Workflow engine (13)#
AI4Life teams up with Galaxy Training Network (GTN) to enhance training resources#
Caterina Fuster-Barceló
Licensed UNKNOWN
Tags: Artificial Intelligence, Workflow Engine, Bioimage Analysis
Content type: Documentation
BiaPy: Bioimage analysis pipelines in Python#
Daniel Franco-Barranco, et al.
BiaPy is an open source Python library for building bioimage analysis pipelines, also called workflows.
Tags: Workflow Engine, Python
Content type: Documentation
BioEngine#
Jeremy Metz, Beatriz Serrano-Solano, Wei Ouyang
Licensed UNKNOWN
BioEnging is a cloud infrastructure to run BioImage model zoo based workflows in the cloud.
Tags: Artificial Intelligence, Workflow Engine
Content type: Publication
BioEngine Documentation#
Wei Ouyang, Nanguage, Jeremy Metz, Craig Russell
Licensed MIT
BioEngine, a Python package designed for flexible deployment and execution of bioimage analysis models and workflows using AI, accessible via HTTP API and RPC.
Tags: Workflow Engine, Deep Learning, Python
Content type: Documentation
Fractal Documentation#
Fractal is a framework to process high-content imaging data at scale and prepare it for interactive visualization.
Tags: Workflow Engine, Python
Content type: Documentation
Galaxy Documentation#
Galaxy is an open source, web-based platform for data intensive biomedical research.
Tags: Workflow Engine
Content type: Documentation
JIPipe: visual batch processing for ImageJ#
Ruman Gerst, Zoltán Cseresnyés, Marc Thilo Figge
JIPipe is an open-source visual programming language for easy-access pipeline development
Tags: Workflow Engine, Imagej
Content type: Publication, Documentation
MiToBo - A Toolbox for Image Processing and Analysis#
Birgit Möller, Markus Glaß, Danny Misiak, Stefan Posch
The Microscope Image Analysis Toolbox is a toolbox with a collection of algorithms for processing and analyzing digital images.
Tags: Workflow Engine, Imagej
Content type: Publication, Documentation
https://openresearchsoftware.metajnl.com/articles/10.5334/jors.103
ModularImageAnalysis (MIA): Assembly of modularisedimage and object analysis workflows in ImageJ#
Stephen J. Cross, Jordan D. J. R. Fisher, Mark A. Jepson
ModularImageAnalysis is a Fiji plugin providing a modular framework for assembling image and object analysis workflows
Tags: Workflow Engine, Imagej
Content type: Publication, Documentation
NextFlow documentation#
Nextflow enables scalable and reproducible scientific workflows using software containers.
Tags: Workflow Engine
Content type: Documentation
Nextflow: Scalable and reproducible scientific workflows#
Floden Evan, Di Tommaso Paolo
Published 2020-12-17
Licensed CC-BY-4.0
Nextflow is an open-source workflow management system that prioritizes portability and reproducibility. It enables users to develop and seamlessly scale genomics workflows locally, on HPC clusters, or in major cloud providers’ infrastructures. Developed since 2014 and backed by a fast-growing community, the Nextflow ecosystem is made up of users and developers across academia, government and industry. It counts over 1M downloads and over 10K users worldwide.
Tags: Workflow Engine
Content type: Slide
Snakemake Documentation#
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
Tags: Workflow Engine, Python
Content type: Documentation
https://snakemake.readthedocs.io/en/stable/
https://academic.oup.com/bioinformatics/article/28/19/2520/290322
WorkflowHub#
Stian Soiland-Reyes, Finn Bacall, Bert Droesbeke, Alan R Williams, Johan Gustafsson, et al.
Licensed BSD-3-CLAUSE
A registry for describing, sharing and publishing scientific computational workflows.
Tags: Bioinformatics, Workflow, Workflow Engine, Python, R
Content type: Collection