Register training material
101 materials found

Resource type: Tutorial 


Tutorial on using MPI with containers

In this material we will briefly touch upon why MPI is such a tricky component, explain the main approaches to combine MPI with containers and discuss when it is actually worthwhile to use MPI containers.

Keywords: MPI, Containers

Resource type: Tutorial

Tutorial on using MPI with containers https://tess.elixir-europe.org/materials/tutorial-on-using-mpi-with-containers In this material we will briefly touch upon why MPI is such a tricky component, explain the main approaches to combine MPI with containers and discuss when it is actually worthwhile to use MPI containers. MPI, Containers
Tutorial on CARNIVAL

This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL

Scientific topics: RNA-Seq, Omics, Gene expression, Molecular interactions, pathways and networks

Operations: RNA-Seq analysis, Network analysis

Keywords: HPC, Signaling, RNAseq, transcriptomics

Resource type: Tutorial

Tutorial on CARNIVAL https://tess.elixir-europe.org/materials/tutorial-on-carnival This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL RNA-Seq Omics Gene expression Molecular interactions, pathways and networks HPC, Signaling, RNAseq, transcriptomics
Tutorials on COBREXA

COBREXA.jl provides tutorials and notebooks with the purpose of explaining the most important concepts and functions for metabolic modelling and model handling to users, and then practicing them. The documentation contains basic tutorials (explaining the core package concepts and basic design...

Scientific topics: Personalised medicine, Simulation experiment

Operations: Modelling and simulation

Keywords: cell-level simulations, Biomodelling, HPC

Resource type: Tutorial

Tutorials on COBREXA https://tess.elixir-europe.org/materials/tutorials-on-cobrexa COBREXA.jl provides tutorials and notebooks with the purpose of explaining the most important concepts and functions for metabolic modelling and model handling to users, and then practicing them. The documentation contains basic tutorials (explaining the core package concepts and basic design ideas), advanced tutorials (describing complicated functionality required for optimised execution of large analyses) and Jupyter notebooks that demonstrate the concepts from tutorials in a more practical setting, with realistic data. Personalised medicine Simulation experiment cell-level simulations, Biomodelling, HPC
Tutorial on CellNOpt

This tutorial aims to be an introduction to i) the preparation of the Prior knowledge network (PKN) of signaling pathways and ii) the training of the PKN against biochemical data to create cell-specific models.

Scientific topics: Personalised medicine, Simulation experiment, Molecular interactions, pathways and networks

Operations: Modelling and simulation

Keywords: HPC, Biomodelling, Signalling

Resource type: Tutorial

Tutorial on CellNOpt https://tess.elixir-europe.org/materials/tutorial-on-cellnopt This tutorial aims to be an introduction to i) the preparation of the Prior knowledge network (PKN) of signaling pathways and ii) the training of the PKN against biochemical data to create cell-specific models. Personalised medicine Simulation experiment Molecular interactions, pathways and networks HPC, Biomodelling, Signalling
Multi-omics data visualization with PathVisio

With this tutorial you can follow a step-by-step guide for visualizing multi-omics data with the pathway drawing software PathVisio

Keywords: biological pathways, Pathways, Pathway analysis

Resource type: Tutorial

Multi-omics data visualization with PathVisio https://tess.elixir-europe.org/materials/multi-omics-data-visualization-with-pathvisio With this tutorial you can follow a step-by-step guide for visualizing multi-omics data with the pathway drawing software PathVisio biological pathways, Pathways, Pathway analysis
Biological network data tutorial

In this skills session, you will learn: how to upload a biological network from STRING how to extend a network using CyTargetLinker how to load a pathway diagram from WikiPathways how to upload a network shared via NDEx how to visualize data in a network how to create a sub network how to...

Keywords: Biological networks, Network Visualization

Resource type: Tutorial

Biological network data tutorial https://tess.elixir-europe.org/materials/biological-network-data-tutorial In this skills session, you will learn: how to upload a biological network from STRING how to extend a network using CyTargetLinker how to load a pathway diagram from WikiPathways how to upload a network shared via NDEx how to visualize data in a network how to create a sub network how to extend a network via R Biological networks, Network Visualization Life Science Researchers PhD students, computer scientists, bioinformaticians and developers who need to maintain/extend existing tools or develop new tools for Galaxy.
SPARQLing Biology: a beginners course

Course given at BioSB 2019 for biologists about SPARQL.

Scientific topics: Biology

Operations: Query and retrieval

Keywords: Sparql queries, Sparql syntax

Resource type: Tutorial

SPARQLing Biology: a beginners course https://tess.elixir-europe.org/materials/sparqling-biology-a-beginners-course Course given at BioSB 2019 for biologists about SPARQL. Biology Sparql queries, Sparql syntax Biologists Chemists
runBioSimulations tutorial and help

runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA),...

Scientific topics: Simulation experiment, Computational biology, Systems biology

Operations: Modelling and simulation

Keywords: biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL

Resource type: Tutorial, Documentation

runBioSimulations tutorial and help https://tess.elixir-europe.org/materials/runbiosimulations-tutorial-and-help runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BNGL, SBML). runBioSimulations also provides a REST API for programmatic access to the same simulation capabilities. The runBioSimulations tutorial and help describes how to use this web application and web service to execute simulations and visualize their results. This includes instructions on how to create COMBINE/OMEX archives of modeling projects. Ion Moraru Bilal Shaikh Gnaneswara Marupilla Simulation experiment Computational biology Systems biology biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL modelers
BioSimulators tutorial and help

BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms,...

Scientific topics: Simulation experiment, Computational biology, Systems biology

Operations: Modelling and simulation

Keywords: Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL

Resource type: Tutorial, Documentation

BioSimulators tutorial and help https://tess.elixir-europe.org/materials/biosimulators-help BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects. The BioSimulators help describes how to use this registry: - How to find a containerized simulation tools that are capable of executing a modeling study. - How to use containerized simulation tools to execute modeling studies. - How to containerize a simulation tool and submit it to the BioSimulators registry. Ion Moraru Bilal Shaikh Simulation experiment Computational biology Systems biology Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL modelers Computational biologists software developers, bioinformaticians
Use Scholia and Wikidata to find scientific literature

Scholia is a useful tool for finding scientific literature. Based on the main topic of a publication, you can find literature similar to a publication you are looking into or literature you didn’t know about or consider. Additionally, you can take advantage of all of the annotation work of others...

Keywords: Literature

Resource type: Tutorial

Use Scholia and Wikidata to find scientific literature https://tess.elixir-europe.org/materials/use-scholia-and-wikidata-to-find-scientific-literature Scholia is a useful tool for finding scientific literature. Based on the main topic of a publication, you can find literature similar to a publication you are looking into or literature you didn’t know about or consider. Additionally, you can take advantage of all of the annotation work of others when finding literature. Proper annotation also makes scientific literature more findable. Literature Researchers
A Tidy Transcriptomics introduction to RNA-Seq analyses

This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages.

Scientific topics: RNA-Seq

Keywords: Differential Expression, Gene Expression, RNA-seq, Transcriptomics

Resource type: Tutorial

A Tidy Transcriptomics introduction to RNA-Seq analyses https://tess.elixir-europe.org/materials/a-tidy-transcriptomics-introduction-to-rna-seq-analyses This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages. RNA-Seq Differential Expression, Gene Expression, RNA-seq, Transcriptomics Biologists
galaxy.sciensano.be

This training is meant specifically for the “Galaxy @Sciensano” that is available at https://galaxy.sciensano.be/ and serves two purposes. First, it serves as an introduction in how to handle and employ the Galaxy instance hosted by Sciensano. Secondly, is also serves as a tutorial into both the...

Scientific topics: Microbiology, Sequencing, Genomics, Public health and epidemiology, Bioinformatics

Resource type: Video, Tutorial

galaxy.sciensano.be https://tess.elixir-europe.org/materials/galaxy-sciensano-training This training is meant specifically for the “Galaxy @Sciensano” that is available at https://galaxy.sciensano.be/ and serves two purposes. First, it serves as an introduction in how to handle and employ the Galaxy instance hosted by Sciensano. Secondly, is also serves as a tutorial into both the basics of next-generation sequencing data analysis, but also more specialized topics of interest in public health (e.g. AMR detection, cgMLST analysis etc., SNP-based outbreak analysis etc.). The training consists specifically out of a series of training videos that are publicly available on YouTube. Microbiology Sequencing Genomics Public health and epidemiology Bioinformatics Microbiologists Public Health Professionals Life Science Researchers
MGnify quick tour

This quick tour provides a brief introduction to MGnify - a free resource for analysis, visualisation and discovery of microbiome (metagenomic, metatranscriptomic, amplicon and assembly) datasets.

Scientific topics: Metagenomics

Keywords: Metagenomics, Sequence analysis, MGnify, Microbiology

Resource type: Tutorial

MGnify quick tour https://tess.elixir-europe.org/materials/mgnify-quick-tour This quick tour provides a brief introduction to MGnify - a free resource for analysis, visualisation and discovery of microbiome (metagenomic, metatranscriptomic, amplicon and assembly) datasets. Ola Tarkowska Lorna Richardson Metagenomics Metagenomics, Sequence analysis, MGnify, Microbiology Life Scientists
DE-Sim examples, tutorials, and documentation

*DE-Sim* is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as [NumPy](https://numpy.org/), [Scipy](https://scipy.org/scipylib/index.html),...

Scientific topics: Computational biology, Mathematics, Computer science, Simulation experiment

Operations: Visualisation, Modelling and simulation

Keywords: data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science

Resource type: examples, Tutorial, Jupyter notebook, API reference

DE-Sim examples, tutorials, and documentation https://tess.elixir-europe.org/materials/de-sim-examples-tutorials-and-documentation *DE-Sim* is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as [NumPy](https://numpy.org/), [Scipy](https://scipy.org/scipylib/index.html), [pandas](https://pandas.pydata.org/), and [SQLAlchemy](https://www.sqlalchemy.org/) to build and simulate complex computational models. Similar to [Simula](http://www.simula67.info/), *DE-Sim* models are implemented by defining logical process objects which read the values of a set of shared variables and schedule events to modify their values at discrete instants in time. This website provides examples, tutorials, and documentation for *DE-Sim*. Computational biology Mathematics Computer science Simulation experiment data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science computational scientists Computational biologists bioinformaticians software engineers programmers
Metagenomics Bioinformatics

Metagenomics, the genomic analysis of microbial communities from samples like water and soil, involves high throughput sequencing of the microbial DNA, collecting, archiving and resharing the genomic data for taxonomic and functional analysis.

Scientific topics: Metagenomics

Keywords: Metagenomics, MGnify, Sequence Analysis, Microbiology

Resource type: Tutorial

Metagenomics Bioinformatics https://tess.elixir-europe.org/materials/metagenomics-bioinformatics Metagenomics, the genomic analysis of microbial communities from samples like water and soil, involves high throughput sequencing of the microbial DNA, collecting, archiving and resharing the genomic data for taxonomic and functional analysis. Alex Mitchell Varsha Kale Rob Finn Guillermo Rangel Pineros Rebecca Campos Metagenomics Metagenomics, MGnify, Sequence Analysis, Microbiology Life Scientists
Datanator tutorial

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA...

Scientific topics: Omics, Bioinformatics, Systems biology, Cell biology, Molecular biology

Operations: Filtering, Query and retrieval

Keywords: genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis

Resource type: Tutorial

Datanator tutorial https://tess.elixir-europe.org/materials/datanator-tutorial Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. This tutorial provides a brief introduction to the Datanator database and web application. The tutorial illustrates how to search the Datanator database and obtain and refine clouds of data about specific metabolites, RNA, proteins, and reactions of interest. Omics Bioinformatics Systems biology Cell biology Molecular biology genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis mololecular cell biologists systems biologists bioinformaticians Computational biologists modelers
Rare Disease Pathway and Network Analysis

The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis.

Keywords: Pathway analysis, Biological networks, Network analysis, Pathways

Resource type: Tutorial

Rare Disease Pathway and Network Analysis https://tess.elixir-europe.org/materials/rare-disease-pathway-and-network-analysis The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis. Pathway analysis, Biological networks, Network analysis, Pathways Life Science Researchers
Constraint-based reconstruction and analysis toolbox tutorials

A suite of >50 tutorials to enable beginners, as well as intermediate and advanced users to practice a wide variety of COBRA methods.

Keywords: Biomodelling

Resource type: Tutorial

Constraint-based reconstruction and analysis toolbox tutorials https://tess.elixir-europe.org/materials/constraint-based-reconstruction-and-analysis-toolbox-tutorials A suite of >50 tutorials to enable beginners, as well as intermediate and advanced users to practice a wide variety of COBRA methods. Biomodelling Biologists, Genomicists, Computer Scientists
OpenRiskNet: Ontology Walkthrough and Workshop

Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.

Scientific topics: Ontology and terminology, Toxicology

Resource type: Tutorial

OpenRiskNet: Ontology Walkthrough and Workshop https://tess.elixir-europe.org/materials/openrisknet-ontology-walkthrough-and-workshop Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology. Ontology and terminology Toxicology Biologists bioinformaticians Chemists
Adding ontology terms

This tutorial describes how terms can be added to the eNanoMapper ontology.

Keywords: enanomapper, ontologies

Resource type: Tutorial

Adding ontology terms https://tess.elixir-europe.org/materials/adding-ontology-terms-2d31ae63-7f7b-45df-aa37-4b1e14209183 This tutorial describes how terms can be added to the eNanoMapper ontology. enanomapper, ontologies post-docs
CWL User Guide

This guide will introduce you to writing tool wrappers and workflows using the Common Workflow Language (CWL). This guide describes the current stable specification, version 1.0.

Keywords: CWL, commonwl, Workflows

Resource type: Tutorial

CWL User Guide https://tess.elixir-europe.org/materials/cwl-user-guide This guide will introduce you to writing tool wrappers and workflows using the Common Workflow Language (CWL). This guide describes the current stable specification, version 1.0. CWL, commonwl, Workflows bioinformaticians tool authors
High Performance Computing (HPC) in Life Sciences

High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used...

Scientific topics: Biology, Bioinformatics, Computer science

Keywords: High performance computing, high-performance computing

Resource type: Tutorial, Slideshow, e-learning

High Performance Computing (HPC) in Life Sciences https://tess.elixir-europe.org/materials/high-performance-computing-hpc-in-life-sciences High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used either as the electronic component of a blended training format or as a self-running learning product. Biology Bioinformatics Computer science High performance computing, high-performance computing PhD students All postgraduates Life Science Researchers
Adding nanomaterial data

This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format.

Scientific topics: Database management, Toxicology

Keywords: nanotoxicology, enanomapper, resource description framework, ontology

Resource type: Tutorial

Adding nanomaterial data https://tess.elixir-europe.org/materials/adding-nanomaterial-data This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format. Database management Toxicology nanotoxicology, enanomapper, resource description framework, ontology programmers data entering
Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How is raw CLIP-Seq data processed and analysed? - How do I find binding motifs and targets for a protein (e.g., RBFOX2)? Objectives of the tutorial: - Remove Adapters, Barcodes and Unique Molecular...

Resource type: Tutorial

Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection https://tess.elixir-europe.org/materials/transcriptomics-clip-seq-data-analysis-from-pre-processing-to-motif-detection Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How is raw CLIP-Seq data processed and analysed? - How do I find binding motifs and targets for a protein (e.g., RBFOX2)? Objectives of the tutorial: - Remove Adapters, Barcodes and Unique Molecular Identifiers (UMIs) from the reads - Align trimmed reads with STAR - De-duplicate the read library - Inspect the read mapping and de-duplication quality - Perform peak calling with PEAKachu - Analyse the peaks and find potential binding motifs and targets - Check the quality of the peak calling
Make your academic life easy with ORCID: an introduction

Many funders and publishers now require you to get an Open Researcher and Contributor ID (ORCID): an identifier that is unique to you and which comes with you wherever you go. It eliminates ambiguity about your name so you can get full credit for your work. Do you have an ORCID id? Are you sure...

Keywords: ORCID

Resource type: Tutorial

Make your academic life easy with ORCID: an introduction https://tess.elixir-europe.org/materials/make-your-academic-life-easy-with-orcid-an-introduction Many funders and publishers now require you to get an Open Researcher and Contributor ID (ORCID): an identifier that is unique to you and which comes with you wherever you go. It eliminates ambiguity about your name so you can get full credit for your work. Do you have an ORCID id? Are you sure how best to use it? Bring your own device to this practical session and register for an ORCID id, explore its features and find out more ORCID Researchers PhD students Staff
InterMine user tutorial

A tutorial for end users of InterMine

Keywords: Data querying, Data analysis, Data download, FAIR

Resource type: Tutorial

InterMine user tutorial https://tess.elixir-europe.org/materials/intermine-user-tutorial A tutorial for end users of InterMine Data querying, Data analysis, Data download, FAIR Life Science Researchers Bioinformaticians
How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene

Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping.

Scientific topics: Genomics, Genetic variation

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial

How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene https://tess.elixir-europe.org/materials/how-to-install-and-load-the-identifier-mapping-service-with-data-needed-for-gene-to-variant-and-variant-to-gene Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping. Genomics Genetic variation ELIXIR RIR, BridgeDb Biologists
#metawinterschool contribution by BiGCaT

Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis.

Scientific topics: Metabolomics

Keywords: Metabolomics, Identifiers, ELIXIR RIR, BridgeDb

Resource type: Tutorial

#metawinterschool contribution by BiGCaT https://tess.elixir-europe.org/materials/metawinterschool-contribution-by-bigcat Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis. Metabolomics Metabolomics, Identifiers, ELIXIR RIR, BridgeDb Biologists
BridgeDbR Tutorial

Bioconductor Vignette on how to use BridgeDb in the R environment for identifier mapping for genes, proteins, and metabolites.

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial, Vignette

BridgeDbR Tutorial https://tess.elixir-europe.org/materials/bridgedbr-tutorial Bioconductor Vignette on how to use BridgeDb in the R environment for identifier mapping for genes, proteins, and metabolites. ELIXIR RIR, BridgeDb Biologists Chemists
Galaxy Server administration - Ansible

Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - Why Ansible? - How and when to use Ansible? - How to write a role? - How to leverage community build roles? Objectives of the tutorial: - Learn Ansible basics - Write a simple role - Install a...

Resource type: Tutorial

Galaxy Server administration - Ansible https://tess.elixir-europe.org/materials/galaxy-server-administration-ansible Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - Why Ansible? - How and when to use Ansible? - How to write a role? - How to leverage community build roles? Objectives of the tutorial: - Learn Ansible basics - Write a simple role - Install a role from Ansible Galaxy