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 …

A survey of data-intensive scientific workflow management

J Liu, E Pacitti, P Valduriez, M Mattoso - Journal of Grid Computing, 2015 - Springer
Nowadays, more and more computer-based scientific experiments need to handle massive
amounts of data. Their data processing consists of multiple computational steps and …

A survey on collecting, managing, and analyzing provenance from scripts

JF Pimentel, J Freire, L Murta… - ACM Computing Surveys …, 2019 - dl.acm.org
Scripts are widely used to design and run scientific experiments. Scripting languages are
easy to learn and use, and they allow complex tasks to be specified and executed in fewer …

Recording provenance of workflow runs with RO-Crate

S Leo, MR Crusoe, L Rodríguez-Navas, R Sirvent… - PLoS one, 2024 - journals.plos.org
Recording the provenance of scientific computation results is key to the support of
traceability, reproducibility and quality assessment of data products. Several data models …

Workflow provenance in the lifecycle of scientific machine learning

R Souza, LG Azevedo, V Lourenço… - Concurrency and …, 2022 - Wiley Online Library
Abstract Machine learning (ML) has already fundamentally changed several businesses.
More recently, it has also been profoundly impacting the computational science and …

[图书][B] Data-intensive workflow management: for clouds and data-intensive and scalable computing environments

DCM De Oliveira, J Liu, E Pacitti - 2019 - books.google.com
Workflows may be defined as abstractions used to model the coherent flow of activities in the
context of an in silico scientific experiment. They are employed in many domains of science …

Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems

M Djaffardjy, G Marchment, C Sebe, R Blanchet… - Computational and …, 2023 - Elsevier
Data analysis pipelines are now established as an effective means for specifying and
executing bioinformatics data analysis and experiments. While scripting languages …

Provenance analytics for workflow-based computational experiments: A survey

W Oliveira, DD Oliveira, V Braganholo - ACM Computing Surveys (CSUR …, 2018 - dl.acm.org
Until not long ago, manually capturing and storing provenance from scientific experiments
were constant concerns for scientists. With the advent of computational experiments …

[HTML][HTML] Validity constraints for data analysis workflows

F Schintke, K Belhajjame, N De Mecquenem… - Future Generation …, 2024 - Elsevier
Porting a scientific data analysis workflow (DAW) to a cluster infrastructure, a new software
stack, or even only a new dataset with some notably different properties is often challenging …

Challenges of provenance in scientific workflow management systems

K Alam, B Roy - 2022 IEEE/ACM Workshop on Workflows in …, 2022 - ieeexplore.ieee.org
Scientific workflow is one of the well-established pillars of large-scale computational science
and emerged as a torchbearer to formalize and structure a massive amount of complex …