The notebook shows how to load an IDR image with labels.

The image is referenced in the paper "NesSys: a novel method for accurate nuclear segmentation in 3D" published August 2019 in PLOS Biology: https://doi.org/10.1371/journal.pbio.3000388 and can be viewed online in the Image Data Resource.

In this notebook, the image is loaded together with the labels and analyzed using StarDist. The StarDist analysis produces a segmentation, which is then viewed side-by-side with the original segmentations ...

Phenotype similarity analysis

A Jupyter Notebook for analyzing phenotyping similarities across user specified genes. Phenotypes are retrieved from the MGI resource

Input

The tool takes as input a list of gene ids (MGI ids or Gene Symbol ids). The elemnts in the list could be separated by a comma, semicolumn, tab or newline.

Operation

The Notebook will create a table where row and columns names are the Gene Symbols of the input elements and each cell will contain the name of the ...

COVID-19 Multiscale Modelling of the Virus and Patients’ Tissue Workflow

Table of Contents

• COVID-19 Multiscale Modelling of the Virus and Patients’ Tissue Workflow
• Table of Contents
• Description
• Contents
• Building Blocks
• Workflows
• Resources
• Tests
• Instructions
• [Local ...

COVID-19 Multiscale Modelling of the Virus and Patients’ Tissue Workflow

Table of Contents

• COVID-19 Multiscale Modelling of the Virus and Patients’ Tissue Workflow
• Table of Contents
• Description
• Contents
• Building Blocks
• Workflows
• Resources
• Tests
• Instructions
• [Local ...

Drug Synergies Screening Workflow

Table of Contents

• Drug Synergies Screening Workflow
• Table of Contents
• Description
• Contents
• Building Blocks
• Workflows
• Resources
• Tests
• Instructions
• Local machine
• Requirements
• Usage steps
• MareNostrum 4

...

Cancer Invasion Workflow

Table of Contents

• Cancer Invasion Workflow
• Table of Contents
• Description
• Contents
• Building Blocks
• Workflows
• Resources
• Tests
• Instructions
• Local machine
• Requirements
• Usage steps
• MareNostrum 4
• [Requirements in ...

Rbbt implementation of the Covid-19 pilot workflow from the Personalized Medicine Center of Excellence.

This workflow processes single cell data to personalize boolean models that are then used in a multi-scale cellular simulation using PhysiBoSS.

COVID-19 Multiscale Modelling of the Virus and Patients’ Tissue Workflow

Table of Contents

• COVID-19 Multiscale Modelling of the Virus and Patients’ Tissue Workflow
• Table of Contents
• Description
• Contents
• Building Blocks
• Workflows
• Resources
• Tests
• Instructions
• [Local ...

Single drug prediction Workflow

Table of Contents

• Single drug prediction Workflow
• Table of Contents
• Description
• Contents
• Building Blocks
• Workflows
• Resources
• Tests
• Instructions
• Local machine
• Requirements
• Usage steps
• MareNostrum 4
• [Requirements ...

metaGOflow: A workflow for marine Genomic Observatories' data analysis

An EOSC-Life project

The workflows developed in the framework of this project are based on pipeline-v5 of the MGnify resource.

This branch is a child of the pipeline_5.1 branch that contains all CWL descriptions of the MGnify ...