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36 materials found

Authors: Jared Simpson  or Michelle Brazas  or Janick Mathys 


Informatics on High-Throughput Sequencing Data 2018 Module 6-De Novo Assmebly

Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data, where the focus is on Illumina reads although information is applicable to all sequencer reads.

Informatics on High-Throughput Sequencing Data 2018 Module 6-De Novo Assmebly https://tess.elixir-europe.org/materials/informatics-on-high-throughput-sequencing-data-2018-module-6-de-novo-assmebly Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data, where the focus is on Illumina reads although information is applicable to all sequencer reads. Researchers Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists Graduate students
Informatics on High-Throughput Sequencing Data 2018 Module 1-Introduction to High-Throughput Sequencing

Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data, where the focus is on Illumina reads although information is applicable to all sequencer reads.

Informatics on High-Throughput Sequencing Data 2018 Module 1-Introduction to High-Throughput Sequencing https://tess.elixir-europe.org/materials/informatics-on-high-throughput-sequencing-data-2018-module-1-introduction-to-high-throughput-sequencing Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data, where the focus is on Illumina reads although information is applicable to all sequencer reads. Researchers Graduate students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists
Bioinformatics for Cancer Genomics 2018 Module 5-Genome Assembly

Course covers the key bioinformatics concepts and tools required to analyze cancer genomic data sets and access and work with data sets in the cloud.

Bioinformatics for Cancer Genomics 2018 Module 5-Genome Assembly https://tess.elixir-europe.org/materials/bioinformatics-for-cancer-genomics-2018-module-5-genome-assembly Course covers the key bioinformatics concepts and tools required to analyze cancer genomic data sets and access and work with data sets in the cloud. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Bioinformatics for Cancer Genomics 2018 Module 4-Genome Alignment

Course covers the key bioinformatics concepts and tools required to analyze cancer genomic data sets and access and work with data sets in the cloud.

Bioinformatics for Cancer Genomics 2018 Module 4-Genome Alignment https://tess.elixir-europe.org/materials/bioinformatics-for-cancer-genomics-2018-module-4-genome-alignment Course covers the key bioinformatics concepts and tools required to analyze cancer genomic data sets and access and work with data sets in the cloud. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Bioinformatics for Cancer Genomics 2017 Module 3-Genome Alignment and Assembly

Course covers the bioinformatics tools required to analyze genomic data sets.

Bioinformatics for Cancer Genomics 2017 Module 3-Genome Alignment and Assembly https://tess.elixir-europe.org/materials/bioinformatics-for-cancer-genomics-2017-module-3-genome-alignment-and-assembly Course covers the bioinformatics tools required to analyze genomic data sets. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Informatics on High-Throughput Sequencing Data 2017 Module 6-De Novo Assembly

Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data with a focus on Illumina reads.

Informatics on High-Throughput Sequencing Data 2017 Module 6-De Novo Assembly https://tess.elixir-europe.org/materials/informatics-on-high-throughput-sequencing-data-2017-module-6-de-novo-assembly Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data with a focus on Illumina reads. Researchers Graduate Students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists
Informatics on High-Throughput Sequencing Data 2017 Module 1-Introduction to High-Throughput Sequencing

Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data with a focus on Illumina reads.

Informatics on High-Throughput Sequencing Data 2017 Module 1-Introduction to High-Throughput Sequencing https://tess.elixir-europe.org/materials/informatics-on-high-throughput-sequencing-data-module-1-introduction-to-high-throughput-sequencing Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data with a focus on Illumina reads. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
High-Throughput Biology 2017 Module 6-De Novo Assembly

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 6-De Novo Assembly https://tess.elixir-europe.org/materials/high-throughput-biology-2017-module-6-de-novo-assembly Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
High-Throughput Biology 2017 Module 1-Introduction to High-Throughput Sequencing

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 1-Introduction to High-Throughput Sequencing https://tess.elixir-europe.org/materials/high-throughput-biology-2017-module-1-introduction-to-high-throughput-sequencing 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
Basic statistics theory

This training gives an introduction to the use of statistics for basic analyses of life sciences data. This training is a prerequisite introduction to a series of hands-on trainings on the statistical analysis of life sciences data: 'Basic statistics in R' and 'Basic statistics in Graphpad...

Basic statistics theory https://tess.elixir-europe.org/materials/basic-statistics-theory This training gives an introduction to the use of statistics for basic analyses of life sciences data. This training is a prerequisite introduction to a series of hands-on trainings on the statistical analysis of life sciences data: 'Basic statistics in R' and 'Basic statistics in Graphpad Prism'. If you want to follow one of these trainings, you have to follow this introduction. Ít will give you all the theoretical background that you need. Those that already have a strong statistical background may register directly for the 'Basic statistics in R, part II' training. Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
Basic bioinformatics concepts, databases and tools

During this 3-day introduction to bioinformatics, BITS will take you along a guided tour that covers all basic aspects of biological sequence analysis. This workshop is an ideal opportunity to get familiar with bioinformatics and its many faces! At the end, you should be able to start tackling...

Scientific topics: Sequence analysis

Basic bioinformatics concepts, databases and tools https://tess.elixir-europe.org/materials/basic-bioinformatics-concepts-databases-and-tools During this 3-day introduction to bioinformatics, BITS will take you along a guided tour that covers all basic aspects of biological sequence analysis. This workshop is an ideal opportunity to get familiar with bioinformatics and its many faces! At the end, you should be able to start tackling any basic bioinformatics problem: how to obtain relevant information about your gene, you know where to get the required sequence data, manipulate the sequences, and how basic software and algorithms function so you can fine-tune it in order the get the most out of your analysis. Sequence analysis Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
Introductory statistics in GraphPad Prism

This training gives an introduction to the use of statistics for basic analyses of life sciences data. The theoretical background obtained in the Basic statistics theory training  will be applied in a hands-on session on real-life data using the statistical software GraphPad...

Introductory statistics in GraphPad Prism https://tess.elixir-europe.org/materials/introductory-statistics-in-graphpad-prism This training gives an introduction to the use of statistics for basic analyses of life sciences data. The theoretical background obtained in the Basic statistics theory training  will be applied in a hands-on session on real-life data using the statistical software GraphPad Prism. BITS distributes the software for free to VIB scientists, for more information you can visit the GraphPad Prism page on the BITS web site. This is the reason why the training is limited to VIB scientists. Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
Introduction to the analysis of NGS data

This training is a prerequisite introduction to a series of trainings on the analysis of NGS data for different applications: 'Hands-on introduction to NGS variant analysis', 'RNA-Seq analysis for differential expression', and 'Hands-on introduction to ChIP-Seq analysis'. If you want to follow...

Scientific topics: Workflows, Sequence assembly

Introduction to the analysis of NGS data https://tess.elixir-europe.org/materials/introduction-to-the-analysis-of-ngs-data This training is a prerequisite introduction to a series of trainings on the analysis of NGS data for different applications: 'Hands-on introduction to NGS variant analysis', 'RNA-Seq analysis for differential expression', and 'Hands-on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings, you have to follow this introduction. The training will give you all the background that you will need in the later NGS trainings. Workflows Sequence assembly Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
Basic statistics in R

This training gives an introduction to the use of the statistical software language R. R is a language for data analysis and graphics. This introduction to R is aimed at beginners. The training covers data handling, graphics, mathematical functions and some statistical techniques. R is for free...

Keywords: Statistical calculation

Basic statistics in R https://tess.elixir-europe.org/materials/basic-statistics-in-r This training gives an introduction to the use of the statistical software language R. R is a language for data analysis and graphics. This introduction to R is aimed at beginners. The training covers data handling, graphics, mathematical functions and some statistical techniques. R is for free and for more information you can visit the site at the CRAN web site. This training is an introduction to the use of R and RStudio and stops at very basic analyses (t-tests and non-parametric equivalents). A full overview of statistical analyses in R including regression, ANOVA will be given in the follow-up training Basic statistics in R, part II Statistical calculation Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
Introduction to Affymetrix microarray analysis

Following this training is a prerequisite to the training on the analysis of Affymetrix microarray data using free Affymetrix software. If you want to follow this training, you have to follow this introduction first. If you want to follow the Genevestigator training or the training on the...

Scientific topics: Expression data visualisation, Gene expression

Introduction to Affymetrix microarray analysis https://tess.elixir-europe.org/materials/introduction-to-affymetrix-microarray-analysis Following this training is a prerequisite to the training on the analysis of Affymetrix microarray data using free Affymetrix software. If you want to follow this training, you have to follow this introduction first. If you want to follow the Genevestigator training or the training on the analysis of public microarray data sets and you have no experience with microarrays, you can also follow this introduction or consult the training material of this introduction. Expression data visualisation Gene expression Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
Analysis of qPCR data using qbase+

This hands-on training provides an introduction to the analysis of qPCR data using Biogazelle's qbase+ software. Although this software allows to do various types of analyses (gene expression, copy number analysis, miRNA profiling), we will focus in the training on gene expression analysis....

Scientific topics: PCR experiment, Gene expression analysis, Gene expression

Analysis of qPCR data using qbase+ https://tess.elixir-europe.org/materials/analysis-of-qpcr-data-using-qbase This hands-on training provides an introduction to the analysis of qPCR data using Biogazelle's qbase+ software. Although this software allows to do various types of analyses (gene expression, copy number analysis, miRNA profiling), we will focus in the training on gene expression analysis. qbase+ software is freely distributed by BITS to VIB scientists. Therefore the training will be limited to VIB scientists. PCR experiment Gene expression analysis Gene expression Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
GOBLET Talk at INCoB 2014

Supporting Trainers to Improve Bioinformatics Education Globally Speaker: Dr. Michelle Brazas A needs assessment isn’t necessary to realize that across the globe, there is a high demand for quality bioinformatics training in all domains of life science. Delivering on this demand however is not...

Keywords: Goblet

GOBLET Talk at INCoB 2014 https://tess.elixir-europe.org/materials/goblet-talk-at-incob-2014 Supporting Trainers to Improve Bioinformatics Education Globally Speaker: Dr. Michelle Brazas A needs assessment isn’t necessary to realize that across the globe, there is a high demand for quality bioinformatics training in all domains of life science. Delivering on this demand however is not trivial. In addition to computational infrastructure and software tools, quality bioinformatics training depends upon excellent trainers and training resources. With a focus on the trainer in the learning equation, the Global Organization for Bioinformatics Learning, Education and Training (GOBLET) aims to facilitate the advancement of bioinformatics education globally by training and supporting a network of bioinformatics trainers. Activities include coordinating training efforts, sharing data sets and teaching materials, discussing best practices and building up teaching standards and teaching recognition. Examples to improve your bioinformatics training programs were provided. Through support and development of trainer excellence, GOBLET is working to improve the global landscape in bioinformatics education. Goblet General Interest 2014-08-14 2017-10-09
Workshop on Education in Bioinformatics 2014 - ISMB 2014 - Benjamin Good

Online Gaming in Bioinformatics: The ‘Fun’ Model to Online Bioinformatics Education Benjamin Good, Senior Staff Scientist, Department of Molecular and Experimental Medicine, The Scripps Research Institute. Dr. Good’s research focuses on games with a purpose in crowdsourcing biological knowledge....

Scientific topics: Bioinformatics

Keywords: Bioinformatics, Gaming, Online learning

Workshop on Education in Bioinformatics 2014 - ISMB 2014 - Benjamin Good https://tess.elixir-europe.org/materials/workshop-on-education-in-bioinformatics-2014-ismb-2014-benjamin-good Online Gaming in Bioinformatics: The ‘Fun’ Model to Online Bioinformatics Education Benjamin Good, Senior Staff Scientist, Department of Molecular and Experimental Medicine, The Scripps Research Institute. Dr. Good’s research focuses on games with a purpose in crowdsourcing biological knowledge. To this end, his research has contributed to the development of a suite of interactive video games that allow for play, learning and contributions to science: genegames.org. Dr. Good spoke on online games for bioinformatics and how they can (or cannot) be used to teach bioinformatics at WEB 2014 at ISMB 2014. Bioinformatics Bioinformatics, Gaming, Online learning General Interest 2014-08-14 2017-10-09
Workshop on Education in Bioinformatics 2014 - ISMB 2014 - David Searls

Self-directed Learning: Does online learning in bioinformatics work? Proposed Speaker: (CONFIRMED) David Searls, Adjunct Associate Professor, Perleman School of Medicine, University of Pennsylvania. Dr. Searls is an independent consultant in bioinformatics and former Senior VP of Bioinformatics...

Keywords: Bioinformatics, Mooc, Online learning

Workshop on Education in Bioinformatics 2014 - ISMB 2014 - David Searls https://tess.elixir-europe.org/materials/workshop-on-education-in-bioinformatics-2014-ismb-2014-david-searls Self-directed Learning: Does online learning in bioinformatics work? Proposed Speaker: (CONFIRMED) David Searls, Adjunct Associate Professor, Perleman School of Medicine, University of Pennsylvania. Dr. Searls is an independent consultant in bioinformatics and former Senior VP of Bioinformatics at GlaxoSmithKline Pharmaceuticals. He recently authored “Ten Simple Rules for Online Learning” and “An Online Bioinformatics Curriculum”. Dr. Searls spoke on the opportunities and challenges of online learning in bioinformatics from a learner's perspective at WEB 2014 at ISMB 2014. Bioinformatics, Mooc, Online learning General Interest 2014-08-14 2017-10-09
Workshop on Education in Bioinformatics 2014 - ISMB 2014 - Michael Love

MOOCs in Bioinformatics: The Online Course Model to Online Bioinformatics Education Dr. Michael Love, edX Faculty and post-doctoral fellow in Dept. Biostatistics, Dana Farber Cancer Institute and Harvard School of Public Health. Dr. Love teaches the Data Analysis for Genomics course offered...

Keywords: Bioinformatics, Mooc

Workshop on Education in Bioinformatics 2014 - ISMB 2014 - Michael Love https://tess.elixir-europe.org/materials/workshop-on-education-in-bioinformatics-2014-ismb-2014-michael-love MOOCs in Bioinformatics: The Online Course Model to Online Bioinformatics Education Dr. Michael Love, edX Faculty and post-doctoral fellow in Dept. Biostatistics, Dana Farber Cancer Institute and Harvard School of Public Health. Dr. Love teaches the Data Analysis for Genomics course offered through edX. His research focuses on inferring biologically meaningful patterns from high-throughput sequencing read counts. He also develops open-source statistical software for the analysis of exome sequencing and RNA sequencing experiments for the Bioconductor Project. Dr. Love spoke on how open online courses operate and how they can (or cannot) be used to teach bioinformatics at WEB 2014 at ISMB 2014. Bioinformatics, Mooc 2014-08-14 2017-10-09
GOBLET Poster at ISMB 2014

This is a PDF of the GOBLET poster presentation at ISMB 2014 in Boston.

Keywords: Goblet survey life scientists

GOBLET Poster at ISMB 2014 https://tess.elixir-europe.org/materials/goblet-poster-at-ismb-2014 This is a PDF of the GOBLET poster presentation at ISMB 2014 in Boston. Goblet survey life scientists 2014-07-07 2017-10-09
RNA-seq Analysis 2014 Module 4 - Isoform discovery and alternative expression

Explore use of Cufflinks in reference annotation based transcript (RABT) assembly mode and ‘de novo’ assembly mode. Both modes require a reference genome sequence.  

Scientific topics: RNA

Keywords: Alternative expression, Transcript isoforms

RNA-seq Analysis 2014 Module 4 - Isoform discovery and alternative expression https://tess.elixir-europe.org/materials/rna-seq-analysis-2014-module-4-isoform-discovery-and-alternative-expression Explore use of Cufflinks in reference annotation based transcript (RABT) assembly mode and ‘de novo’ assembly mode. Both modes require a reference genome sequence.   RNA Alternative expression, Transcript isoforms Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-27 2017-10-09
RNA-seq Analysis 2014 Module 3 - Expression and Differential Expression

Get FPKM style expression estimates using Cufflinks Perform differential expression analysis with Cuffdiff Perform summary analysis with CummeRbund Downstream interpretation of expression analysis (multiple testing, clustering, heatmaps, classification, pathway analysis, etc.)  

Keywords: Differential expression, Transript expression

RNA-seq Analysis 2014 Module 3 - Expression and Differential Expression https://tess.elixir-europe.org/materials/rna-seq-analysis-2014-module-3-expression-and-differential-expression Get FPKM style expression estimates using Cufflinks Perform differential expression analysis with Cuffdiff Perform summary analysis with CummeRbund Downstream interpretation of expression analysis (multiple testing, clustering, heatmaps, classification, pathway analysis, etc.)   Differential expression, Transript expression Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-27 2017-10-09
RNA-seq Analysis 2014 Module 2 - Alignment and Visualization

Use of Bowtie/TopHat ‘Regular mode’ vs. ‘Fusion mode’ Introduction to the BAM format Basic manipulation of BAMs with samtools, etc. Visualization of RNA-seq alignments - IGV BAM read counting and determination of variant allele expression status    

Keywords: Data visualization, Rna seq alignment

RNA-seq Analysis 2014 Module 2 - Alignment and Visualization https://tess.elixir-europe.org/materials/rna-seq-analysis-2014-module-2-alignment-and-visualization Use of Bowtie/TopHat ‘Regular mode’ vs. ‘Fusion mode’ Introduction to the BAM format Basic manipulation of BAMs with samtools, etc. Visualization of RNA-seq alignments - IGV BAM read counting and determination of variant allele expression status     Data visualization, Rna seq alignment Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-27 2017-10-09
RNA-seq Analysis 2014 Module 1 - Introduction to RNA-seq Analysis

Basic introduction to biology of RNA-seq Experimental design considerations Commonly asked questions Data visualization using IGV  

Keywords: Experimental design rna seq, Igv, Introduction rna seq analysis

RNA-seq Analysis 2014 Module 1 - Introduction to RNA-seq Analysis https://tess.elixir-europe.org/materials/rna-seq-analysis-2014-module-1-introduction-to-rna-seq-analysis Basic introduction to biology of RNA-seq Experimental design considerations Commonly asked questions Data visualization using IGV   Experimental design rna seq, Igv, Introduction rna seq analysis Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-27 2017-10-09
Pathway and Network Analysis 2014 Module 5 - Network Visualization

Introduction to network visualization Visualizing omics data on a network or pathway Active modules in Cytoscape

Keywords: Cytoscape, Network visualization

Pathway and Network Analysis 2014 Module 5 - Network Visualization https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-5-network-visualization Introduction to network visualization Visualizing omics data on a network or pathway Active modules in Cytoscape Cytoscape, Network visualization Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09
Pathway and Network Analysis 2014 Module 4 - Pathway and Network Analysis

Introduction to pathway and network analysis Basic network concepts Types of pathway and network information Pathway Databases: Reactome, KEGG, etc. Pathway analysis of large scale genomics data sets, including cancer genomics

Keywords: Biological networks, Kegg, Pathway analysis, Reactome

Pathway and Network Analysis 2014 Module 4 - Pathway and Network Analysis https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-4-pathway-and-network-analysis Introduction to pathway and network analysis Basic network concepts Types of pathway and network information Pathway Databases: Reactome, KEGG, etc. Pathway analysis of large scale genomics data sets, including cancer genomics Biological networks, Kegg, Pathway analysis, Reactome Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09
Pathway and Network Analysis 2014 Module 3 - Gene Regulation Analysis

Overview of transcription Data sources for regulatory data - Chromatin IP, DNA hypersensitivity, other chip data Basics of processing data Pattern discovery

Keywords: Pattern discovery, Transcriptional regulation

Pathway and Network Analysis 2014 Module 3 - Gene Regulation Analysis https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-3-gene-regulation-analysis Overview of transcription Data sources for regulatory data - Chromatin IP, DNA hypersensitivity, other chip data Basics of processing data Pattern discovery Pattern discovery, Transcriptional regulation Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09
Pathway and Network Analysis 2014 Module 2 - Finding Over-represented Pathways

Over-representation analysis (ORA) Statistics for detecting over-representation e.g. hypergeometric test, GSEA Multiple testing correction: Bonferroni, Benjamini-Hochberg FDR Filtering Gene Ontology e.g. using evidence codes

Keywords: Gsea, Over representation analysis

Pathway and Network Analysis 2014 Module 2 - Finding Over-represented Pathways https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-2-finding-over-represented-pathways Over-representation analysis (ORA) Statistics for detecting over-representation e.g. hypergeometric test, GSEA Multiple testing correction: Bonferroni, Benjamini-Hochberg FDR Filtering Gene Ontology e.g. using evidence codes Gsea, Over representation analysis Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09
Pathway and Network Analysis 2014 Module 1 - Introduction to Gene Lists

Gene list analysis overview: Workflow of concepts and tools from gene list to pathway analysis Where do gene lists come from? Working with gene function information

Keywords: Gene lists, Gene ontology

Pathway and Network Analysis 2014 Module 1 - Introduction to Gene Lists https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-1-introduction-to-gene-lists Gene list analysis overview: Workflow of concepts and tools from gene list to pathway analysis Where do gene lists come from? Working with gene function information Gene lists, Gene ontology Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09