11 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…
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…
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…
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)…
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…
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…