Proteomics is the large-scale experimental study of the proteome, all the proteins produced or modified by an organism or system. Proteomics can tell us about when and where proteins are expressed, protein production and degradation rates, the characterisation of protein post-translational modifications (e.g. phosphorylation), elucidating protein structures, and protein-protein interactions.This information can be combined with data from other omics disciplines (genomics, metagenomics, metabolomics) ...

Tools and workflows around Next Generation File Formats

EuroScienceGateway will leverage a distributed computing network across 13 European countries, accessible via 6 national, user-friendly web portals, facilitating access to compute and storage infrastructures across Europe as well as to data, tools, workflows and services that can be customized to suit researchers’ needs.EuroScienceGateway will deliver a robust, scalable, seamlessly integrated open infrastructure for data-driven research, contributing an innovative and customizable service for ...

Software and data format standards for management of microscopy image data. Joint project between international private and public research

TRE-FX is assembling leading technology providers from ELIXIR-UK and HDR UK, with three TRE providers and two leading analysis platforms to show through a real reference implementation how we can use secure Research Objects to move between TREs while still supporting the Five Safes principles that govern and protect patient data; all overseen by patient representatives.

Personalized Medicine Center of Excellence

Kataegis refers to the occurrence of regional hypermutation and is a phenomenon observed in a wide range of malignancies. Using changepoint detection katdetectr aims to identify putative kataegis foci from common data-formats housing genomic variants. Katdetectr has shown to be a robust package for the detection, characterization and visualization of kataegis.

Computational Science at Helmholtz-Zentrum Dresden-Rossendorf (HZDR)

A collection of workflows related to air quality predictions, with a focus on the UK.

The principle models used are WRF and EMEP.

Our research is focused on understanding the clinical and genetic basis of inherited heart disease. We use a range of approaches including human gene discovery studies, basic cellular systems, animal models of human disease, and population-based psychosocial and public health studies.Our research involves state-of-the-art approaches including whole exome sequencing, mRNA and microRNA profiling, and RNASeq. Most importantly, we have the key clinical resources, including well phenotyped individual ...

Download all genome from https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide with filter host:viridiplantae and Refseq on.

Poster and presentation video by Ambarish Kumar

Protein domains can be viewed as building blocks, essential for understanding structure-function relationships in proteins. However, each domain database classifies protein domains using its own methodology. Thus, in many cases, boundaries between different domains or families differ from one domain database to the other, raising the question of domain definition and enumeration. The answer to this question cannot be found in a single database. Rather, expert integration and curation of various ...

Introduction

This repository contains all the custom scripts used in the evaluation and comparison of Katdetectr as described in the corresponding Technical Note (under submission).

Usage

All required files were deposited on Zenodo. These can directly be downloaded using zen4R and be used as input.

# Increase the timeout (due to some large files). 
options(timeout=5000)
...

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.

This original image was converted into the Zarr format. The analysis results produced by the authors of the paper were converted into labels and linked to the Zarr file which was placed into a public ...

Learning objectives

• Read data to analyse from an object store.
• Analyse data in parallel using Dask.
• Show how to use public resources to train neural network.
• Load labels associated to the original data
• Compare results with ground truth.

The authors of the PLOS Biology paper, "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures" published in August 2019: https://doi.org/10.1371/journal.pbio.3000388, considered several image ...

IDR is based on OMERO and thus all what we show in this notebook can be easily adjusted for use against another OMERO server, e.g. your institutional OMERO server instance.

The main objective of this notebook is to demonstrate how public resources such as the IDR can be used to train your neural network or validate software tools.

The authors of the PLOS Biology paper, "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures" published in August ...

Learning Objectives

• How to access genomic resource via its Python API
• How to access image resource via its Python API
• Relate image data to genomic data

Diabetes related genes expressed in pancreas

This notebook looks at the question Which diabetes related genes are expressed in the pancreas? Tissue and disease can be modified.

Steps:

• Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the ...

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 ...

Name: Matrix multiplication with Files Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs

Description

Matrix multiplication is a binary operation that takes a pair of matrices and produces another matrix.

If A is an n×m matrix and B is an m×p matrix, the result AB of their multiplication is an n×p matrix defined only if the number of columns m in A is equal to the number of rows m in B. When multiplying A and B, the elements ...

Name: Matrix Multiplication Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs

Description

Matrix multiplication is a binary operation that takes a pair of matrices and produces another matrix.

If A is an n×m matrix and B is an m×p matrix, the result AB of their multiplication is an n×p matrix defined only if the number of columns m in A is equal to the number of rows m in B. When multiplying A and B, the elements of the ...

Gene similariy anaylsis across IMPC physiological systems

A Jupyter Notebook tool for analysing user specified genes cross the different IMPC physiological systems.

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 program will create an heatmap representing the number of phenotypes and the mp term list for each gene contained in an [IMPC physiological ...

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 ...

hutch-workflow executes rquest in one shot.

ZARP

...