incorporating high-throughput computation and big-data analysis as fundamental pillars of the scientific discovery process. This has necessitated the development of tools and techniques to deal with the…
Sebastian Pohl, Nourhan Elfaramawy, Kedi Cao, Birte Kehr + 1 more
'Matthias Weidlich'] Scientific workflows automate the analysis of large-scale scientific data, fostering the reuse of data processing operators as well as the reproducibility and traceability of analysis results. In exploratory research, however, workflows are continuously adapted, utilizing a wide range of tools and…
Caspar Schmitt, T. Kuhr
A workflow describes the entirety of processing steps in an analysis, such as employed in many fields of physics. Workflow management makes the dependencies between individual steps of a workflow and their computational requirements explicit, such that entire workflows can be executed in a stand-alone manner. Though…
Gregor von Laszewski, J. P. Fleischer, Geoffrey Fox
In this paper, we summarize our effort to create and utilize a simple framework to coordinate computational analytics tasks with the help of a workflow system. Our design is based on a minimalistic approach while at the same time allowing to access computational resources offered through the owner's computer, HPC…
Marcin Cieślik, Cameron Mura
Background Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In…
Boris Yamrom, Yoon-ha Lee, Steven Marks, Lubomir Chorbadjiev + 2 more
Snakemake is one of the most popular workflow management systems, particularly in biological sciences. Snakemake workflows are highly portable, scalable, and transparent. Moreover, they enable the painless reproduction of published results and adaption to similar data processing and analysis projects. Here we present…
Malwina Kotowicz, Magdalena Shumanska, Sven Fengler, Birgit Kurkowsky + 14 more
'Birgit Kurkowsky' 'Anja Meyer-Berhorn' 'Elisa Moretti' 'Josephine Blersch' 'Gisela Schmidt' 'Jakob Kreye' 'Scott van Hoof' 'Elisa Sánchez-Sendín' 'S. Momsen Reincke' 'Lars Krüger' 'Harald Prüß' 'Philip Denner' 'Eugenio Fava' 'Dominik Stappert' 'Bhanwar Lal Puniya'] Data management and sample tracking in complex…
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…
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…
Taylor Reiter, Phillip T. Brooks, Luiz Irber, Shannon E.K. Joslin + 4 more
As the scale of biological data generation has increased, the bottleneck of research has shifted from data generation to analysis. Researchers commonly need to build computational workflows that include multiple analytic tools and require incremental development as experimental insights demand tool and parameter…
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…
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…
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…
Hugo López-Fernández, Osvaldo Graña-Castro, Alba Nogueira-Rodríguez, Miguel Reboiro-Jato + 2 more
'Miguel Reboiro-Jato' 'Daniel Glez-Peña' 'Robert Winkler'] Compi is an application framework to develop end-user, pipeline-based applications with a primary emphasis on: (i) user interface generation, by automatically generating a command-line interface based on the pipeline specific parameter definitions; (ii)…
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…
Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
With pull-based workflow tools such as Snakemake or Luigi, it is easy to reproduce a particular output file on-demand because the scheduling mechanism is optimized for the use case of asking for a specific file and calculating all the tasks required to be executed based on that. With push-based workflow tools, however…
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…
Authors not listed
Deriving versatile and robust mechanistic models from experimental data is a key challenge in engineering and natural sciences. This is especially true in chemical reaction engineering, where reactor manufacturers and operators increasingly pursue the development and maintenance of digital twins that rely on frequent…
Authors not listed
This paper presents GLAS (Git-based Lab Automated Scheduler or Get Lab Automation Simplified), an open-source, robust, and highly expandable Git-based architecture designed for laboratory automation. GLAS can be deployed in both partially and fully automated experimental science laboratories, enabling the development…
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…