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1395 materials found

Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment

Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment

Keywords: biohackaton 2018

Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment https://tess.elixir-europe.org/materials/improve-shiny-and-rstudio-integration-within-galaxy-using-galaxy-interactive-environment Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment biohackaton 2018
Galaxy training material improvement and extension

Galaxy training material improvement and extension

Keywords: biohackaton 2018

Galaxy training material improvement and extension https://tess.elixir-europe.org/materials/galaxy-training-material-improvement-and-extension Galaxy training material improvement and extension biohackaton 2018
Pathway effect prediction for protein targets

Pathway effect prediction for protein targets

Keywords: biohackaton 2018

Pathway effect prediction for protein targets https://tess.elixir-europe.org/materials/pathway-effect-prediction-for-protein-targets Pathway effect prediction for protein targets biohackaton 2018
OmicsPath: Finding Relevant omics datasets using pathway information

OmicsPath: Finding Relevant omics datasets using pathway information

Keywords: biohackaton 2018

OmicsPath: Finding Relevant omics datasets using pathway information https://tess.elixir-europe.org/materials/omicspath-finding-relevant-omics-datasets-using-pathway-information OmicsPath: Finding Relevant omics datasets using pathway information biohackaton 2018
Prototyping the new PSICQUIC 2.0

Prototyping the new PSICQUIC 2.0

Keywords: biohackaton 2018

Prototyping the new PSICQUIC 2.0 https://tess.elixir-europe.org/materials/prototyping-the-new-psicquic-2-0 Prototyping the new PSICQUIC 2.0 biohackaton 2018
Support tools for rapid adoption of compact identifiers in the publishing process

Support tools for rapid adoption of compact identifiers in the publishing process

Keywords: biohackaton 2018

Support tools for rapid adoption of compact identifiers in the publishing process https://tess.elixir-europe.org/materials/support-tools-for-rapid-adoption-of-compact-identifiers-in-the-publishing-process Support tools for rapid adoption of compact identifiers in the publishing process biohackaton 2018
Enrichment and propagation of metagenomic experimental metadata

Enrichment and propagation of metagenomic experimental metadata

Keywords: biohackaton 2018

Enrichment and propagation of metagenomic experimental metadata https://tess.elixir-europe.org/materials/enrichment-and-propagation-of-metagenomic-experimental-metadata Enrichment and propagation of metagenomic experimental metadata biohackaton 2018
Putting structured data into individual entry pages in biological database

Putting structured data into individual entry pages in biological database

Keywords: biohackaton 2018

Putting structured data into individual entry pages in biological database https://tess.elixir-europe.org/materials/putting-structured-data-into-individual-entry-pages-in-biological-database Putting structured data into individual entry pages in biological database biohackaton 2018
ProtVista (protein annotation viewer) extension using Bioschemas data

ProtVista (protein annotation viewer) extension using Bioschemas data

Keywords: biohackaton 2018

ProtVista (protein annotation viewer) extension using Bioschemas data https://tess.elixir-europe.org/materials/protvista-protein-annotation-viewer-extension-using-bioschemas-data ProtVista (protein annotation viewer) extension using Bioschemas data biohackaton 2018
Using blockchain in biomedical provenance, the identifiers use case

Using blockchain in biomedical provenance, the identifiers use case

Keywords: biohackaton 2018

Using blockchain in biomedical provenance, the identifiers use case https://tess.elixir-europe.org/materials/using-blockchain-in-biomedical-provenance-the-identifiers-use-case Using blockchain in biomedical provenance, the identifiers use case biohackaton 2018
Development of BioJS components

Development of BioJS components

Keywords: biohackaton 2018

Development of BioJS components https://tess.elixir-europe.org/materials/development-of-biojs-components Development of BioJS components biohackaton 2018
How to install and deploy Beacon

**This is an OPEN-ACCESS online tutorial where you can learn how to install and deploy Beacon.**

Scientific topics: Genomics

Keywords: genomics, open access, eLearning, EeLP

Resource type: Video, Manual, Slides, Installation instructions

How to install and deploy Beacon https://tess.elixir-europe.org/materials/how-to-install-and-deploy-beacon **This is an OPEN-ACCESS online tutorial where you can learn how to install and deploy Beacon.** Juha Tornroos Sabela de la Torre Jordi Rambla Genomics genomics, open access, eLearning, EeLP life scientists Researchers
Using Bioinformatics to Understand Genetic Diseases: A Practical Guide

This Practical Guide in the Bringing Bioinformatics into the Classroom series outlines a number of basic bioinformatics approaches that can be used to understand the molecular basis of genetic diseases. A rare variation in the insulin gene is discussed, and the impact of the variation on the gene...

Keywords: Basic bioinformatics, Bioinformatics schools, Gene finding, Genetic mutation, Insulin structure, Sequence alignment, Sequence database searching, Training material

Using Bioinformatics to Understand Genetic Diseases: A Practical Guide https://tess.elixir-europe.org/materials/using-bioinformatics-to-understand-genetic-diseases-a-practical-guide This Practical Guide in the Bringing Bioinformatics into the Classroom series outlines a number of basic bioinformatics approaches that can be used to understand the molecular basis of genetic diseases. A rare variation in the insulin gene is discussed, and the impact of the variation on the gene product, and how this results in disease, is explored. Specifically, this Guide introduces a range of commonly used bioinformatics tools and databases with which to analyse both DNA and protein sequences, and protein structures. On reading the Guide and completing the exercises, users will be able to: i) investigate the locations of genes on the human genome using a genome browser; ii) compare DNA sequences using an alignment tool; iii) translate a DNA sequence into its protein product; iv) search a protein structure database, and visualise the 3D structure of insulin; and v) infer whether insulin is specific to humans by using protein sequence database search tools. Basic bioinformatics, Bioinformatics schools, Gene finding, Genetic mutation, Insulin structure, Sequence alignment, Sequence database searching, Training material 2019-03-18
Data processing with R tidyverse

R is a powerful language for data science in many disciplines of research with a steep learning curve. The tidyverse group of packages provide a dialect that greatly simplifies: * data importing * cleaning * processing * visualization as well as providing reproducible workflows using...

Keywords: R-programming

Resource type: course materials

Data processing with R tidyverse https://tess.elixir-europe.org/materials/data-processing-with-r-tidyverse R is a powerful language for data science in many disciplines of research with a steep learning curve. The tidyverse group of packages provide a dialect that greatly simplifies: * data importing * cleaning * processing * visualization as well as providing reproducible workflows using pipelines (`%>%`) Adopt Hadley Wickham, Chief Scientist at RStudio, philosophy: take each step of data science and replace many intricacies of R with clear, consistent and easy to learn syntax. RStudio will be the software to use since it eases package management, scripting, plotting and data handling. R-programming Researchers
Groovy Cheminformatics with the Chemistry Development Kit

Book that describes the cheminformatics functionality of the Chemistry Development Kit taking advantage of the Groovy programming language.

Scientific topics: Chemistry, Cheminformatics

Resource type: Book

Groovy Cheminformatics with the Chemistry Development Kit https://tess.elixir-europe.org/materials/groovy-cheminformatics-with-the-chemistry-development-kit Book that describes the cheminformatics functionality of the Chemistry Development Kit taking advantage of the Groovy programming language. Chemistry Cheminformatics PhD candidates Master students Chemists Biologists
MATHEMATICS BOOT CAMP: Introduction to Complex Systems Tools

This repository contains didactic material used in an introductory course of mathematics at the Center for Complex Systems and Brain Sciences in Florida Atlantic University by Viktor K. Jirsa.

Scientific topics: Computational biology, Mathematics

Keywords: ComputationalBiology, Neuroscience, complex systems, Mathematics

Resource type: Notes, Scripts

MATHEMATICS BOOT CAMP: Introduction to Complex Systems Tools https://tess.elixir-europe.org/materials/mathematics-boot-camp-introduction-to-complex-systems-tools This repository contains didactic material used in an introductory course of mathematics at the Center for Complex Systems and Brain Sciences in Florida Atlantic University by Viktor K. Jirsa. Felix Almonte Collins Assisi Frederick Carver Gautam Vallabha Jaime Morris Ajay Pillai Armin Fuchs Computational biology Mathematics ComputationalBiology, Neuroscience, complex systems, Mathematics Undergraduate students
Plant Bioinformatics

The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply...

Keywords: life-sciences, physical-science-and-engineering, health-informatics, research-methods

Plant Bioinformatics https://tess.elixir-europe.org/materials/plant-bioinformatics The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply and in a high-throughput manner. These data sets in turn allow us to generate hypotheses at the click of a mouse. For instance, knowing where and when a gene is expressed can help us narrow down the phenotypic search space when we don't see a phenotype in a gene mutant under "normal" growth conditions. Coexpression analyses and association networks can provide high-quality candidate genes involved in a biological process of interest. Using Gene Ontology enrichment analysis and pathway visualization tools can help us make sense of our own 'omics experiments and answer the question "what processes/pathways are being perturbed in our mutant of interest?" Structure: each of the 6 week hands-on modules consists of a ~2 minute intro, a ~20 minute theory mini-lecture, a 1.5 hour hands-on lab, an optional ~20 minute lab discussion if experiencing difficulties with lab, and a ~2 minute summary. Tools covered: Module 1: GENOMIC DBs / PRECOMPUTED GENE TREES / PROTEIN TOOLS. Araport, TAIR, Gramene, EnsemblPlants Compara, PLAZA; SUBA4 and Cell eFP Browser, 1001 Genomes Browser Module 2: EXPRESSION TOOLS. eFP Browser / eFP-Seq Browser, Araport, Genevestigator, TravaDB, NCBI Genome Data Viewer for exploring RNA-seq data for many plant species other than Arabidopsis, MPSS database for small RNAs Module 3: COEXPRESSION TOOLS. ATTED II, Expression Angler, AraNet, AtCAST2 Module 4: PROMOTER ANALYSIS. Cistome, Athena, ePlant Module 5: GO ENRICHMENT ANALYSIS AND PATHWAY VIZUALIZATION. AgriGO, AmiGO, Classification SuperViewer, TAIR, g:profiler, AraCyc, MapMan (optional: Plant Reactome) Module 6: NETWORK EXPLORATION. Arabidopsis Interactions Viewer 2, ePlant, TF2Network, Virtual Plant, GeneMANIA [Material updated in June 2019] life-sciences, physical-science-and-engineering, health-informatics, research-methods
A network biology workflow to study transcriptomics data of the diabetic liver

Description of a network biology workflow for pathway and network analysis methods to study the rewiring of the diabetic liver.

Keywords: Biological networks, Network Visualization

A network biology workflow to study transcriptomics data of the diabetic liver https://tess.elixir-europe.org/materials/a-network-biology-workflow-to-study-transcriptomics-data-of-the-diabetic-liver Description of a network biology workflow for pathway and network analysis methods to study the rewiring of the diabetic liver. Susan Coort Martina Kutmon Chris Evelo Biological networks, Network Visualization
Learning structural bioinformatics and evolution with a snake puzzle

We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding.

Scientific topics: Protein structure analysis, Molecular biology, Evolutionary biology, Bioinformatics

Resource type: course materials

Learning structural bioinformatics and evolution with a snake puzzle https://tess.elixir-europe.org/materials/learning-structural-bioinformatics-and-evolution-with-a-snake-puzzle We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. Protein structure analysis Molecular biology Evolutionary biology Bioinformatics Master students Undergraduate students
Bioinformática con Ñ

"Bioinformática con Ñ" is a project born in 2013 aimed to provide specialized educational bibliography on Bioinformatics for Spanish speakers. The first release, published in 2014 and edited by Álvaro Sebastián and Alberto Pascual-García, consists on more than 500 pages where the following...

Scientific topics: Systems biology, Bioinformatics

Keywords: introduction to bioinformatics, structural biology, biomolecular databases, Systems biology, phylogenetics, Programming, Sequence Analysis, DNA RNA, Virtual Screening, molecular evolution, molecular dynamics, Molecular docking, normal modes analysis, Proteins, protein folding, protein structure alignment, chromatin structure, intrinsically disordered proteins, data minning, R-programming, parallel computing, bibliography management

Resource type: Book

Bioinformática con Ñ https://tess.elixir-europe.org/materials/bioinformatica-con-n "Bioinformática con Ñ" is a project born in 2013 aimed to provide specialized educational bibliography on Bioinformatics for Spanish speakers. The first release, published in 2014 and edited by Álvaro Sebastián and Alberto Pascual-García, consists on more than 500 pages where the following matters are covered: biomedical databases, sequence analysis, phylogeny and evolution, structural biology, including diverse topics such as docking, virtual screening or molecular dynamics, statistics and R, systems biology, programming skills, data mining, parallel computation, bibliography management and science article writing. Portada: Enrique Sahagún Systems biology Bioinformatics introduction to bioinformatics, structural biology, biomolecular databases, Systems biology, phylogenetics, Programming, Sequence Analysis, DNA RNA, Virtual Screening, molecular evolution, molecular dynamics, Molecular docking, normal modes analysis, Proteins, protein folding, protein structure alignment, chromatin structure, intrinsically disordered proteins, data minning, R-programming, parallel computing, bibliography management Anyone interested in bioinformatics
FAIRsharing Educational Material

Whether you are a researcher, standard/database developer, funder, journal editor, librarian or data manager, FAIRsharing can help you understand which standards are mature and appropriate to your use case. By mapping the relationships between standards and the databases that implement them, or...

Keywords: Databases, Standards, Data Policies, FAIR

Resource type: Metadata Registry

FAIRsharing Educational Material https://tess.elixir-europe.org/materials/fairsharing-educational-material Whether you are a researcher, standard/database developer, funder, journal editor, librarian or data manager, FAIRsharing can help you understand which standards are mature and appropriate to your use case. By mapping the relationships between standards and the databases that implement them, or the policies that recommend them, FAIRsharing enables you to make an informed decision as to which standard or database to use or endorse. In this training, educational material, we describe the FAIRsharing resource and explain how you can use it to find the appropriate resource for your work. Databases, Standards, Data Policies, FAIR Researchers data managers data stewards Policy makers database managers biocurators standard developers
Adding schema.org to a GitHub Pages site

This guide will show you how to do add schema.org to GitHub Pages.

Scientific topics: Computer science

Keywords: Mark-up, Bioschemas, Interoperability

Resource type: Training materials

Adding schema.org to a GitHub Pages site https://tess.elixir-europe.org/materials/adding-schema-org-to-a-github-pages-site This guide will show you how to do add schema.org to GitHub Pages. Raniere Silva Computer science Mark-up, Bioschemas, Interoperability web developers System administrators
RRegrs package

This tutorial explains how to use a collection of R regression tools for estimating the optimal model via a fully validated procedure.

Keywords: Regression Models

RRegrs package https://tess.elixir-europe.org/materials/rregrs-package This tutorial explains how to use a collection of R regression tools for estimating the optimal model via a fully validated procedure. Regression Models PhD students post-docs
How to use the AffyQC web tool of ArrayAnalysis.org for quality control and pre-processing of Affymetrix microarray data

This tutorial explains how to use the AffyQC web tool of ArrayAnalysis.org for quality control and pre-processing of Affymetrix microarray data.

Keywords: Microarray data analysis, Quality control and data pre-processing, Affymetrix microarrays, Systems biology, Pathway and network analyis

How to use the AffyQC web tool of ArrayAnalysis.org for quality control and pre-processing of Affymetrix microarray data https://tess.elixir-europe.org/materials/how-to-use-the-affyqc-web-tool-of-arrayanalysis-org-for-quality-control-and-pre-processing-of-affymetrix-microarray-data This tutorial explains how to use the AffyQC web tool of ArrayAnalysis.org for quality control and pre-processing of Affymetrix microarray data. Microarray data analysis, Quality control and data pre-processing, Affymetrix microarrays, Systems biology, Pathway and network analyis PhD students post-docs
How to use the statistics module of ArrayAnalysis.org for statistics analysis of microarray data

This tutorial how to statistically analyze microarray data with ArrayAnalysis.org website.

Keywords: ArrayAnalysis.org, microarray

How to use the statistics module of ArrayAnalysis.org for statistics analysis of microarray data https://tess.elixir-europe.org/materials/how-to-use-the-statistics-module-of-arrayanalysis-org-for-statistics-analysis-of-microarray-data This tutorial how to statistically analyze microarray data with ArrayAnalysis.org website. ArrayAnalysis.org, microarray post-docs
How to make a new pathway for WikiPathways using PathVisio

This tutorial explains how to a new pathway for WikiPathways using PathVisio.

Keywords: Systems biology, Pathway analysis, Network analysis, Microarray data analysis, Nanomaterials

How to make a new pathway for WikiPathways using PathVisio https://tess.elixir-europe.org/materials/how-to-make-a-new-pathway-for-wikipathways-using-pathvisio This tutorial explains how to a new pathway for WikiPathways using PathVisio. Systems biology, Pathway analysis, Network analysis, Microarray data analysis, Nanomaterials PhD students post-docs
Omics descriptors calculation R package

This tutorial explains how to generate a new set of GO descriptors using two novel created R packages.

Keywords: Gene Ontology

Omics descriptors calculation R package https://tess.elixir-europe.org/materials/omics-descriptors-calculation-r-package This tutorial explains how to generate a new set of GO descriptors using two novel created R packages. Gene Ontology PhD students post-docs
PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. [Materials](ftp://ftp.psb.ugent.be/pub/plaza/workshop/ELIXIR/)

Scientific topics: Plant biology, Functional genomics, Comparative genomics, Evolutionary biology, Phylogenomics, Genotype and phenotype

Operations: Annotation, Visualisation, Comparison

Keywords: plants, Plants bioinformatics, genomics, Visualisation, Annotation

Resource type: Training materials

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics https://tess.elixir-europe.org/materials/plaza-is-a-plant-oriented-online-resource-for-comparative-evolutionary-and-functional-genomics PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. [Materials](ftp://ftp.psb.ugent.be/pub/plaza/workshop/ELIXIR/) Plant biology Functional genomics Comparative genomics Evolutionary biology Phylogenomics Genotype and phenotype plants, Plants bioinformatics, genomics, Visualisation, Annotation Life Science Researchers plant researchers experimeintal biologist researchers postdoctoral researchers Research Assistants and Research Associates PhD
Galaxy Proteomics workshop Prague 2018

Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic

Scientific topics: Proteomics

Keywords: Galaxy, training, proteomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

Galaxy Proteomics workshop Prague 2018 https://tess.elixir-europe.org/materials/galaxy-proteomics-workshop-prague-2018 Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic Andrea Argentini Frederik Coppens Pavel Dvorak Matthias Fahrner Melanie Foell Björn Grüning Martin Hubalek Hana Pergl Sustkova Marek Vrbacky Proteomics Galaxy, training, proteomics, eLearning, EeLP life scientists Researchers PhD Students
Working with Ranges infrastructure: annotating and understanding regions

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Operations: Annotation

Working with Ranges infrastructure: annotating and understanding regions https://tess.elixir-europe.org/materials/working-with-ranges-infrastructure-annotating-and-understanding-regions Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.