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16 materials found

Authors: Obi Griffith  or blankclemens  or Bruno Gaeta  or Yo Yehudi  or Will Hsiao 


Infectious Disease Genomic Epidemiology 2018 Module 1-Introduction to Public Health Microbiology and Genomic Epidemiology

Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools.

Infectious Disease Genomic Epidemiology 2018 Module 1-Introduction to Public Health Microbiology and Genomic Epidemiology https://tess.elixir-europe.org/materials/infectious-disease-genomic-epidemiology-2018-module-1-introduction-to-public-health-microbiology-and-genomic-epidemiology Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools. Researchers Post-Doctoral Fellows Graduate students Biologists, Genomicists, Computer Scientists
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
InterMine user manual

Documentation for end users on how to search for data, run simple and complex queries, analyse results and download data from any instance of InterMine.

Keywords: Data querying, data visualization, Data download, FAIR

Resource type: Documentation

InterMine user manual https://tess.elixir-europe.org/materials/intermine-user-manual Documentation for end users on how to search for data, run simple and complex queries, analyse results and download data from any instance of InterMine. Data querying, data visualization, Data download, FAIR Life Science Researchers Bioinformaticians
InterMine operator manual

Documentation on how to install, configure and operate an InterMine instance.

Keywords: Data integration, Data analysis, Data publishing, FAIR

Resource type: Documentation

InterMine operator manual https://tess.elixir-europe.org/materials/intermine-operator-manual Documentation on how to install, configure and operate an InterMine instance. Data integration, Data analysis, Data publishing, FAIR Bioinformaticians software engineers
Analysis of Metagenomic Data 2018 Module 2-Marker Gene-Based Analysis

Course providing an introduction to metagenomic data analysis followed by hands-on practical tutorials demonstrating the use of metagenome analysis tools.

Analysis of Metagenomic Data 2018 Module 2-Marker Gene-Based Analysis https://tess.elixir-europe.org/materials/analysis-of-metagenomic-data-2018-module-2-marker-gene-based-analysis Course providing an introduction to metagenomic data analysis followed by hands-on practical tutorials demonstrating the use of metagenome analysis tools. Researchers Graduate students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists
Analysis of Metagenomic Data 2018 Module 1-Introduction to Metagenomics

Course providing an introduction to metagenomic data analysis followed by hands-on practical tutorials demonstrating the use of metagenome analysis tools.

Analysis of Metagenomic Data 2018 Module 1-Introduction to Metagenomics https://tess.elixir-europe.org/materials/analysis-of-metagenomic-data-2018-module-1-introduction-to-metagenomics Course providing an introduction to metagenomic data analysis followed by hands-on practical tutorials demonstrating the use of metagenome analysis tools. Researchers Graduate Students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists
Informatics for RNA-Seq Analysis 2018 Module 3-Expression and Differential Expression

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2018 Module 3-Expression and Differential Expression https://tess.elixir-europe.org/materials/informatics-for-rna-seq-analysis-2018-module-3-expression-and-differential-expression Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows
Informatics for RNA-Seq Analysis 2017 Module 3-Expression and Differential Expression

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2017 Module 3-Expression and Differential Expression https://tess.elixir-europe.org/materials/informatics-for-rna-seq-analysis-2017-module-3-expression-and-differential-expression Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Graduate Students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Infectious Disease Genomic Epidemiology 2017 Module 1-Introduction to Public Health Microbiology and Genomic Epidemiology

Course provides an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools.

Infectious Disease Genomic Epidemiology 2017 Module 1-Introduction to Public Health Microbiology and Genomic Epidemiology https://tess.elixir-europe.org/materials/infectious-disease-genomic-epidemiology-module-1-introduction-to-public-health-microbiology-and-genomic-epidemiology Course provides an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools. Researchers Graduate Students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
High-Throughput Biology 2017 Module 9-Expression and Differential Expression

Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.

High-Throughput Biology 2017 Module 9-Expression and Differential Expression https://tess.elixir-europe.org/materials/high-throughput-biology-2017-module-9-expression-and-differential-expression Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate students Post-Doctoral Fellows Researchers Biologists, Genomicists, Computer Scientists
Development in Galaxy - Galaxy Webhooks

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What are Galaxy Webhooks? - How to create them? Objectives of the tutorial: - Discover what Galaxy...

Resource type: Tutorial

Development in Galaxy - Galaxy Webhooks https://tess.elixir-europe.org/materials/development-in-galaxy-galaxy-webhooks Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What are Galaxy Webhooks? - How to create them? Objectives of the tutorial: - Discover what Galaxy Webhooks are - Be able to create Webhooks - Be able to add a Galaxy Webhook in a Galaxy instance
Introduction to Galaxy Analyses - Galaxy 101

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - Which coding exon has the...

Resource type: Tutorial

Introduction to Galaxy Analyses - Galaxy 101 https://tess.elixir-europe.org/materials/galaxy-introduction-galaxy-101 Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - Which coding exon has the highest number of single nucleotide polymorphisms (SNPs) on human chromosome 22? Objectives of the tutorial: - Familiarize yourself with the basics of Galaxy - Learn how to obtain data from external sources - Learn how to run tools - Learn how histories work - Learn how to create a workflow - Learn how to share your work
Introduction to Galaxy Analyses - From peaks to genes

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How to use Galaxy? - How to get...

Resource type: Tutorial

Introduction to Galaxy Analyses - From peaks to genes https://tess.elixir-europe.org/materials/galaxy-introduction-from-peaks-to-genes Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How to use Galaxy? - How to get from peak regions to a list of gene names? Objectives of the tutorial: - Familiarize yourself with the basics of Galaxy - Learn how to obtain data from external sources - Learn how to run tools - Learn how histories work - Learn how to create a workflow - Learn how to share your work
Similarity searching, multiple sequence alignment and protein families - undergraduate lab

Lab 3 in a series of labs given as part of a "bioinformatics for biologists" course targeted at 2nd/3rd year undergraduates and focusing on informed use of tools. Some instructions are specific to our local computer lab setup but overall the content should be adaptable. Note that because some of...

Keywords: Blast, Hmmer, Interpro, Multiple sequence alignment, Similarity searching

Similarity searching, multiple sequence alignment and protein families - undergraduate lab https://tess.elixir-europe.org/materials/similarity-searching-multiple-sequence-alignment-and-protein-families-undergraduate-lab Lab 3 in a series of labs given as part of a "bioinformatics for biologists" course targeted at 2nd/3rd year undergraduates and focusing on informed use of tools. Some instructions are specific to our local computer lab setup but overall the content should be adaptable. Note that because some of the exercises make use of public databases they need to be checked and in some cases updated every time the lab is run. The lab is meant to be easily assessed using an online quiz (I use moodle). I provides a hands on introduction to NCBI BLAST, Interproscan, Clustal, MUSCLE and T-COFFEE, and HMMER.  Blast, Hmmer, Interpro, Multiple sequence alignment, Similarity searching biology and bioinformatics sophomore undergraduates 2013-11-12 2017-10-09
Multiple sequence alignment and phylogeny - undergraduate lab

This is lab 4 in a series of labs given as part of an undergraduate "Bioinformatics for biologists" course delivered to 2nd and 3rd year biology and bioinformatics undergraduate students, as part of a course focusing on using bioinformatics tools. Some instructions in it are specific to our lab...

Keywords: Clustalw, Multiple sequence alignment, Phylip, Phylogeny

Multiple sequence alignment and phylogeny - undergraduate lab https://tess.elixir-europe.org/materials/multiple-sequence-alignment-and-phylogeny-undergraduate-lab This is lab 4 in a series of labs given as part of an undergraduate "Bioinformatics for biologists" course delivered to 2nd and 3rd year biology and bioinformatics undergraduate students, as part of a course focusing on using bioinformatics tools. Some instructions in it are specific to our lab environment - including some not so current programs (clustalw, treetool, seaview, phylip) as that's what we have installed at the moment and they're stable, but the content can easily be adapted to other environments and programs. The lab is meant to be easily assessed and I get the students to answer the question in a moodle quiz which makes marking easier. The lab follows some lectures on multiple sequence alignment and molecular phylogeny. Clustalw, Multiple sequence alignment, Phylip, Phylogeny biology and bioinformatics sophomore undergraduates 2013-11-12 2017-10-09
Sequence comparison - undergraduate lab

This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of...

Keywords: Dotmatrix plots, Scoring matrices, Sequence alignment

Sequence comparison - undergraduate lab https://tess.elixir-europe.org/materials/sequence-comparison-undergraduate-lab This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of the lab should be easy to adapt to other environments. This lab makes use of EMBOSS programs, prss in the FASTA package, as well as the NCBI BLAST website. I usually deliver this lab after a series of lectures discussing dotmatrix plots and sequence alignment. Students enter their answers to the questions into a quiz set up within moodle which allows for easier marking. Dotmatrix plots, Scoring matrices, Sequence alignment Undergraduate students 2013-11-12 2017-10-09