TeSS Training eSupport System

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, health-informatics

Plant Bioinformatics https://www.coursera.org/learn/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 life-sciences, health-informatics

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://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-971 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

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://www.fairsharing.org/educational 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. Peter McQuilton Susanna-Assunta Sansone 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://bioschemas.gitbook.io/training-portal/how-to/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. Niall Beard 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://enanomapper.github.io/tutorials/RRegrs/RRegrs.html 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://enanomapper.github.io/tutorials/QCandpreprocessing/QCandpreprocessing.html 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://enanomapper.github.io/tutorials/Statistics/readme.html 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. Anwesha Bohler Egon Willighagen Friederike Ehrhart Lars Eijssen Linda Rieswijk Penny Nymark 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://enanomapper.github.io/tutorials/Pathway/Pathway.html 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://enanomapper.github.io/tutorials/Omics%20descriptors%20calculation/Omics%20descriptors%20calculation%20R%20package.html 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://bioinformatics.psb.ugent.be/plaza/ 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/) Klaas Vandepoele Michiel Van Bel Emmelien Vancaester 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://elixir.mf.uni-lj.si/course/view.php?id=41 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 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