13 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…
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…
Scott White, John Quinn, Jennifer Enzor, Janet Staats + 6 more
'Sarah M. Mosier' 'James Almarode' 'Thomas N. Denny' 'Kent J. Weinhold' 'Guido Ferrari' 'Cliburn Chan'] An important challenge for primary or secondary analysis of cytometry data is how to facilitate productive collaboration between domain and quantitative experts. Domain experts in cytometry laboratories and core…
Amruta Kale, Ziheng Sun, Xiaogang Ma
Computational workflows are widely used in data analysis, enabling automated tracking of steps and storage of provenance information, leading to innovation and decision-making in the scientific community. However, the growing popularity of workflows has raised concerns about reproducibility and reusability which can…
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…
Damien J. Mannion, Maria del Mar Quiroga, Jacob M. Paul, Marta I. Garrido
The processing of neuroimaging data typically involves a complicated set of operations, which often require different software packages and have intensive computational and storage demands. Although there are many options available for the neuroimaging researcher to establish their preferred set of processing…
Daniel J.B. Clarke, John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino + 38 more
'Giacomo B. Marino' 'Anna I. Byrd' 'Mano R. Maurya' 'Sumana Srinivasan' 'Keyang Yu' 'Varduhi Petrosyan' 'Matthew E. Roth' 'Miroslav Milinkov' 'Charles Hadley King' 'Jeet Kiran Vora' 'Jonathon Keeney' 'Christopher Nemarich' 'William Khan' 'Alexander Lachmann' 'Nasheath Ahmed' 'Alexandra Agris' 'Juncheng Pan' 'Srinivasan…
Michael J. Roach, N. Tessa Pierce-Ward, Radoslaw Suchecki, Vijini Mallawaarachchi + 6 more
'Vijini Mallawaarachchi' 'Bhavya Papudeshi' 'Scott A. Handley' 'C. Titus Brown' 'Nathan S. Watson-Haigh' 'Robert A. Edwards' 'Scott Markel'] Introduction As bioinformatics analyses increase in size and complexity, workflow managers are becoming more popular for building pipelines [1-3]. Workflow managers, such as…
Azza E. Ahmed, Joshua M. Allen, Tajesvi Bhat, Prakruthi Burra + 16 more
'Christina E. Fliege' 'Steven N. Hart' 'Jacob R. Heldenbrand' 'Matthew E. Hudson' 'Dave Deandre Istanto' 'Michael T. Kalmbach' 'Gregory D. Kapraun' 'Katherine I. Kendig' 'Matthew Charles Kendzior' 'Eric W. Klee' 'Nate Mattson' 'Christian A. Ross' 'Sami M. Sharif' 'Ramshankar Venkatakrishnan' 'Faisal M. Fadlelmola'…
Károly Bósa, Paul Heinzlreiter
Background Data preparation is a fundamental aspect of data engineering, a prerequisite for later tasks such as data visualization, reporting, and training machine learning models. Despite the recurring patterns in data transformation processes, the specific steps often vary depending on the project context, data…
Le Zhang, Daniela Cassol, Brendan Gongol, Thomas Girke
Workflow management systems (WMS) are essential for creating and automating multi-step data analyses and ensuring the reproducibility of biological insights. Although numerous WMS solutions exist, few provide deep integration of command-line software with the R and Bioconductor ecosystems, where a substantial portion…
Francesco Strozzi, Roel Janssen, Ricardo Wurmus, Michael R. Crusoe + 7 more
'George Githinji' 'Paolo Di Tommaso' 'Dominique Belhachemi' 'Steffen Möller' 'Geert Smant' 'Joep de Ligt' 'Pjotr Prins'] Biological, clinical, and pharmacological research now often involves analyses of genomes, transcriptomes, proteomes, and interactomes, within and between individuals and across species. Due to large…
Fabrice Allain, Julien Roméjon, Philippe La Rosa, Frédéric Jarlier + 2 more
'Nicolas Servant' 'Philippe Hupé'] With the advent of high-throughput biotechnological platforms and their ever-growing capacity, life science has turned into a digitized, computational and data-intensive discipline. As a consequence, standard analysis with a bioinformatics pipeline in the context of routine production…