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14 events found

Organizer: INRA, URGI platform  or bioinformatics.ca 

  • High-Throughput Biology: From Sequence to Networks

    20 - 26 March 2017

    Cold Spring Harbor, United States of America

    High-Throughput Biology: From Sequence to Networks https://tess.elixir-europe.org/events/high-throughput-biology-from-sequence-to-networks With the introduction of next generation sequencing platforms, it is becoming feasible to consider sequencing approaches to address many research projects. Now more than ever, having knowledge of the available bioinformatic resources and the informatic skills to analyze such data is critical. The Canadian Bioinformatics Workshops, in collaboration with Cold Spring Harbor Laboratory, has developed a comprehensive 7-day course covering the key bioinformatics concepts and tools required to analyze DNA- and RNA-sequence reads using a reference genome. Participants will gain experience in cloud computing and data visualization tools, which will be applied throughout the course. Beginning with an understanding of the workflow involved to move from platform images to sequence generation, participants will gain practical experience and skills to be able to evaluate sequence read quality, map reads to a reference and analyze sequence reads for variation and expression level. The workshop will conclude with analyzing and conducting pathway and network analysis on the resultant ‘gene’ list. The tutorials are designed as self-contained units that include example data (e.g. Illumina paired-end data) and detailed instructions for installation of all required bioinformatics tools. 2017-03-20 09:00:00 UTC 2017-03-26 17:00:00 UTC bioinformatics.ca Cold Spring Harbor, Cold Spring Harbor, United States of America Cold Spring Harbor Cold Spring Harbor Suffolk County United States of America Molecular interactions, pathways and networks RNA-Seq alignment DNA-Seq [] course_info@bioinformatics.ca [] [] 30 workshops_and_courses registration_of_interest []
  • Infectious Disease Genomic Epidemiolgy

    1 - 3 May 2017

    Vancouver, Canada

    Infectious Disease Genomic Epidemiolgy https://tess.elixir-europe.org/events/infectious-disease-genomic-epidemiolgy With increasing adoption of Next Generation Sequencing technologies to infectious disease surveillance and outbreak investigations, genomic epidemiology (combining pathogen genomics data with epidemiological investigations to track the spread of infectious diseases) is poised to change the practices of public health and infection controls and provides unprecedented amount of data for pathogen evolution studies. The CBW has developed a 3-day course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use selected analysis tools. The tutorials are designed as self-contained units that include example data and detailed instructions for installation of all required bioinformatics tools or access to publicly available web applications. Participants will gain practical experience and skills to be able to: Understand next generation sequencing (NGS) platforms as applied to pathogen genomics and metagenomics sequencing Analyze NGS data for pathogen surveillance and outbreak investigations Analyze antimicrobial resistance genes Detect emerging pathogens in metagenomics data Perform phylogeographic analysis Use different visualization tools for genomic epidemiology analysis 2017-05-01 08:30:00 UTC 2017-05-03 17:00:00 UTC bioinformatics.ca Vancouver, Vancouver, Canada Vancouver Vancouver Greater Vancouver Canada Public health and epidemiology [] course_info@bioinformatics.ca [] [] workshops_and_courses registration_of_interest []
  • Bioinformatics of Genomic Medicine

    10 - 11 May 2017

    Toronto, Canada

    Bioinformatics of Genomic Medicine https://tess.elixir-europe.org/events/bioinformatics-of-genomic-medicine Genomic medicine is the practice of utilizing multi-omic (genomic, transcriptomic, epigenomic) data to improve the diagnosis and treatment of patients. The CBW has developed a 2-day course that will explore various aspects of genomic medicine, covering and teaching popular tools and methods in the field. The course will start with topics that are important to the analysis of genetic disorders, including phenotyping and the annotation of genetic variants. Next, we will cover multi-omic approaches that can be used to identify homogenous clusters of patients, build patient trajectories to identify likely outcomes, and improve these outcomes through better selection of therapies. Participants will gain practical experience and skills to be able to: Identify disease variants: Conduct basic exome analysis to identify disease-causing mutations Perform deep phenotyping of patients using the Human Phenotype Ontology (HPO) Conduct detailed variant annotation and prioritization Perform patient classification: Understand and select appropriate epigenomic datasets for patient classification Conduct data fusion to identify homogenous patient subgroups Identify potential therapies based on molecular profiles 2017-05-10 08:30:00 UTC 2017-05-11 17:00:00 UTC bioinformatics.ca Toronto, Toronto, Canada Toronto Toronto Toronto Division Canada Preclinical and clinical studies [] course_info@bioinformatics.ca [] [] workshops_and_courses registration_of_interest []
  • Informatics on High-throughput Sequencing Data

    25 - 26 May 2017

    Toronto, Canada

    Informatics on High-throughput Sequencing Data https://tess.elixir-europe.org/events/informatics-on-high-throughpuut-sequencing-data With the introduction of high-throughput sequencing platforms, it is becoming feasible to consider sequencing approaches to address many research projects. However, knowing how to manage and interpret the large volume of sequence data resulting from such technologies is less clear. The CBW has developed a popular 2-day course covering the bioinformatics tools available for managing and interpreting high-throughput sequencing data, where the focus is on Illumina reads although the information is applicable to all sequencer reads. Beginning with an understanding of the workflow involved to move from platform images to sequence generation, participants will gain practical experience and skills to be able to: Assess sequence quality Map sequence data onto a reference genome (required) Perform de novo assembly tasks Quantify sequence data Integrate biological context with sequence information 2017-05-25 08:30:00 UTC 2017-05-26 17:00:00 UTC bioinformatics.ca Toronto, Toronto, Canada Toronto Toronto Toronto Division Canada DNA-Seq [] course_info@bioinformatics.ca [] [] 30 workshops_and_courses registration_of_interest []
  • Bioinformatics for Cancer Genomics

    29 May - 3 June 2017

    Toronto, Canada

    Bioinformatics for Cancer Genomics https://tess.elixir-europe.org/events/bioinformatics-for-cancer-genomics-8a6f462a-84bb-4aca-8634-9ae69d538eff Cancer research has rapidly embraced high throughput technologies into its research, using various microarray, tissue array, and next generation sequencing platforms. The result has been a rapid increase in cancer data output and data types. Now more than ever, having the informatic skills and knowledge of available bioinformatic resources specific to cancer is critical. The CBW has developed a 5-day workshop covering the key bioinformatics concepts and tools required to analyze cancer genomic data sets. Participants will gain practical experience and skills to: Visualize genomic data; Analyze cancer –omic data for gene expression, genome rearrangement, somatic mutations, and copy number variation; Analyze and conduct pathway analysis on the resultant cancer gene list; Integrate clinical data. 2017-05-29 09:00:00 UTC 2017-06-03 00:00:00 UTC bioinformatics.ca Toronto, Toronto, Canada Toronto Toronto Toronto Division Canada [] organizers [] [] workshops_and_courses registration_of_interest []
  • Informatics and Statistics for Metabolomics

    6 - 7 June 2017

    Toronto, Canada

    Informatics and Statistics for Metabolomics https://tess.elixir-europe.org/events/informatics-and-statistics-for-metabolomics-79e429cd-7ef2-4cb8-9ea8-2068a39dc855 Using high-throughput technologies, life science researchers can identify and characterize all the small molecules or metabolites in a given cell, tissue, or organism. The CBW course covers many topics ranging from understanding metabolomics technologies, data collection and analysis, using pathway databases, performing pathway analysis, conducting univariate and multivariate statistics, working with metabolomic databases, and exploring chemical databases. Hands-on practical tutorials using various data sets and tools will assist participants in learning metabolomics analysis techniques. Participants will gain practical experience and skills to be able to: Design appropriate metabolome-focused experiments Understand the advantages and limitations of metabolomic data analysis Devise an appropriate bioinformatics workflow for processing and analyzing metabolomic data Apply appropriate statistics to undertake rigorous data analysis Visualize datasets to gain intuitive insights into the composition and/or activity of their metabolome 2017-06-06 08:30:00 UTC 2017-06-07 17:00:00 UTC bioinformatics.ca Toronto, Toronto, Canada Toronto Toronto Toronto Division Canada Metabolomics [] course_info@bioinformatics.ca [] [] 30 workshops_and_courses registration_of_interest []
  • Introduction to R

    12 June 2017

    Toronto, Canada

    Introduction to R https://tess.elixir-europe.org/events/introduction-to-r-49424f47-7823-41b6-a83a-e2f3774ec109 R is rapidly becoming the most important scripting language for both experimental- and computational biologists. It is well designed, efficient, widely adopted and has a very large base of contributors who add new functionality for all modern aspects of data analysis and visualization. Moreover it is free and open source. However, R's great power and expressivity can at first be difficult to approach without guidance, especially for those who are new to programming. This workshop introduces the essential ideas and tools of R. Participants will gain practical experience and skills to be able to: Meet the challenges of data handling; Break down problems into structured parts; Use R syntax, functions and packages; Understand best practices for scientific computational work. 2017-06-12 08:30:00 UTC 2017-06-12 17:00:00 UTC bioinformatics.ca Toronto, Toronto, Canada Toronto Toronto Toronto Division Canada [] [] [] 30 workshops_and_courses registration_of_interest []
  • Exploratory Analysis of Biological Data using R

    13 - 14 June 2017

    Toronto, Canada

    Exploratory Analysis of Biological Data using R https://tess.elixir-europe.org/events/exploratory-analysis-of-biological-data-using-r-718f6e8a-2a6b-4ab5-8af1-d70ba923fd54 Before we can begin to apply rigorous statistical tools to research data, we often need to approach our data intuitively, and look for meaningful associations, surprising patterns, or irregularities, to formulate hypotheses. This is Exploratory Data Analysis (EDA). This workshop introduces the essential tools and strategies that are available for EDA through the free statistical workbench R. Steps covered in this workshop are broadly relevant for many areas of modern, quantitative biology such as flow cytometry, expression profile analysis, function prediction and more. Participants will gain practical experience and skills to be able to: Use R and its analysis tools, read and modify code, and explore protocols that can be adapted for their own research tasks. Write R functions and analysis scripts. Plot and visualize data using the elementary built-in routines via their (sometimes bewildering) array of parameters to sophisticated, publication-ready presentations. 2017-06-13 08:30:00 UTC 2017-06-14 17:00:00 UTC bioinformatics.ca Toronto, Toronto, Canada Toronto Toronto Toronto Division Canada [] course_info@bioinformatics.ca [] [] 30 workshops_and_courses registration_of_interest []
  • Epigenomic Data Analysis

    15 - 16 June 2017

    Montreal, Canada

    Epigenomic Data Analysis https://tess.elixir-europe.org/events/epigenomic-data-analysis-814bc674-0a0a-42a1-9bd5-bbc43ae8b2b6 High-throughput sequencing of Chromatin-Immunoprecipitated libraries (ChIP-seq) and of bisulfite converted DNA (WGBS) have become increasingly common and have largely supplanted microarrays for chromatin and DNA methylation profiling. When processed appropriately, ChIP-seq data provides base-pair resolution representations of transcription factor DNA-binding events and nucleosome (histone) modifications genome-wide. Similarly, WGBS can provide a quantitative genome wide profile of cytosine methylation. The CBW has developed a 2-day course providing an introduction to histone ChIP-seq and WGBS data analysis followed by integrated tutorials demonstrating the use of open source ChIP-Seq and WGBS analysis packages. The tutorials are designed as self-contained units that include example data and detailed instructions for installation of all required bioinformatics tools (FASTQC, BWA, MACS2, FindER, samtools, Picard, BisSNP). The course also includes an overview of integrative epigenomic tools that have been developed to explore ChIP-Seq and WGBS data together with other epigenomic datasets such as RNA-seq, DHS-seq and ATAC-seq. Participants will gain practical experience and skills to be able to: Align ChIP-seq and WGBS sequence data to a reference genome (required) Identify narrow and broad peaks from ChIP-seq data Identify methylated levels from WGBS data Visualize and summarize the output of ChIP-Seq and WGBS analyses Explore integrative tools for epigenomic data sets 2017-06-15 08:30:00 UTC 2017-06-16 17:00:00 UTC bioinformatics.ca Montreal, Montreal, Canada Montreal Montreal Montreal Canada ChIP-seq Epigenomics [] course_info@bioinformatics.ca [] [] 30 workshops_and_courses registration_of_interest []
  • Microbiome Summer School

    19 - 22 June 2017

    Québec City, Canada

    Microbiome Summer School https://tess.elixir-europe.org/events/microbiome-summer-school Bioinformatics has become an important part of many areas of health research. Several fields of research such as microbiome, cancer, immunology and clinical research are generating massive amounts of data that need appropriate computational tools for their analysis and interpretation. Moreover, a need for bioinformatics training is more pressing than ever as big data are more and more present in health research. The Canadian Institutes of Health Research (CIHR), Université Laval Big Data Research Centre, the Canada Excellence Research Chairs (CERC) Program, and CBW are offering a 4-day workshop centered on the microbiome. This workshop will provide an introduction to the use of bioinformatics in microbiome research as well as big data analytics applied to this field. Participants will gain practical experience and skills to be able to: Design appropriate microbiome-focused experiments Understand the advantages and limitations of metagenomic data analysis Devise an appropriate bioinformatics workflow for processing and analyzing metagenomic sequence data (marker-gene, shotgun metagenomic, and metatranscriptomic data) Apply appropriate statistics to undertake rigorous data analysis Visualize datasets to gain intuitive insights into the composition and/or activity of their data set Use machine learning approaches to solve problems 2017-06-19 08:30:00 UTC 2017-06-22 17:00:00 UTC bioinformatics.ca Québec City, Québec City, Canada Québec City Québec City Communauté-Urbaine-de-Québec Canada Machine learning [] course_info@bioinformatics.ca [] [] workshops_and_courses registration_of_interest []
  • Pathway and Network Analysis of –omics Data

    26 - 28 June 2017

    Toronto, Canada

    Pathway and Network Analysis of –omics Data https://tess.elixir-europe.org/events/pathway-and-network-analysis-of-omics-data-6c38c613-511c-4975-a95f-fb31c6ad563d The CBW has developed a 2.5-day course covering the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information. The workshop focuses on the principles and concepts required for analyzing and conducting pathway and network analysis on a gene list from any organism, although focus will be on human and model eukaryotic organisms. Participants will gain practical experience and skills to be able to: Get more information about a gene list; Discover what pathways are enriched in a gene list (and use it for hypothesis generation); Find out how a set of genes is connected by e.g. protein interactions and identify pathways, systems and modules within this network; Predict gene function and extend a gene list; Identify master regulators, such as transcription factors, active in the experiment. We will develop a unified analysis flow chart throughout the course that students will be able to follow after the workshop to conduct their own analysis. 2017-06-26 08:30:00 UTC 2017-06-28 17:00:00 UTC bioinformatics.ca Toronto, Toronto, Canada Toronto Toronto Toronto Division Canada Molecular interactions, pathways and networks [] course_info@bioinformatics.ca [] [] 30 workshops_and_courses registration_of_interest []
  • Cloud Computing in Bioinformatics with Big Data

    5 - 6 July 2017

    Toronto, Canada

    Cloud Computing in Bioinformatics with Big Data https://tess.elixir-europe.org/events/cloud-computing-in-bioinformatics-with-big-data Several big data genomics projects, including the ICGC, are deciding to host their data in the Cloud and to provide access to configurable virtual machines (VM) with which to compute on this data (thereby removing the need to purchase and maintain your own compute cluster). Similarly, many labs are moving to renting compute time from various cloud providers. Analysis of a single genome or a smaller selected subset differs from analysis of multiple genomes, particularly in the compute infrastructure required. To navigate through working in this new compute space, the CBW has developed a 2-day course providing an introduction to security and privacy issues related to working on human genome data and the processes necessary to access such data. After reviewing cloud computing infrastructure, the workshop will also provide a hands-on introduction to launching and configuring your own virtual machine (VM), accessing cloud-based data sets, and how to scale up the number of VMs to meet your analysis needs. Customizing VMs with your own tools and cloud-computing best practices will also be discussed. Participants will gain practical experience and skills to be able to: Launch their own virtual machine (VM) Configure a VM with prepackaged tools Pull in data sets from Cloud repositories Follow best practices in data and workflow management Customize a VM with their own tools Scale up their VM to meet their analysis needs 2017-07-05 08:30:00 UTC 2017-07-06 17:00:00 UTC bioinformatics.ca Toronto, Toronto, Canada Toronto Toronto Toronto Division Canada [] course_info@bioinformatics.ca [] [] 30 workshops_and_courses registration_of_interest []
  • Informatics for RNA-seq Analysis

    10 - 12 July 2017

    Toronto, Canada

    Informatics for RNA-seq Analysis https://tess.elixir-europe.org/events/informatics-for-rna-seq-analysis-d573f303-974d-4819-ac09-3d7db5c256b8 High-throughput sequencing of RNA libraries (RNA-seq) has become increasingly common and largely supplanted gene microarrays for transcriptome profiling. When processed appropriately, RNA-seq data has the potential to provide a considerably more detailed view of the transcriptome. The CBW has developed a 3-day course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. The tutorials are designed as self-contained units that include example data (Illumina paired-end RNA-seq data) and detailed instructions for installation of all required bioinformatics tools (HISAT, StringTie, etc.). De novo assembly of transcripts will be covered. Participants will gain practical experience and skills to be able to: Perform command-line Linux based analysis on the cloud Assess quality of RNA-seq data Align RNA-seq data to a reference genome Estimate known gene and transcript expression Perform differential expression analysis Discover novel isoforms Assemble RNA-seq data into transcripts Visualize and summarize the output of RNA-seq analyses in R 2017-07-10 08:30:00 UTC 2017-07-12 17:00:00 UTC bioinformatics.ca Toronto, Toronto, Canada Toronto Toronto Toronto Division Canada RNA-Seq alignment [] course_info@bioinformatics.ca [] [] 30 workshops_and_courses registration_of_interest []
  • Manual curation of Transposable element annotation

    4 - 6 February 2019

    Versailles, France

    Manual curation of Transposable element annotation https://tess.elixir-europe.org/events/manual-curation-of-transposable-element-annotation URGI organizes a BYOD-­style (Bring Your Own Data) training course on manual curation of transposable elements reference sequences obtained with REPET pipelines. For pre-registration, please fill the form before December 26, 2018, we will answer you before January 3rd, 2019: https://goo.gl/forms/ordIgogDuQffuQbZ2 Preliminary program Day 1: - Presentation of REPET outputs of TEdenovo and TEannot pipelines needed to curate the consensus library - Presentation of tools used to assist curation/validation of TE consensus - Presentation of use cases Day 2 and 3 -Practice on your data or a set of precomputed data Prerequesite You have already launched TEdenovo and TEannot pipelines using REPET version 2.5 The MySQL database is still alive OR You have already participated to a TE annotation training (@URGI or in the frame of an Elixir Genome assembly and annotation Course)In this case we’ll provide you a precomputed dataset for the training Fees : 150 € (Payment modalities will be sent once registration accepted) 2019-02-04 09:00:00 UTC 2019-02-06 17:00:00 UTC INRA, URGI platform INRA, URGI, Bat 18 ­ Route de Saint­Cyr ­ RD10, Versailles, France INRA, URGI, Bat 18 ­ Route de Saint­Cyr ­ RD10 Versailles France 78000 Bioinformatics Genomics INRA urgi-contact@inra.fr [] Bioinformatician, Bioanalysts 10 workshops_and_courses registration_of_interest Transposable elementsManual curationGenome sequence analysis
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