Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers

L Wratten, A Wilm, J Göke - Nature methods, 2021 - nature.com
The rapid growth of high-throughput technologies has transformed biomedical research.
With the increasing amount and complexity of data, scalability and reproducibility have …

Containerization technologies: Taxonomies, applications and challenges

O Bentaleb, ASZ Belloum, A Sebaa… - The Journal of …, 2022 - Springer
Modern scientific research challenges require new technologies, integrated tools, reusable
and complex experiments in distributed computing infrastructures. But above all, computing …

NCI imaging data commons

A Fedorov, WJR Longabaugh, D Pot, DA Clunie… - Cancer research, 2021 - AACR
Abstract The National Cancer Institute (NCI) Cancer Research Data Commons (CRDC) aims
to establish a national cloud-based data science infrastructure. Imaging Data Commons …

Workflows community summit 2022: A roadmap revolution

RF da Silva, RM Badia, V Bala, D Bard… - arXiv preprint arXiv …, 2023 - arxiv.org
Scientific workflows have become integral tools in broad scientific computing use cases.
Science discovery is increasingly dependent on workflows to orchestrate large and complex …

Data integration challenges for machine learning in precision medicine

M Martínez-García, E Hernández-Lemus - Frontiers in medicine, 2022 - frontiersin.org
A main goal of Precision Medicine is that of incorporating and integrating the vast corpora on
different databases about the molecular and environmental origins of disease, into analytic …

Design considerations for workflow management systems use in production genomics research and the clinic

AE Ahmed, JM Allen, T Bhat, P Burra, CE Fliege… - Scientific reports, 2021 - nature.com
The changing landscape of genomics research and clinical practice has created a need for
computational pipelines capable of efficiently orchestrating complex analysis stages while …

Wfbench: Automated generation of scientific workflow benchmarks

T Coleman, H Casanova, K Maheshwari… - 2022 IEEE/ACM …, 2022 - ieeexplore.ieee.org
The prevalence of scientific workflows with high computational demands calls for their
execution on various distributed computing platforms, including large-scale leadership-class …

[HTML][HTML] Distributed workflows with Jupyter

I Colonnelli, M Aldinucci, B Cantalupo… - Future Generation …, 2022 - Elsevier
The designers of a new coordination interface enacting complex workflows have to tackle a
dichotomy: choosing a language-independent or language-dependent approach. Language …

MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development

GE Parada, R Munita, I Georgakopoulos-Soares… - Genome biology, 2021 - Springer
Background Microexons, exons that are≤ 30 nucleotides, are a highly conserved and
dynamically regulated set of cassette exons. They have key roles in nervous system …

A DICOM framework for machine learning and processing pipelines against real-time radiology images

P Kathiravelu, P Sharma, A Sharma, I Banerjee… - Journal of Digital …, 2021 - Springer
Real-time execution of machine learning (ML) pipelines on radiology images is difficult due
to limited computing resources in clinical environments, whereas running them in research …