Provide an integrated, comprehensive, modular modelling and testing framework

Develop multi-scale workflows applicable beyond the identified test-areas enabling improved physical understanding and progress beyond state-of-the-art in the earthquake process.

Develop and implement 6 DTCs covering earthquake-related aspects over long and short time scales

Test the 6 DTC-E at 4 relevant sites: Euro-Med (SD8), Central Apennines and Alto-Tiberina (SD9), Bedretto Lab (SD10) and the Alps (SD11).

FAIR data specialists and research software engineers working towards interlinking, harmonization and facilitation of access to geobiodiversity research data.

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 ...

Provenance registration is becoming more and more important, as we increase the size and number of experiments performed using computers. In particular, when provenance is recorded in HPC environments, it must be efficient and scalable. In this paper, we propose a provenance registration method for scientific workflows, efficient enough to run in supercomputers (thus, it could run in other ...

Keynote Presented at the ICTeSSH 2021 Conference to Social Science and Humanities. ICTeSSH 2021, 30th June 2021

https://ictessh.uns.ac.rs/ In data intensive science multi-step tool-chains are widely used to help scientists manage, analyze, and share increasing volumes of complex data. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for scalable data processing, the exchange of processing know-how, and ...

Keynote JOBIM 2021 (French Bioinformatics Conference)

FAIR Computational Workflows https://jobim2021.sciencesconf.org/ 8 July 2021

Computational workflows capture precise descriptions of the steps and data dependencies needed to carry out computational data pipelines, analysis and simulations in many areas of Science, including the Life Sciences. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for ...

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 ...

Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 7.5 km2 large Reserve Naturelle Nationale du Bagnas ('Bagnas') in France (3.514360 E, 43.314332 N). The work has been performed in the context of the EU project MAMBO (Modern ...

This KNIME workflow is designed to facilitate the loading of image data from OMERO. It includes key preprocessing steps for VAST data, such as metadata creation and the linking of Key-Value Pairs.

• Fetching Images: The first step involves fetching images from a locally accessible folder.
• User Authentication: Users are prompted to input their OMERO username and password through a Java snippet. This information is then converted into variables that can be used by the Python script node. ...

Workflow to perform nuclei cell counting on High Content Screening (HCS) Data and upload result into OMERO

In this workflow, cell images are first uploaded to both Galaxy and OMERO using the “OMERO Image Import” tool. Concurrently, image processing is performed. After thresholding and binarization, key features of nuclei, such as area, label number, and perimeter, are computed from the processed images and saved as a CSV file. The result file is then attached to each image stored in OMERO using ...

General workflow to upload data into OMERO using Galaxy

A dataset for testing can be found at: https://zenodo.org/records/14205500

Important Security Note: It is crucial to be aware that storing credentials as variables can pose security risks, particularly if accessed by administrators. Therefore, it is essential to handle user credentials securely and in accordance with best practices.

General workflow to upload data into OMERO using KNIME

The workflow consists of two main branches: the Green Branch, which imports a folder containing images, and the Purple Branch, which enables the annotation of metadata as key-value pairs.

• Fetching Images: The first step involves fetching images from a locally accessible folder.
• User Authentication: Users are prompted to input their OMERO username and password through a Java snippet. This information is then converted into ...

ONT Artificial Deletion Filter-Delter

A tool to filter short artificial deletion variations by Oxford Nanopore Technologies (ONT) R9 and R10 flow cells and chemistries.

Requirements

The tool has been tested on Ubuntu 20.04 with 256GB RAM, 64 CPU cores and a NVIDIA GPU with 48GB RAM. The minimal requirements should be >= 64GB RAM and a NVIDIA GPU with >= 8GB RAM. Other operating systems like Windows or Mac were not tested.

ONT softwares like Guppy, ...

Nextflow Pipeline for DeepVariant

This repository contains a Nextflow pipeline for Google’s DeepVariant, optimised for execution on NCI Gadi.

Quickstart Guide

1. Edit the pipeline_params.yml file to include:

• samples: a list of samples, where each sample includes the sample name, BAM file path (ensure corresponding .bai is in the same directory), path to an optional regions-of-interest BED file (set to '' if not required), and the model type.
• ref: path to the reference FASTA (ensure ...

Name: PhysioNet CascadeCSVM Kfold Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

Kfold to evaluate CascadeCSVM accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0

Name: PhysioNet kNN Kfold Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

Kfold to evaluate kNN accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0

Name: PhysioNet RF Kfold Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

Kfold to evaluate RandomForest accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0

A R workflow for proteomics data analysis is reported. This pipeline was basing on protein expression projects, stored on the PRIDE database and reported on the COVID-19 Data portal. This is an R pipeline to analyze protein expression data, built on lung cell lines infected by SARS-CoV-2 variants: ​B.1, Delta, and Omicron BA.1 (Mezler et al. 2023) https://www.ebi.ac.uk/pride/archive/projects/PXD037265. This pipeline can obtain DEPs for each variant, starting from normalized protein expression ...

Name: GridSearchCV Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

GridSearch of kNN algorithm for the iris.csv dataset (https://gist.githubusercontent.com/netj/8836201/raw/6f9306ad21398ea43cba4f7d537619d0e07d5ae3/iris.csv). This application used dislib-0.9.0

Name: GridSearchCV Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

GridSearch of kNN algorithm for the iris.csv dataset (https://gist.githubusercontent.com/netj/8836201/raw/6f9306ad21398ea43cba4f7d537619d0e07d5ae3/iris.csv). This application used dislib-0.9.0

cfDNA UniFlow is a unified, standardized, and ready-to-use workflow for processing whole genome sequencing (WGS) cfDNA samples from liquid biopsies. It includes essential steps for pre-processing raw cfDNA samples, quality control and reporting. Additionally, several optional utility functions like GC bias correction and estimation of copy number state are included. Finally, we provide specialized methods for extracting coverage derived signals and visualizations comparing cases and controls. ...

Name: KMeans Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

KMEans for clustering the housing.csv dataset (https://github.com/sonarsushant/California-House-Price-Prediction/blob/master/housing.csv). This application used dislib-0.9.0

Variant Interpretation Pipeline (VIP) that annotates, filters and reports prioritized causal variants in humans, see https://github.com/molgenis/vip for more information.

Workflow for gene set enrichment analsysis (GSEA) and co-expression analysis (WGCNA) on transcriptomics data to analyze pathways affected in Porto-Sinusoidal Vascular Disease.

JAX NGS Operations Nextflow DSL2 Pipelines

This repository contains production bioinformatic analysis pipelines for a variety of bulk 'omics data analysis. Please see the Wiki documentation associated with this repository for all documentation and available analysis workflows.

Name: Incrementation and Fibonacci Access Level: public License Agreement: Apache2 Platform: COMPSs

Description

Brief Overview: Demonstrates COMPSs task parallelism with increment and Fibonacci computations. Helps to understand COMPSs.

Detailed Description:

1. Performs multiple increments of input values in parallel using COMPSs.
2. Concurrently calculates Fibonacci numbers using recursive COMPSs tasks.
3. Demonstrates task synchronization via compss_wait_on.

Execution

...

Calculates the Fibonacci series up to a specified length.

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) ...

Summary

This pipeline contains the following functions: (1) Data processing to handle the tansformations needed to obtain the original pathway scores of the samples according to single sample analysis GSEA (2) Model training based on the disease and healthy sample pathway scores, to classify them (3) Scoring matrix weights optimization according to a gold standard list of drugs (those that went on clinical trials or are approved for the disease).It tests the weights in a range of 0 to 30 (you ...

The Polygenic Score Catalog Calculator (pgsc_calc)

...

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...