Non-profit Korean Community of Bioinformatics

PiFlow is an open source, ready-to-use workflow management systems. It has won 2023 TOP 100 Open Source Achievement Award by BenchCouncil, and its latest version was released in October 2024. PiFlow is dedicated to helping both data scientists and non-technical users to solve complex tasks by providing out-of-the-box solutions.

French Biodiversity e-infrastructure

Our lab, affiliated with Genoscope and the Institut de Biologie François Jacob of CEA, is part of a leading research institution with over 20,000 employees across nine centers in France, focusing on defense, low carbon energies, technological, and fundamental research.Genoscope, founded in 1996, shifted to environmental genomics in 2006, collaborating with the national scientific community on diverse projects. Affiliated with Paris-Saclay University, Genoscope specializes in biodiversity exploitation ...

Our group is engaged in the developing of novel bioinformatics approaches for assisting study of RNA modification and post-translational modifications(PTMs).

The Workflow and Ecosystem Services (WES) group at Oak Ridge Leadership Computing Facility (OLCF) is committed to enhancing automated workflows to enable efficient and reliable execution of research applications across distributed computing environments. Our primary focus is designing and implementing technologies that seamlessly integrate diverse computational, storage, and visualization resources, while leveraging advanced network capabilities to facilitate data movement. We aim to empower ...

Disease Ontology (DO) enrichment analysis is an effective means to discover the associations between genes and diseases. However, most current DO-based enrichment methods were unable to solve the over enriched problem caused by the “true-path” rule. To address this problem, we presents EnrichDO, a double weighted iterative model, which is based on the latest annotations of the human genome with DO terms and integrates the DO graph topology on a global scale. On one hand, to reinforce the saliency ...

interTwin co-designs and implements the prototype of an interdisciplinary Digital Twin Engine (DTE) – an open source platform based on open standards that offers the capability to integrate with application-specific Digital Twins (DTs). Its functional specifications and implementation are based on a co-designed interoperability framework and conceptual model of a DT for research – the DTE blueprint architecture. The ambition of interTwin is to create consensus on a common approach to the ...

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 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 ...

Workflow (hybrid) metagenomic assembly and binning

• Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
• FastQC (control)
• fastp (quality trimming)
• kraken2 (taxonomy)
• bbmap contamination filter
• Workflow Longread Quality:
• NanoPlot (control)
• filtlong (quality trimming)
• kraken2 (taxonomy)
• minimap2 contamination filter
• Kraken2 taxonomic classification of FASTQ reads
• SPAdes/Flye (Assembly)
• Pilon/Medaka/PyPolCA (Assembly polishing)
• QUAST (Assembly ...

gimp-image-annotator

gimp-image-annotator or GIÀ, a lightweight GIMP plug-in to alllow for computer vision-assisted image annotation using the powerful GIMP selection toolbox.

Installation

Follow the guide here: https://en.wikibooks.org/wiki/GIMP/Installing_Plugins to find how to install GIMP plug-ins on your system, save the file image-annotator.py in GIMP's plug-in folder.

In GIMP v2.x, the plug-in system relies on deprecated python2. On Windows, a version of python2 is included in ...

Article abstract

Permeability is an important molecular property in drug discovery, as it co-determines pharmacokinetics whenever a drug crosses the phospholipid bilayer, e.g., into the cell, in the gastrointestinal tract or across the blood-brain barrier. Many methods for the determination of permeability have been developed, including cell line assays, cell-free model systems like PAMPA mimicking, e.g., gastrointestinal epithelia or the skin, as well as the Black lipid membrane (BLM) and ...

M6Allele Pipeline & M6Allele algorithm

Introduction

We have developed an algorithm called M6Allele for identifying allele-specific m6A modifications. To facilitate its usage by researchers, we have also encapsulated our analysis process into a pipeline. You can learn more about the pipeline and the algorithm's usage from the following two modules:

• Pipeline
• M6Allele algorithm

M6Allele Pipeline

PARAMETER INTRODUCTION

• -g/--gtf : ...

EnrichDO

EnrichDO is a double weighted iterative model by integrating the DO graph topology on a global scale. It was based on the latest annotations of the human genome with DO terms, and double weighted the annotated protein-coding genes. On one hand, to reinforce the saliency of direct gene-DO annotations, different initial weights were assigned to directly annotated genes and indirectly annotated genes, respectively. On the other hand, to detect locally most significant node between ...

GALOP - Genome Assembly using Long reads Pipeline

This repository contains an exact copy of the standard Genoscope long reads assembly pipeline.

At the moment, this is not intended for users to download as it uses grid submission commands that will only work at Genoscope. As time goes on, we intend to make this pipeline available to a broader audience. However, genome assembly and polishing commands are accessible in the lib/assembly.py and lib/polishing.py files.

galop.py -h 
Mandatory
...

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. ...

This is an aggregation of the work done in Seq4AMR consisting of the following workflows:

• WF1: AbritAMR / AMRFinderPlus
• WF2: Sciensano (not currently included)
• WF3: SRST2
• WF4: StarAMR

Installation

• You will need to:
• run the [RGI Database ...

The Polygenic Score Catalog Calculator (pgsc_calc)

...

Metagenome-Atlas

![Mastodon ...

Subset data on the Mediterreanean see and extract and visualise the Phosphate variable

Workflow permettant de prendre en entrée les résultats du challenge IA-biodiv par tâche, le fichier de référence par tâche afin de faire tourner un jupyter notebook produisant les scores pour chaque consortium participant.

beacon-omop-worker-survival-analysis

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 ...

Workflow for microbial (meta-)genome annotation

Input is a (meta)genome sequence in fasta format.

• bakta

• KoFamScan (optional)

• InterProScan (optional)

• eggNOG mapper (optional)

• To RDF conversion with SAPP (optional, default on) --> SAPP conversion Workflow in WorkflowHub

git: https://gitlab.com/m-unlock/cwl

Workflow for converting (genome) annotation tool output into a GBOL RDF file (TTL/HDT) using SAPP

Current formats / tools:

• EMBL format
• InterProScan (JSON/TSV)
• eggNOG-mapper (TSV)
• KoFamScan (TSV)

git: https://gitlab.com/m-unlock/cwl

SAPP (Semantic Annotation Platform with Provenance):
https://gitlab.com/sapp
https://academic.oup.com/bioinformatics/article/34/8/1401/4653704

Current version of this workflow: https://workflowhub.eu/workflows/1109. Please use only with the new version. KNIME workflow to gather ChEMBL permeability data is availbale: https://workflowhub.eu/workflows/1169.

demux_doublet_sim

Repository for Nextflow pipeline used in demuxSNP demultipelxing paper

Overall workflow

1. Simulate doublets

2. Benchmark methods

• Experiments 1: Vary doublet rate
• Experiment 2: Vary SNP subsetting

Inputs

Most inputs are specified in nextflow.config: container__souporcell: path to souporcell apptainer image, ideally at top level of project. bam_path: Path to demultiplexed bam files. barcodes_path: Path to demultiplexed barcodes. tenx: Path to barcodes.tsv, features.tsv ...