Resource type: Tutorial
This section provides a step-by-step by tutorial on how to develop Building Blocks using the permedcoe package and an application that uses them.
Scientific topics: Personalised medicine, Workflows, Bioinformatics
Keywords: HPC, building blocks
Resource type: Tutorial
This tutorial provides an introduction to how to access a computing cluster, manage your data and submit jobs using a batch job system.
Keywords: HPC
Resource type: Tutorial
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, Computer Programming, Documentation and help
Resource type: Tutorial
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
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: Simulation experiment, Personalised medicine
Operations: Modelling and simulation
Keywords: cell-level simulations, Biomodelling, HPC
Resource type: Tutorial
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: Molecular interactions, pathways and networks, Simulation experiment, Personalised medicine
Operations: Modelling and simulation
Keywords: HPC, Biomodelling, Signalling
Resource type: Tutorial
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
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
Course given at BioSB 2019 for biologists about SPARQL.
Scientific topics: Biology
Operations: Query and retrieval
Keywords: Sparql queries, Sparql syntax
Resource type: Tutorial
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
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
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
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
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
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.
This course is suitable those with an undergraduate degree in a life science subject would be an...
Scientific topics: Metagenomics
Keywords: Metagenomics, Sequence analysis, MGnify, Microbiology
Resource type: Tutorial
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, Scipy,...
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
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.
This course covers the use of publicly available...
Scientific topics: Metagenomics
Keywords: Metagenomics, MGnify, Sequence Analysis, Microbiology
Resource type: 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
The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis. The tutorials are freely available on pathway drawing, pathway curation, pathway analysis, and network analysis.
Keywords: Pathway analysis, Biological networks, Network analysis, Pathways
Resource type: Tutorial
A suite of >50 tutorials to enable beginners, as well as intermediate and advanced users to practice a wide variety of COBRA methods. Each tutorial is presented in a variety of formats, including as a MATLAB live script, which is an interactive document, or narrative...
Keywords: Biomodelling
Resource type: Tutorial
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
This tutorial describes how terms can be added to the eNanoMapper ontology.
Keywords: enanomapper, ontologies
Resource type: Tutorial
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
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
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
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
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
InterMine integrates biological data sources, making it easy to query and analyse data. It is a downloadable platform that operators can install and integrate with their own systems.
InterMine is a generic model-based platform that is used to provide data to end users in many different life...
Keywords: Data querying, Data analysis, Data download, FAIR
Resource type: Tutorial
Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping. It explains how to download the IMS Docker and identifier mapping databases (link sets), load the link sets, and test the web interface.
Scientific topics: Genomics, Genetic variation
Keywords: ELIXIR RIR, BridgeDb
Resource type: Tutorial
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