This is a general team for the BGE project for any members affiliated directly or indirectly with the BGE project.

To request joining this team, make sure sure your WorkflowHub institution matches one of the listed BGE partners.

Within Biodiversity Genomics Europe (BGE), under the Metabarcoding for Biomonitoring Task 6.2, we have developed a standard operating procedure (SOP) for the metabarcoding of bulk arthropod samples, covering the laboratory workflows that follow terrestrial field sampling for the High Mountain Systems and Pollinator Communities case studies. This SOP was developed using the FAVIS: Fast and Versatile Protocol for Metabarcoding of Bulk Insect Samples (https://dx.doi.org/10.17504/protocols.io.kqdg36261g25/v2), ...

This is a project specific guide for the Bioiversity Genomics Europe (BGE project use of WorkflowHub.

SOP for DNA extraction and Illumina amplicon library preparation of encapsulated water samples collected for the Case Study "Detection of Non-Indigenous Marine Species from Port Water Samples" withing the scope of BGE (Biodiversity Genomics Europe) project.

Based off the International Barcode of Life microplate instructions, with permission of iBOL (https://ibol.org/).

Within Biodiversity Genomics Europe (BGE), under the Metabarcoding for Biomonitoring Task 6.2, we have developed a standard operating procedure (SOP) for the DNA extraction and Illumina amplicon library preparation of soil core samples for the characterization of Prokaryotic and Eukaryotic biodiversity from soil samples. This SOP covers the laboratory workflows that follow terrestrial field sampling for the case study "Ecological Restoration - Soil Chronosequences" (https://doi.org/10.48546/workflowhub.sop.19.1). ...

Within the Biodiversity Genomics Europe project, the "High Mountain Systems - Arthropods" case study was designed to evaluate how arthropod communities change along altitudinal gradients in seven selected mountain systems across different countries in Europe, establishing baseline sampling in mountain ranges to track biodiversity shifts associated with climate change. This SOP describes the sampling design and fieldwork methodology for retrieving arthropod bulk samples for metabarcoding analyses. ...

Within the Biodiversity Genomics Europe project, the "Pollinator Communities" case study was designed to evaluate pollinator diversity in urban gardens in comparison with agricultural fields, to understand the role of urban habitats for pollinator conservation. This SOP describes the sampling design and Malaise trap fieldwork to retrieve pollinator bulk samples for metabarcoding analysis. This case study involved paired sampling, choosing one large garden and one agricultural field with no more ...

Within the Biodiversity Genomics Europe project, the "Ecological Restoration - Soil" case study was designed to evaluate changes in soil biodiversity during the process of ecological succession, sampling a chronosequence of replicated plots at different stages of restoration since land abandonment. The present SOP describes soil sampling under sterile and cold conditions for metabarcoding analyses. This case study involved sampling four successional stages, represented by specific vegetation types ...

The EuroScienceGateway project is producing and maintaining workflows. We need to register those workflows in WorkflowHub:

• To give visibility to the workflows created by the project and by the different networks and communities within the project
• To give visibility to the workflows used by project that were created
• To share workflows across the project, within project networks and externally
• To credit and cite the people making the workflows and the ...

eDNA Protocols for BGE (Biodiversity Genomics Europe) Work package 6, task 6.2

This is a general collection of workflows used by or developed by members of the BGE project.

...

Barcode gene Extraction and Evaluation from Genome Skims (BeeGees) Snakemake workflow

Snakemake workflow for recovering high-quality barcode sequences at scale, built around MitoGeneExtractor and adapted for genome skims of museum specimens.

Contents

• Requirements
• Workflow
• Installation and set up
• Cluster configuration
• Results structure
• [Validation ...

ANNOTATO - Annotation workflow To Annotate Them Oll

• ANNOTATO - Annotation workflow To Annotate Them Oll
• Overview of the workflow
• Input data
• Pipeline steps
• Output data
• Prerequisites
• Installation
• Running ANNOTATO
• Before running the pipeline (IMPORTANT) ...

skim2mito

skim2mito is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.

Contents

• Setup
• Example data
• Input
• Output
• Filtering contaminants
• [Assembly and ...

Objective. Biomarkers have become important for the prognosis and diagnosis of various diseases. High-throughput methods such as RNA-sequencing facilitate the detection of differentially expressed genes (DEGs), hence potential biomarker candidates. Individual studies suggest long lists of DEGs, hampering the identification of clinically relevant ones. Concerning preeclampsia, a major obstetric burden with high risk for adverse maternal and/or neonatal outcomes, limitations in diagnosis and ...

This portion of the workflow produces sets of feature Counts ready for analysis by limma/etc.

Associated Tutorial

This workflows is part of the tutorial Pathway analysis with the MINERVA Platform, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA

This portion of the workflow produces sets of feature Counts ready for analysis by limma/etc.

RNA-Seq reads to counts

Associated Tutorial

This workflows is part of the tutorial 1: RNA-Seq reads to counts, available in the GTN

Thanks to...

Tutorial Author(s): Maria Doyle, Belinda Phipson, ...

Library curation BOLD

This repository contains scripts and synonymy data for pipelining the automated curation of BOLD data dumps in BCDM TSV ...

Bactria: BarCode TRee Inference

...

ROIforMSI

Source codes for manuscript "Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation"

"ExampleWorkflow.ipynb" is a methods document to demonstrate the workflow of our multimodal fusion-based spatial segmentation.

"Utilities.py" contains all the tools to implement our method.

"gui.py" and "registration_gui.py" are files to implement linear and nonlinear registration.

(Licence: GPL-3)

We present an R script that describes the workflow for analysing honey bee (Apis mellifera) wing shape. It is based on a dataset of wing images and landmark coordinates available at Zenodo: https://doi.org/10.5281/zenodo.8128010. The dataset can be used as a reference for the identification of local bees from southern Kazakhstan, which most probably belong to the subspecies Apis mellifera pomonella. It was compared with data from Nawrocka et al. (2018), available at Zenodo: ...

Learning Objectives

• How to build complex queries using the IDR searcher to retrieve data from the Image Data Resource (IDR)
• How to load binary data from IDR using its Python API

Launch

This notebook can be launched using Google Colab.

This notebook is about pre-processing the Auditory Brainstem Response (ABR) raw data files provided by Ingham et. al to create a data set for Deep Learning models.

The unprocessed ABR data files are available at Dryad.

Since the ABR raw data are available as zip-archives, these have to be unzipped and the extracted raw data files parsed so that the time ...

PanGIA: A universal framework for identifying association between ncRNAs and diseases

PanGIA is a deep learning model for predicting ncRNA-disease associations.

Model Architecture

Installation

conda create -n pangia python=3.11 
conda activate pangia 
pip install -r requirements.txt 

Prepare Datasets

The raw data can be downloaded from the following sources:

• miRNA: The associations between miRNAs and diseases were obtained from the HMDD v4.0 ...

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 ...

We present an R script that describes the workflow for analysing honey bee (Apis mellifera) wing shape. It is based on a large dataset of wing images and landmark coordinates available at Zenodo: https://doi.org/10.5281/zenodo.7244070. The dataset can be used as a reference for the identification of unknown samples. As unknown samples, we used data from Nawrocka et al. (2018), available at Zenodo: https://doi.org/10.5281/zenodo.7567336. Among others, the script can be used to identify the geographic ...

AutoEncoders for Anomaly Detection tutorial using BioExcel Building Blocks (biobb)

This tutorial involves the use of a multilayer AutoEncoder (AE) for feature extraction and pattern recognition by analyzing Molecular Dynamic Simulations, step by step, using the BioExcel Building Blocks library (biobb).

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB ...