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

The Hurwitz Lab was established in August, 2014 at the University of Arizona in the Department of Biosystems Engineering. Our lab focuses on large-scale –omics datasets, high-throughput computing, and big data analytics. We leverage these technologies to answer questions related to the relationship between microbes, their hosts, and the environment.

Machine Learning Made Easy (MLme) is a novel tool that simplifies machine learning (ML) for researchers. By integrating four essential functionalities, namely data exploration, AutoML, CustomML, and visualization, MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. MLme serves as a valuable resource that empowers researchers of all technical levels to leverage ML for insightful data analysis and enhance research outcomes. By simplifying ...

CImorgh IT solutions is a bioinformatics and healthcare company located in Iran.

Our goal is deciphering the complexity of microbial metabolism, its evolutionary and biotechnological implications through a multidisciplinary approach. By assuming that the whole is greater than the sum of its parts, we aim to contribute to a better understanding of the emergent properties of microbial systems at subcellular, cellular and supracellular levels. We pursuit the rational re-design of these system properties towards novel biotechnological and medical applications.

Proteomics is the large-scale experimental study of the proteome, all the proteins produced or modified by an organism or system. Proteomics can tell us about when and where proteins are expressed, protein production and degradation rates, the characterisation of protein post-translational modifications (e.g. phosphorylation), elucidating protein structures, and protein-protein interactions.This information can be combined with data from other omics disciplines (genomics, metagenomics, metabolomics) ...

The Workflow and Ecosystems Services (WES) Group enables data stewardship and enriched scalable data access capabilities, and it develops end-to-end scientific workflow technologies for user programs at the Oak Ridge Leadership Computing Facility (OLCF).

A series of tools and an open database of polygenic scores and the relevant metadata required for accurate application and evaluation.

Research areas: - Structure, evolution and maintenance of telomeres and their roles in chromosome stability, DNA repair and plant speciation - Epigenetic mechanisms in the regulation of gene expression, chromatin assembly, genome stability and telomere homeostasis - Transcription, replication and DNA repair in the context of nuclear and nucleolar architecture

Team of contributors working on the ARA (Automated Record Analysis) pipeline.ARA is an automatic pipeline for exploration of SRA datasets with sequences as a query.

This team is a testing grounds for the DeSci Labs research object development team.

An open-source bioinformatics community, based in Japan. Members include academic and private companies. Working with the topics such as workflow sharing and cloud computing infrastructure.

The Biodata Analysis Group (also known as the Bioinformatics Lab at the Institute of Applied Biosciences (INAB / CERTH)) is active in Bioinformatics research, focusing on the design of new algorithms and pipelines.We are a group of enthusiastic researchers, active in the following key fields:- Machine Learning and Data Mining- Multi-omics data integration- Training for Life Sciences

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

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

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 ...

This repository contains the python code to reproduce the experiments in Dłotko, Gurnari "Euler Characteristic Curves and Profiles: a stable shape invariant for big data problems"

This workflow represents the Default ML Pipeline for AutoML feature from MLme. Machine Learning Made Easy (MLme) is a novel tool that simplifies machine learning (ML) for researchers. By integrating four essential functionalities, namely data exploration, AutoML, CustomML, and visualization, MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. MLme serves as a valuable resource that empowers researchers of all technical levels to leverage ...

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: ...

The Polygenic Score Catalog Calculator (pgsc_calc)

...

This workflow is designed to analyze to a multi-omics data set that comprises genome-wide DNA methylation profiles, targeted metabolomics, and behavioral data of two cohorts that participated in the ACTION Biomarker Study (ACTION, Aggression in Children: Unraveling gene-environment interplay to inform Treatment and InterventiON strategies. (Boomsma 2015, Bartels 2018, Hagenbeek 2020, van Dongen 2021, Hagenbeek 2022). The ACTION-NTR cohort consists of twins that are either longitudinally concordant ...

GERONIMO

Introduction

GERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models. These models are based on the alignment of sequences and the consensus of secondary structures. The pipeline is built using Snakemake, a workflow management tool that allows for the reproducible execution of analyses on various computational platforms.

The idea for developing GERONIMO emerged from a comprehensive search for [telomerase ...

About SnakeMAGs

SnakeMAGs is a workflow to reconstruct prokaryotic genomes from metagenomes. The main purpose of SnakeMAGs is to process Illumina data from raw reads to metagenome-assembled genomes (MAGs). SnakeMAGs is efficient, easy to handle and flexible to different projects. The workflow is CeCILL licensed, implemented in Snakemake (run on multiple cores) and available ...

This repository hosts Metabolome Annotation Workflow (MAW). The workflow takes MS2 .mzML format data files as an input in R. It performs spectral database dereplication using R Package Spectra and compound database dereplication using SIRIUS OR MetFrag . Final candidate selection is done in Python using RDKit and PubChemPy.

ARA (Automated Record Analysis) : An automatic pipeline for exploration of SRA datasets with sequences as a query

Requirements

• Docker

• Please checkout the Docker installation guide.

or

• Mamba package manager

• Please checkout the mamba or micromamba official installation guide.

• We prefer mamba over conda since it is faster and uses ...

prepareChIPs

This is a simple snakemake workflow template for preparing single-end ChIP-Seq data. The steps implemented are:

1. Download raw fastq files from SRA
2. Trim and Filter raw fastq files using AdapterRemoval
3. Align to the supplied genome using bowtie2
4. Deduplicate Alignments using Picard MarkDuplicates
5. Call Macs2 Peaks using macs2

A pdf of the rulegraph is available here

Full details for each step are given below. Any additional ...

BatchConvert

A command line tool for converting image data into either of the standard file formats OME-TIFF or OME-Zarr.

The tool wraps the dedicated file converters bfconvert and bioformats2raw to convert into OME-TIFF or OME-Zarr, respectively. The workflow management system NextFlow is used to perform conversion in parallel for batches of images.

The tool also wraps s3 and Aspera clients (go-mc and aspera-cli, respectively). ...

A CWL-based pipeline for calling small germline variants, namely SNPs and small INDELs, by processing data from Whole-genome Sequencing (WGS) or Targeted Sequencing (e.g., Whole-exome sequencing; WES) experiments.

On the respective GitHub folder are available:

• The CWL wrappers and subworkflows for the workflow
• A pre-configured YAML template, based on validation analysis of publicly available HTS data

Briefly, the workflow performs the following steps:

1. Quality control of Illumina reads ...

A CWL-based pipeline for calling small germline variants, namely SNPs and small INDELs, by processing data from Whole-genome Sequencing (WGS) or Targeted Sequencing (e.g., Whole-exome sequencing; WES) experiments.

On the respective GitHub folder are available:

• The CWL wrappers and subworkflows for the workflow
• A pre-configured YAML template, based on validation analysis of publicly available HTS data

Briefly, the workflow performs the following steps:

1. Quality control of Illumina reads ...

A CWL-based pipeline for processing ChIP-Seq data (FASTQ format) and performing:

• Peak calling
• Consensus peak count table generation
• Detection of super-enhancer regions
• Differential binding analysis

On the respective GitHub folder are available:

• The CWL wrappers for the workflow
• A pre-configured YAML template, based on validation analysis of publicly available HTS data
• Tables of metadata (EZH2_metadata_CLL.csv and H3K27me3_metadata_CLL.csv), based on the same validation ...

A CWL-based pipeline for processing RNA-Seq data (FASTQ format) and performing differential gene/transcript expression analysis.

On the respective GitHub folder are available:

• The CWL wrappers for the workflow
• A pre-configured YAML template, based on validation analysis of publicly available HTS data
• A table of metadata (mrna_cll_subsets_phenotypes.csv), based on the same validation analysis, to serve as an input example for the design of comparisons during differential expression ...

SARS-CoV-2 variant prediction using Read It And Keep, fastp, bbmap and iVar

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).

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).