Lab for Stem Cell Biology and Metabolic Diseases

SeBiMER is the Bioinformatics Core Facility of IFREMER, the French National Institute for Ocean Science. SeBiMER is in charge of providing a large community of marine biologists with all the requirements (knowledge, softwares and data) to handle small and large scale bioinformatics projects, in a broad range of fields such as metabarcoding (eDNA), (meta-)transcriptomics and genomes assembly & annotaton.

The Biomolecular Artificial Intelligence & Digital Biochemistry (BAID) team is an interdisciplinary research group committed to addressing critical challenges in biomolecular science and biomedicine, such as the inefficiency of traditional drug discovery pipelines, limited understanding of molecular mechanisms, and data scarcity in therapeutic development. To overcome these issues, our research goal is to discover, design, and develop innovative advanced AI models and computational frameworks ...

The ACCR group headed by Prof. Dr. Florian Rambow focuses on resolving and perturbing cancer cell fate decisions to prevent cancer progression and therapy resistance. We leverage the power of spatially resolved single-cell approaches in combination with computational biology to investigate cell state plasticity and the contribution of the tumor microenvironment. Our primary aim is to advance translational precision oncology.

For managing the workflows associated with the CrustyBase web application.

https://tucca-cellag.github.io/

Scipion team located at the National Centre for Biotechnology (CNB, CSIC)

This team and associated Galaxy workflows are maintained by the European Galaxy Team.

Implementation of CausalCoxMGM algorithm and scripts for analysis of simulated and real-world biomedical datasets.

The Computational Earth Sciences (CES) group is a multidisciplinary team with different technical profiles that closely relates to all the other groups in the department. CES supports scientists in their daily work and provides a framework for the most efficient use of IT resources, specializing in HPC. At the same time, the group has different research lines related to profiling and optimization and porting Earth modeling codes toward Exascale computing. The group has links and collaborations ...

Workflows from the Industrial Biotechnology Innovation and Synthetic Biology Accelerator (IBISBA 1.0) project, which is funded by the European Union Horizon 2020 program INRAIA-02 under grant agreement 730976.

The workflows also appear on https://hub.ibisba.eu

This is metadata of human trafficking research conducted by Daniel Tesfa in Tigray and Addis Ababa between October 2024 and March 2025.

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

This document provides a detailed explanation of all the workflows, including their functionalities, problems they address, advantages, disadvantages, implementation requirements, and open points for future versions.

In the age of high-throughput data, computational workflows have made data processing tasks flexible, manageable, and automated. To administer different computational activities in a workflow, different workflow management systems (WMS) are used that necessitate a sophisticated level of standardisation. Standardisation and reproducibility can be achieved by using standard formats for specifying workflows, such as Common Workflow Language (CWL), and provenance gathering with the standard W3C PROV ...

Poster and presentation video by Ambarish Kumar

This is human trafficking vecabulory that explains how terms are used to explore the human trafficking context in Ethiopia.

ConceptScheme URI https://workflowhub.eu/events/11 PREFIX vocab https://workflowhub.eu/events/11 dct:title Human Trafficking Vocabulary dct:description Welcome to Human Trafficking Vocabulary dct:creater https://orcid.org/0000-0002-5115-0231

URI skos:prefLabel@en skos:altLabel@en skos:definition@en skos:narrower(separator=",") skos:notation@en vocab:type_of_data Data Type ...

This workflow is part of the EJP RD case study on CAKUT published here: Bayjanov, J.R., Doornbos, C., Ozisik, O. et al. Integrative analysis of multi-omics data reveals importance of collagen and the PI3K AKT signalling pathway in CAKUT. Sci Rep 14, 20731 (2024). https://doi.org/10.1038/s41598-024-71721-8

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 ...

DeepAnnotation can be used to perform genomic selection (GS), which is a promising breeding strategy for agricultural breeding. DeepAnnotation predicts phenotypes from comprehensive multi-omics functional annotations with interpretable deep learning framework. The effectiveness of DeepAnnotation has been demonstrated in predicting three pork production traits (lean meat percentage at 100 kg [LMP], loin muscle depth at 100 kg [LMD], back fat thickness at 100 kg [BF]) on a population of 1940 Duroc ...

High-throughput phenotyping is addressing the current bottleneck in phenotyping within breeding programs. Imaging tools are becoming the primary resource for improving the efficiency of phenotyping processes and providing large datasets for genomic selection approaches. The advent of AI brings new advantages by enhancing phenotyping methods using imaging, making them more accessible to breeding programs. In this context, we have developed an open Python workflow for analyzing morphology, colour ...

Documentation: https://sanjaynagi.github.io/AmpSeeker/ ...

Code for the high risk autism phenotype paper

This repository implements a fully reproducible pipeline for the autism signature project. It uses invoke tasks and a Docker container for consistent, cross-platform execution.

The entire workflow—data fetching, processing, and figure generation—can be reproduced in a few commands. Much of the code in this repo originated from [ASD ...

Introduction

samba-norovirus is an adaptation of the samba workflow for the specific needs in metabarcoding analyses of norovirus. It is a FAIR scalable workflow integrating, into a unique tool, state-of-the-art bioinformatics and statistical methods to conduct reproducible metabarcoding and eDNA analyses using Nextflow (Di Tommaso et al., 2017). SAMBA performs complete metabarcoding analysis by:

...

SynProtX

An official implementation of our research paper "SynProtX: A Large-Scale Proteomics-Based Deep Learning Model for Predicting Synergistic Anticancer Drug Combinations".

SynProtX is a deep learning model that integrates large-scale proteomics data, molecular graphs, and chemical fingerprints to predict synergistic effects of anticancer drug combinations. It provides robust ...

SAMBA is a FAIR scalable workflow integrating, into a unique tool, state-of-the-art bioinformatics and statistical methods to conduct reproducible eDNA analyses using Nextflow. SAMBA starts processing by verifying integrity of raw reads and metadata. Then all bioinformatics processing is done using commonly used procedure (QIIME 2 and DADA2) but adds new steps relying on dbOTU3 and microDecon to build high quality ASV count tables. Extended statistical analyses are also performed. Finally, SAMBA ...

Introduction

wombat-p pipelines is a bioinformatics analysis pipeline that bundles different workflow for the analysis of label-free proteomics data with the purpose of comparison and benchmarking. It allows using files from the proteomics metadata standard SDRF.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses ...

Click-qPCR

Ultra-simple tool for interactive qPCR data analysis developed by R and Shiny.

Read this document in Japanese (日本語版のユーザーガイドはこちら)

Overview

Click-qPCR is a user-friendly Shiny web application designed for the straightforward analysis of real-time quantitative PCR (qPCR) data.

This tool is readily accessible via a web browser at https://kubo-azu.shinyapps.io/Click-qPCR/, requiring no local installation for end-users. ...

SeuratExtend: An Enhanced Toolkit for scRNA-seq Analysis

Overview

SeuratExtend is an R package designed to provide an improved and easy-to-use toolkit for scRNA-seq analysis and visualization, built upon the Seurat object. While Seurat is a widely-used tool in the R community that offers a foundational framework for scRNA-seq analysis, it has limitations when it comes to more advanced analysis and customized visualization. SeuratExtend expands upon Seurat by offering an array of ...

Annual percentage Change for population in Germany (1950 - 2025)

This workflow run was executed on Galaxy (Workflow Rerun Information)

Workflow: Climate Stripes

Execution Status: scheduled

Executed: 2025-05-27 14:14:07.240149

Workflow Inputs

Formal Input Definitions

• Germany-Population-Annual--Change-2025-05-27-15-17.csv (File)

• Column name to use for plotting (Text)

• Plot Title (Text)

• nxsplit (Integer)

• Description: Number of values per intervals

...

This is the workflow for thesis: A FAIR Data Pipeline for Ecosystem Research, with Machine Learning and Marine Acoustic Data (Jiamian He)

A workflow for performing alignment and phylogeny using protein sequences from the CrusTome database. See crustybase.org/crustome for more information.

Calculate extended gamma-ray source halo using crbeam simulation

This workflows contains a pipeline in Scipion that performs the following steps:

1.1) Import small molecules: introduces a set of small molecular structures in the pipeline as prospective ligands

1.2) Import atomic structure: introduces a protein atomic structure in the pipeline as receptor.

2.1) Ligand preparation: uses RDKit to prepare the small molecules optimizing their 3D structure.

2.2) Receptor preparation: uses bioPython to prepare the receptor structure, removing waters, adding hydrogens ...

This workflow performs the most basic Virtual Drug Screening Pipeline to import a set of small molecules and dock them to an imported protein structure.

This workflow was built for the 2024 Bioinformatics Bootcamp at The Open University. It is meant to occur after the (universal) Filter, plot and explore tutorial to allow analysis of a single cluster.

BVSim: A Benchmarking Variation Simulator Mimicking Human Variation Spectrum

Table of Contents

• Getting Started
• Installation
• General Functions and Parameters
• Shared Parameters
• Output Naming Conventions
• [Write the Relative ...

CausalCoxMGM

Implementation of CausalCoxMGM algorithm and scripts for analysis of simulated and real-world biomedical datasets.

Installation

To install CoxMGM and CausalCoxMGM, run the following command in the terminal:

R CMD INSTALL rCausalMGM 

or alternatively:

R CMD INSTALL rCausalMGM/rCausalMGM_1.0.tar.gz 

Demonstration of CausalCoxMGM with the WHAS500 dataset

First, we begin by loading the necessray R packages for this analysis.

library(rCausalMGM) 
library(survival)
...

EuCanImage FHIR ETL Implementation

This repository contains the ETL implementation for EuCanImage, encouraging semantic interoperability of the clinical data obtained in the studies by transforming it into a machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create the dictionaries following a FHIR compliant structure.

• Code Language is written in Python 3.11. ...

A set of generic and automatic workflows designed to: 

• Run on-the-fly and unattended.

• Maintain robust stability for a wide range of samples.

• Covers steps from movies to CTF estimation (for the moment).

• Monitor the acquisition process and provide user feedback.

• Comprise three proposed workflows, each with an additional layer of complexity.

Collection of workflows exploring data in the Image Data Resource (IDR).

TronFlow is an open source collection of computational workflows originally conceived for tumor-normal somatic variant calling over whole exome data and the manipulation of BAM and VCF files with the aim of having comparable and analysis-ready data. Over time, we have extended it to germline variant calling, copy numbers and other related technologies and analyses.

Its modular architecture covers different analytical and methodological use cases that allow analysing FASTQ files into analysis-ready ...