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WP3 Discoverability hackathon v2 on Feb 8th

COVID-19 Data Portal Knowledge Molecular biology Clinical data Socioeconomic data EOSC ecosystem Hackathons Metadata FAIRsharing Social sciences
Using Large Language Models for Biodata Exploration: From Theory to Practice

• beginner
machine learning mark ibberson group training
theislab/single-cell-tutorial

RNA-Seq Single-cell sequencing Transcriptomics Python RNA-seq
RockefellerUniversity/RU_VisualizingGenomicsData

Data visualisation Genomics Data visualization R
opensciency/sprint-content

Data management FAIR data
bioinformatics-core-shared-training/SingleCell_RNASeq_Jan23

Sequencing RNA-Seq Single-cell sequencing Transcriptomics R Next generation sequencing RNA-seq
Computer Software, workflow

How to use V-pipe (SARS-CoV-2 data)

• beginner
Virology Genetic variation Workflows Variant calling Alignment Read pre-processing coronavirus NGS bioinformatics Variant-calling
Course design: Considerations for trainers – a Professional Guide

Curriculum development, course design, learning outcomes, Bloom's Taxonomy, assessment, course evaluation, training trainers, training material
Training materials

Using bioinformatics to hunt SARS-CoV-2, its variants & its origins – a practical guide

• beginner
Bioinformatics for schools, basic bioinformatics, SARS-CoV-2 pandemic, genome analysis, protein sequence analysis, protein structure analysis, virus variants, spike protein, training material
ncl-icbam/ismb-tutorial-2023

Sequencing Transcriptomics Next generation sequencing Spatial transcriptomics
IFB-ElixirFr/EBAII

ChIP-seq Sequencing RNA-Seq Variant pattern analysis R Unix/Linux Next generation sequencing RNA-seq Variant analysis
IFB Shiny training

•• intermediate
R-programming Reproducible Science
RockefellerUniversity/RU_tidyverse_core

R script R
GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - An automated SARS-CoV-2 genome surveillance system built around Galaxy

Galaxy, Build, pathogen surveillance system, automated, automation, SARS-CoV-2, genome surveillance, system Galaxy, Building, pathogen surveillance system, Automating, automation, workflows, command line Galaxy, Building, pathogen surveillance system, Removal,human reads, SARS-CoV-2, sequencing data Galaxy, Building, pathogen surveillance system, Upload data, ENA Galaxy, Building, pathogen surveillance system, usegalaxy, SARS-CoV-2, Bot Galaxy, Sequencing data analysis, spectrum, viral genomes Galaxy, Tuberculosis Sequence Analysis, Concepts, drug-resistance, prediction, mutation-based, clustering Galaxy, Tuberculosis Sequence Analysis, Identifying, tuberculosis transmission, links, SNPs, transmission clusters Galaxy, Tuberculosis Sequence Analysis, Implementation, NGS, TB- WHO, documents, considerations Galaxy, Tuberculosis Sequence Analysis, Tuberculosis, Variant Analysis …
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Building RO-Crates - An overview of the RO-Crate concept and its implementations

Galaxy, FAIR data, data provenance, RO-Crate, Publishing Galaxy, FAIR data, data provenance, RO-Crate, Publishing Workflow, GitHub repositories Galaxy, FAIR data, data provenance, RO-Crate, Publishing Workflow, Submitting workflows, LifeMonitor Galaxy, FAIR data, data provenance, RO-Crate, Publishing, Workflow, Registering, WorkflowHub Galaxy, FAIR data, data provenance, RO-Crate, Python Galaxy, FAIR data, data provenance, RO-Crate, RO-Crate concept, RO-Crate implementations Galaxy, FAIR data, data provenance, RO-Crate, Workflow Run, RO-Crate Introduction
UniProt: Focus on Plant Proteins

• beginner
e-learning

BLAST and multiple sequence alignment (MSA) programs

• beginner
Sequence analysis Blast Multiple sequence alignment
Docker and Singularity for Reproducible Research: Getting Started with Containers

• beginner
reproducibility container data management data security high-performance computing
BLAST and multiple sequence alignment (MSA) programs

• beginner
Blast E learning Multiple sequence alignment
hadley/r4ds

R script Quarto R Data science
jeroenjanssens/data-science-at-the-command-line

Unix/Linux
WCSCourses/SARS-COV-2_B4B

Genomics Variant pattern analysis Unix/Linux Variant analysis
bioinformaticsdotca/MET_2023

Metabolomics
e-learning

UNIX Fundamentals

• beginner
Computer science Problem based learning Programming Unix
Tutorial, Slideshow, e-learning

High Performance Computing (HPC) in Life Sciences

• beginner
Computer science Bioinformatics Biology High performance computing high-performance computing
e-learning

ISMARA: A tool to infer genome-wide regulatory interactions

• beginner
Systems biology Gene regulation Transcription factors and regulatory sites Computational modelling
tidyverse/datascience-box

R script R Data science
e-learning

Cellosaurus : A resource on cell lines

• beginner
Biosciences Experimental design and studies basic research Reproducibility cell line
e-learning

neXtProt : Exploring human proteins

• beginner
Proteins Proteomics Proteins (proteins) human
Vital-IT Infrastructure Usage

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WP3 Discoverability hackathon v2 on Feb 8th

Using Large Language Models for Biodata Exploration: From Theory to Practice

theislab/single-cell-tutorial

RockefellerUniversity/RU_VisualizingGenomicsData

opensciency/sprint-content

bioinformatics-core-shared-training/SingleCell_RNASeq_Jan23

How to use V-pipe (SARS-CoV-2 data)

Course design: Considerations for trainers – a Professional Guide

Using bioinformatics to hunt SARS-CoV-2, its variants & its origins – a practical guide

ncl-icbam/ismb-tutorial-2023

IFB-ElixirFr/EBAII

IFB Shiny training

RockefellerUniversity/RU_tidyverse_core

GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - An automated SARS-CoV-2 genome surveillance system built around Galaxy

GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Building RO-Crates - An overview of the RO-Crate concept and its implementations

UniProt: Focus on Plant Proteins

BLAST and multiple sequence alignment (MSA) programs

Docker and Singularity for Reproducible Research: Getting Started with Containers

BLAST and multiple sequence alignment (MSA) programs

hadley/r4ds

jeroenjanssens/data-science-at-the-command-line

WCSCourses/SARS-COV-2_B4B

bioinformaticsdotca/MET_2023

UNIX Fundamentals

High Performance Computing (HPC) in Life Sciences

ISMARA: A tool to infer genome-wide regulatory interactions

tidyverse/datascience-box

Cellosaurus : A resource on cell lines

neXtProt : Exploring human proteins

Vital-IT Infrastructure Usage

Interactive Visualization with Python

Introduction to Machine Learning with Python

When immunology meets bioinformatics

Data Analysis and Representation in Python

Diving into deep learning - theory and applications with PyTorch

First Steps with Python in Life Sciences

Ensuring More Accurate, Generalisable, and Interpretable Machine Learning Models for Bioinformatics

NGS - Quality Control, Alignment, Visualisation

Enrichment Analysis

Docker and Singularity for Reproducible Research: Getting Started with Containers

Snakemake for Reproducible Research: Getting Started with Workflows

Biodiversity bioinformatics: from large-scale phylogenomics to gene families and functions

NGS - Genome Variant Analysis

Make your research FAIRer with Quarto, GitHub and Zenodo

UNIX Shell Scripting in Life Sciences

Best Practices in Programming

Introduction to bulk RNA-Seq: From Quality Control to Pathway Analysis

Causal Inference

First Steps with R in Life Sciences

Federated Learning in Bioinformatics

Introduction to Sequencing Data Analysis

Federated Learning in Bioinformatics

Introduction to High-performance Computing (sciCORE Cluster)

Reproducible and Scalable Research with Snakemake and Software Containers

Optimizing Python Code for Better Performance

Biology-informed Multiomics Data Integration and Visualization

Summer School Machine Learning and AI

Introduction to High-performance Computing (sciCORE Cluster)

R-packaging

Best Practices for Investigating Gene Expression Differences by Biological Sex

SIB Swiss Institute of Bioinformatics

Glittr.org

BY-COVID