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105 materials found

Resource type: PDF  or Tutorial 


Tutorial on developing Building Blocks

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

Tutorial on working with computing clusters

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

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, Computer Programming, Documentation and help

Resource type: Tutorial

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

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: Simulation experiment, Personalised medicine

Operations: Modelling and simulation

Keywords: cell-level simulations, Biomodelling, HPC

Resource type: Tutorial

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

Operations: Modelling and simulation

Keywords: HPC, Biomodelling, Signalling

Resource type: Tutorial

Elaboración de un Plan de Gestión de Datos (DMP): teoria y práctica

PDF with slides of the course in Spanish:
- Data management definitions
- DMP Objectives
- DMP Content and structure
- Competencies needed
- Practical session: DMP content analysis and evaluation

Scientific topics: Data management, FAIR data

Keywords: ELIXIR-CONVERGE, DMP, data management plan, research data management, FAIR principles, DMP tools, DMP templates, tools, template, competency, DMP evaluation, evaluation, on-line, e-learning, Spanish

Resource type: PDF, e-learning, slideck/ presentation

Research Data Management Introduction for researchers

Short summary of the previous session
1.Scope of the DM
2.DMP Content and structure
Practical activities
3.Planning the DM of a simple project
4.DMP evaluation

Scientific topics: Data management, FAIR data

Keywords: ELIXIR-CONVERGE, DMP, data management plan, research data management, FAIR principles, DMP tools, DMP templates, tools, template, competency, DMP evaluation, evaluation, on-line, e-learning

Resource type: PDF, e-learning, slideck/ presentation

Data Management Plans and Policies

PDF with slides of the course:
- Data management definitions
- RDM and DM policy
- DMPs: content and competencies
- DMPs for European and National funded projects

Scientific topics: Data management, FAIR data

Keywords: ELIXIR-CONVERGE, DMP, data management plan, research data management, FAIR principles, DMP tools, DMP templates, tools, template, competency, on-line, e-learning

Resource type: PDF, e-learning, slideck/ presentation

Elaboración de un Plan de Gestión de Datos (DMP): teoria y práctica

PDF with slides of the course in Spanish
- Data management definitions
- DMP Objectives
- DMP Content and structure
- Competencies needed
- Practical session: DMP content analysis and evaluation

Scientific topics: FAIR data, Data management

Keywords: ELIXIR-CONVERGE, DMP, DMP tools, DMP templates, DMP evaluation, Data managment plan, research data management, FAIR principles, tools, template, competency, evaluation, online, e-learning, Spanish

Resource type: PDF, e-learning, slideck/ presentation

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

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

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

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

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

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

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

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

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.

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 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, 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 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.

This course covers the use of publicly available...

Scientific topics: Metagenomics

Keywords: Metagenomics, MGnify, Sequence Analysis, Microbiology

Resource type: Tutorial

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

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. 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

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. 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

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

An introduction to the role of experimental data in Intellectual Property

data ownership
the role of experimental data in acquiring a patent
the role of data in establishing a prior use right
trade secrets

Keywords: patents

Resource type: PDF

Helis Academy - Data Management Plans, why and how?

Research Data Management
The organisation of data throughout the research project
everyday management of research data (storage, file naming, preservation)
how will data be preserved and shared after the project is completed?

Scientific topics: Data management

Keywords: Data managment plan, Data Life Cycle

Resource type: Slides, PDF

Adding ontology terms

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

Keywords: enanomapper, ontologies

Resource type: Tutorial

IUPHAR/BPS Guide to Pharmacology online tutorial

The International Union of Basic and Clinical Pharmacology (IUPHAR) / British Pharmacological Society (BPS) Guide to PHARMACOLOGY is an expert-curated resource of ligand-activity-target relationships, the majority of which come from high-quality pharmacological and medicinal chemistry literature....

Scientific topics: Drug discovery, Pharmacology

Resource type: PDF

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