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 …

The machine learning life cycle and the cloud: implications for drug discovery

O Spjuth, J Frid, A Hellander - Expert opinion on drug discovery, 2021 - Taylor & Francis
Introduction: Artificial intelligence (AI) and machine learning (ML) are increasingly used in
many aspects of drug discovery. Larger data sizes and methods such as Deep Neural …

[HTML][HTML] Sustainable data analysis with Snakemake

F Mölder, KP Jablonski, B Letcher, MB Hall… - …, 2021 - ncbi.nlm.nih.gov
Data analysis often entails a multitude of heterogeneous steps, from the application of
various command line tools to the usage of scripting languages like R or Python for the …

Predicting blood–brain barrier permeability of molecules with a large language model and machine learning

ETC Huang, JS Yang, KYK Liao, WCW Tseng… - Scientific Reports, 2024 - nature.com
Predicting the blood–brain barrier (BBB) permeability of small-molecule compounds using a
novel artificial intelligence platform is necessary for drug discovery. Machine learning and a …

KoopaML: a graphical platform for building machine learning pipelines adapted to health professionals

F García-Peñalvo, A Vázquez-Ingelmo… - 2024 - reunir.unir.net
Machine Learning (ML) has extended its use in several domains to support complex
analyses of data. The medical field, in which significant quantities of data are continuously …

MasterOfPores: a workflow for the analysis of oxford nanopore direct RNA sequencing datasets

L Cozzuto, H Liu, LP Pryszcz, TH Pulido… - Frontiers in …, 2020 - frontiersin.org
The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for
direct measurement of RNA molecules without the need of conversion to complementary …

[HTML][HTML] Cinco de Bio: A Low-Code Platform for Domain-Specific Workflows for Biomedical Imaging Research

C Brandon, S Boßelmann, A Singh, S Ryan… - …, 2024 - mdpi.com
Background: In biomedical imaging research, experimental biologists generate vast
amounts of data that require advanced computational analysis. Breakthroughs in …

KubeAdaptor: a docking framework for workflow containerization on Kubernetes

C Shan, Y Xia, Y Zhan, J Zhang - Future Generation Computer Systems, 2023 - Elsevier
As Kubernetes becomes the infrastructure of the cloud-native era, the integration of workflow
systems with Kubernetes is gaining more and more popularity. However, when migrating the …

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 …

Predicting off-target binding profiles with confidence using conformal prediction

S Lampa, J Alvarsson, S Arvidsson Mc Shane… - Frontiers in …, 2018 - frontiersin.org
Ligand-based models can be used in drug discovery to obtain an early indication of
potential off-target interactions that could be linked to adverse effects. Another application is …