Workflows associated with the ELIXIR Biodiversity Community. The domain focuses on genomics, ecology, biogeography and the evolution of wildlife across all kingdoms of life.

WhiteSymmetry

An Interpretable Graph-Regularized Optimal Transport Framework for Diagonal Single-Cell Integrative Analysis

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.

KececiLayout

Kececi Layout (Keçeci Yerleşimi): A deterministic graph layout algorithm designed for visualizing linear or sequential structures with a characteristic "zig-zag" or "serpentine" pattern.

Python implementation of the Keçeci layout algorithm for graph visualization. Description / Açıklama

This algorithm arranges nodes sequentially along a primary axis and offsets them alternately along a secondary axis. It's particularly useful for path graphs, chains, or showing progression.

Bu ...

Keçeci Fractals: Keçeci Fraktals

Keçeci Circle Fractal: Keçeci-style circle fractal.

Description / Açıklama

Keçeci Circle Fractal: Keçeci-style circle fractal.:

Many systems encountered in nature and engineering exhibit complex and hierarchical geometric structures. Fractal geometry provides a powerful tool for understanding and modeling these structures. However, existing deterministic circle packing fractals, such as the Apollonian gasket, often adhere to fixed geometric rules and may fall ...

Keçeci Binomial Squares (Keçeci Binom Kareleri): Keçeci's Arithmetical Square (Keçeci Aritmetik Karesi, Keçeci'nin Aritmetik Karesi)

Description / Açıklama

Keçeci Binomial Squares (Keçeci Binom Kareleri): Keçeci's Arithmetical Square (Keçeci Aritmetik Karesi, Keçeci'nin Aritmetik Karesi):

Keçeci Binomial Squares (Keçeci Binom Kareleri): The Keçeci Binomial Square is a series of binomial coefficients forming a square region within Khayyam (مثلث خیام), Pascal, Binomial Triangle, selected from a ...

Keçeci Numbers: Keçeci Sayıları

Description / Açıklama

Keçeci Numbers (Keçeci Sayıları): Keçeci Numbers; An Exploration of a Dynamic Sequence Across Diverse Number Sets: This work introduces a novel numerical sequence concept termed "Keçeci Numbers." Keçeci Numbers are a dynamic sequence generated through an iterative process, originating from a specific starting value and an increment value. In each iteration, the increment value is added to the current value, and this "added value" is recorded ...

grikod2 (Gri Kod, Gray Code)

A Python library for converting binary numbers to Gray Code with ease. Tanım (Türkçe)

Gri Kod: grikod2 İkili sayıları Gri Koda çevirir. Description (English)

Gri Kod: grikod2 converts binary numbers to Gray Code. Kurulum (Türkçe) / Installation (English) Python ile Kurulum / Install with pip, conda, mamba

pip install grikod2 -U python -m pip install -U grikod2 conda install bilgi::grikod2 -y mamba install bilgi::grikod2 -y

• pip uninstall grikod2 -y

• pip install ...

Grikod (Gri Kod, Gray Code)

Tanım (Türkçe) Gri Kod: Grikod İkili sayıları Gri Koda çevirir.

Description (English) Gri Kod: Grikod converts binary numbers to Gray Code.

Kurulum (Türkçe) / Installation (English) Python ile Kurulum / Install with pip, conda, mamba pip install grikod -U python -m pip install -U grikod conda install bilgi::grikod -y mamba install bilgi::grikod -y

• pip uninstall grikod -y

• pip install -U grikod
• python -m pip install -U grikod PyPI

Test Kurulumu / Test Installation ...

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 guidance for understanding and implementing the set of workflows included in this collection. It outlines best practices and recommendations to ensure successful setup and execution of automated and real-time image processing pipelines.

Guidelines for using Scipion in the context of on-the-fly image processing at cryo-EM facilities. This document is divided into three main sections:

• On-the-fly processing: Monitoring data acquisition in real time.

• Processing workflows and templates: Building familiarity with creating and customizing workflows and templates in Scipion.

• Scipion with queue systems: Demonstrating Scipion’s behavior and integration with SLURM-based queueing systems.

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 ...

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using Relion.

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using Relion.

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using CryoSPARC.

Adapting to Tilted Samples

To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle ...

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using CryoSPARC.

Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using Relion.

Adapting to Tilted Samples

To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle high drift and lower resolution commonly observed in tilted samples. Key adjustments include:

• Motion Correction Filters: Max ...

Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using Relion.

Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using CryoSPARC.

Adapting to Tilted Samples

To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle high drift and lower resolution commonly observed in tilted samples. Key adjustments include:

• Motion Correction Filters: ...

Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using CryoSPARC.

Image processing from movies to micrographs, including CTF estimation and quality filters for image curation.

Adapting to Tilted Samples

To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle high drift and lower resolution commonly observed in tilted samples. Key adjustments include:

• Motion Correction Filters: Max per-frame shift = 30; Global drift = 120.

• CTF Consensus Filters: Adapted to 6.5 Å and 8.5 Å resolution cutoffs.

• **Defocus ...

Image processing pipeline from movies to micrographs, including CTF estimation and quality filters for image curation.

ONTeater is a eukaryotic genome assembly pipeline intended to produce highly-contiguous genomes with a single input of Oxford NanoPore Tech (ONT) longread data, although PacBio is accepted as well. Information can be found here. Originally developed to support genome assembly efforts by OIKOS genomics, predominantly of nonmodel vertebrate species.

A Retrieval-Augmented Knowledge Mining Method with Deep Thinking LLMs for Biomedical Research and Clinical Support

Introduction

Knowledge graphs and large language models (LLMs) serve as key tools for biomedical knowledge integration and reasoning, facilitating the structured organization of literature and the discovery of deep semantic relationships. However, existing methods still face challenges in knowledge mining and cross-document reasoning: knowledge graph construction is constrained ...

A Retrieval-Augmented Knowledge Mining Method with Deep Thinking LLMs for Biomedical Research and Clinical Support

Introduction

Knowledge graphs and large language models (LLMs) serve as key tools for biomedical knowledge integration and reasoning, facilitating the structured organization of literature and the discovery of deep semantic relationships. However, existing methods still face challenges in knowledge mining and cross-document reasoning: knowledge graph construction is constrained ...

Using:

• vadr annotation (virus model must be selected in options)
• vardict variant caller
• coverage depth Provides summarizing files:
• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only

SINGLE-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.

IMPORTANT:

• For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
• SELECT the mot ADAPTED VADR MODEL for annotation (see vadr parameters).

PAIRED-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.

IMPORTANT:

• For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
• SELECT THE MOST ADAPTED VADR MODEL for annotation (see vadr parameters).

Using:

• vadr annotation (virus model must be selected in options)
• vardict variant caller
• coverage depth Provides summarizing files:
• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only

Using:

• vadr annotation (virus model must be selected in options)
• vardict variant caller
• coverage depth Provides summarizing files:
• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only (can be opened in Excel/LibreOffice)

Using:

• vadr annotation (virus model must be selected in options)
• vardict variant caller
• coverage depth Provides summarizing files:
• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only (can be opened in Excel/LibreOffice)

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 ...

A collection of image processing templates designed to support data collection and automated processing for Single Particle Analysis (SPA) in cryo-electron microscopy. The workflows range from simple pipelines—including movie alignment, CTF estimation, and quality assessment—to fully automated 2D and 3D processing. Please select the workflow that best suits your needs.

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 ...