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34 materials found

Authors: Jared Simpson  or Michelle Brazas  or Robin Haw 


Pathways and Network Analysis of -Omics data 2018 Module 4-More Depth on Network and Pathway Analysis

Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information.

Pathways and Network Analysis of -Omics data 2018 Module 4-More Depth on Network and Pathway Analysis https://tess.elixir-europe.org/materials/pathways-and-network-analysis-of-omics-data-2018-module-4-more-depth-on-network-and-pathway-analysis Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information. Researchers Post-Doctoral Fellows Graduate Students Biologists, Genomicists, Computer Scientists
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 14-Variants to Networks

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 14-Variants to Networks https://tess.elixir-europe.org/materials/bioinformatics-for-cancer-genomics-2018-module-14-variants-to-networks 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 Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists Graduate Students
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
Pathways and Network Analysis with -Omics Data 2017 Module 4-More Depth on Network and Pathway Analysis

Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.

Pathways and Network Analysis with -Omics Data 2017 Module 4-More Depth on Network and Pathway Analysis https://tess.elixir-europe.org/materials/pathways-and-network-analysis-with-omics-data-2017-module-4-more-depth-on-network-and-pathway-analysis Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.
Bioinformatics for Cancer Genomics 2017 Module 8-Variants to Networks

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

Bioinformatics for Cancer Genomics 2017 Module 8-Variants to Networks https://tess.elixir-europe.org/materials/bioinformatics-for-cancer-genomics-2017-module-8-variants-to-networks Course covers the bioinformatics tools required to analyze genomic data sets.
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 15-More Depth on Network and Pathway Analysis

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 15-More Depth on Network and Pathway Analysis https://tess.elixir-europe.org/materials/high-throughput-biology-2017-module-15-more-depth-on-network-and-pathway-analysis 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 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
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
Flow Cytometry 2013 Module 4 - 1D Static gating

How to create a constant gate for the whole data set for one channel by first creating a sample representative of the whole data set How to apply a static gate to all samples and count the proportions of cells lying on either side of the gate Visualizing the proportions using a density...

Keywords: 1d static gating, Flow cytometry data

Flow Cytometry 2013 Module 4 - 1D Static gating https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-4-1d-static-gating How to create a constant gate for the whole data set for one channel by first creating a sample representative of the whole data set How to apply a static gate to all samples and count the proportions of cells lying on either side of the gate Visualizing the proportions using a density plot, histogram, bean/violin plot Automating a sequential gating strategy in R to obtain cell proportions for a desired phenotype 1d static gating, Flow cytometry data 2013-06-26 2017-10-09
Flow Cytometry 2013 Module 6 - Clustering and Additional FCM Tools

Lecture on FlowCAP (Flow Cytometry: Critical Assessment of Population Identification Methods) project K-means explained flowMeans: smart k-means for FCM data flowClust3.0, SPADE, flowBin, flowFP, SamSPECTRAL clustering Biomarker discovery: flowType and RchyOptimyx, advanced tools used...

Keywords: Biomarker discovery, Flow cytometry data, Flowcap

Flow Cytometry 2013 Module 6 - Clustering and Additional FCM Tools https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-6-clustering-and-additional-fcm-tools Lecture on FlowCAP (Flow Cytometry: Critical Assessment of Population Identification Methods) project K-means explained flowMeans: smart k-means for FCM data flowClust3.0, SPADE, flowBin, flowFP, SamSPECTRAL clustering Biomarker discovery: flowType and RchyOptimyx, advanced tools used to explore novel phenotypes and find ones which correlate with a clinical diagnosis More R: Bioconductor.org, an open source software project full of bioinformatics packages created for R, including sample work flows GenePattern.org: web-interface for running analysis modules such as sample deidentication, extracting specic keywords, quality control, normalization, clustering, classification FlowRepository.org: online FCM data repository to share public or private data sets with collaborators while providing detailed descriptions of the experiment set up and each FCS file Biomarker discovery, Flow cytometry data, Flowcap 2013-06-26 2017-10-09