Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities

S Cohen-Boulakia, K Belhajjame, O Collin… - Future Generation …, 2017 - Elsevier
With the development of new experimental technologies, biologists are faced with an
avalanche of data to be computationally analyzed for scientific advancements and …

Scientific workflows: moving across paradigms

CS Liew, MP Atkinson, M Galea, TF Ang… - ACM Computing …, 2016 - dl.acm.org
Modern scientific collaborations have opened up the opportunity to solve complex problems
that require both multidisciplinary expertise and large-scale computational experiments …

Methods included: standardizing computational reuse and portability with the common workflow language

MR Crusoe, S Abeln, A Iosup, P Amstutz… - Communications of the …, 2022 - dl.acm.org
Methods included: standardizing computational reuse and portability with the Common
Workflow Language Page 1 54 COMMUNICATIONS OF THE ACM | JUNE 2022 | VOL. 65 …

Tximeta: Reference sequence checksums for provenance identification in RNA-seq

MI Love, C Soneson, PF Hickey… - PLoS computational …, 2020 - journals.plos.org
Correct annotation metadata is critical for reproducible and accurate RNA-seq analysis.
When files are shared publicly or among collaborators with incorrect or missing annotation …

Packaging research artefacts with RO-Crate

S Soiland-Reyes, P Sefton, M Crosas, LJ Castro… - Data …, 2022 - content.iospress.com
An increasing number of researchers support reproducibility by including pointers to and
descriptions of datasets, software and methods in their publications. However, scientific …

Big data hurdles in precision medicine and precision public health

M Prosperi, JS Min, J Bian, F Modave - BMC medical informatics and …, 2018 - Springer
Background Nowadays, trendy research in biomedical sciences juxtaposes the term
'precision'to medicine and public health with companion words like big data, data science …

A characterization of workflow management systems for extreme-scale applications

RF Da Silva, R Filgueira, I Pietri, M Jiang… - Future Generation …, 2017 - Elsevier
Automation of the execution of computational tasks is at the heart of improving scientific
productivity. Over the last years, scientific workflows have been established as an important …

Scientific workflows: Past, present and future

M Atkinson, S Gesing, J Montagnat, I Taylor - Future Generation Computer …, 2017 - Elsevier
This special issue and our editorial celebrate 10 years of progress with data-intensive or
scientific workflows. There have been very substantial advances in the representation of …

Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online …

Y Guitton, M Tremblay-Franco, G Le Corguillé… - … International Journal of …, 2017 - Elsevier
Metabolomics is a key approach in modern functional genomics and systems biology. Due
to the complexity of metabolomics data, the variety of experimental designs, and the …

FAIR computational workflows

C Goble, S Cohen-Boulakia, S Soiland-Reyes… - Data …, 2020 - direct.mit.edu
Computational workflows describe the complex multi-step methods that are used for data
collection, data preparation, analytics, predictive modelling, and simulation that lead to new …