Content Providers

  • Genomics Core KU Leuven/UZ Leuven

    The Genomics Core is a facility that advances the development and implementation of novel genomic...

    0 upcoming events (1 past event)
    Genomics Core KU Leuven/UZ Leuven https://tess.elixir-europe.org/content_providers/genomics-core-ku-leuven-uz-leuven The Genomics Core is a facility that advances the development and implementation of novel genomic technologies. The facility provides technological and intellectual support for scientific applications as well as next generation genetic diagnosis. The genomics core partners within the Universitaire ziekenhuizen KULeuven to enable the BELAC-accredited breast cancer (BRCA) genetic test as well as non-invasive prenatal testing (NIPT).
  • Flemish Supercomputer Centre

    The Flemish Supercomputer Centre (VSC) is a virtual centre making supercomputer infrastructure...

    0 upcoming events (66 past events)
    Flemish Supercomputer Centre https://tess.elixir-europe.org/content_providers/flemish-supercomputer-centre The Flemish Supercomputer Centre (VSC) is a virtual centre making supercomputer infrastructure available for both the academic and industrial world. This centre is managed by the Research Foundation - Flanders (FWO) in partnership with the five Flemish university associations. /system/content_providers/images/000/000/067/original/logo_VSC_CMYK-1.png?1487672198
  • VIB Bioinformatics Core

    Provider of Bioinformatics and software training, plus informatics services and resource...

    49 training materials
    18 upcoming events (142 past events)
    VIB Bioinformatics Core https://tess.elixir-europe.org/content_providers/bitsvib Provider of Bioinformatics and software training, plus informatics services and resource management support. /system/content_providers/images/000/000/042/original/bioinformatics_core_cmyk_pos.jpg?1539150443
  • VIB Conferences

    VIB is a life sciences research institute in Flanders, Belgium. More than 1470 scientists from...

    1 upcoming event (19 past events)
    VIB Conferences https://tess.elixir-europe.org/content_providers/vib-conferences VIB is a life sciences research institute in Flanders, Belgium. More than 1470 scientists from over 66 countries perform basic research into the molecular foundations of life. The institute offers a program of international VIB conferences in various VIB research fields. From day one VIB has supported and sponsored scientific conferences to help VIB scientists network with their colleagues. In 2014 the VIB Conference Series was launched to further expand these activities and support them with a dedicated professional team. The aims of the conference series are: to showcase cutting edge research and exciting technological solutions presented by leading scientist in the life sciences fields to offer junior researchers the opportunity to present their work during poster sessions and learn from the world’s experts during the Meet the Expert sessions to establish opportunities for collaborations between scientists during an accompanying social program including lunches, conference dinners and receptions /system/content_providers/images/000/000/054/original/vib_conferences_series_rgb_pos.png?1538645378
  • UCLouvain Bioinformatics Platform

    The platform's goak is to collaborate throughput the scientific community at the UCLouvain and...

    1 training material
    0 upcoming events (2 past events)
    UCLouvain Bioinformatics Platform https://tess.elixir-europe.org/content_providers/uclouvain-bioinformatics-platform The platform's goak is to collaborate throughput the scientific community at the UCLouvain and offer technical and methodological bioinformatics support, including, among others: support the bioinformatics aspects of grant proposals and experimental designs high throughput omics data analysis such as genomics, epigenetics and transcriptomics (RNASeq or microarrays) or mass spectrometry based proteomics and metabolomics help in utilisation of public databases (TCGA, Gtex, CCLE, ENCODE, ...) development of dedicated algorithms and software. The platform also organises workshops in data analysis and bioinformatics to introduce particpants to widely used languages such as R, and get them started in the analysis of their own omics data. For additional information and any collaboration requests, please contact us by email at contact-cbio@uclouvain.be describing your needs, including, if data is already available, the underlying technology and experimental design. Members Prof Laurent Gatto Mr Theo Killian Dr Axelle Loriot Contact: contact-cbio@uclouvain.be CBIO - de Duve Institute - UCLouvain Avenue Hippocrate, 75 - bte B1.74.10 1200 Brussels, Belgium
  • Showing 30 materials out of 50. View all results.
    Hands-on introduction to NGS variant analysis

    This training gives an introduction to the use of popular NGS analysis software packages at the command line. It reviews several exchangeable tools and provide hints to evaluate quality and content of DNA-Seq data by a biologist.   This training does not cover all methods available today. It does...

    Scientific topics: DNA

    Hands-on introduction to NGS variant analysis https://tess.elixir-europe.org/materials/hands-on-introduction-to-ngs-variant-analysis This training gives an introduction to the use of popular NGS analysis software packages at the command line. It reviews several exchangeable tools and provide hints to evaluate quality and content of DNA-Seq data by a biologist.   This training does not cover all methods available today. It does not aim at bringing users to a professional NGS analyst level but provides enough information to allow biologists understand what DNA sequencing practically is and to communicate with NGS experts for more in-depth needs. DNA Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09
    Mass spectrometry data processing

    In this training session we start by reviewing the types of mass spectrometer, and what the properties of their output data are. Out of our understanding of the data, we learn to extract meaningful interpretations.

    Scientific topics: Proteomics

    Mass spectrometry data processing https://tess.elixir-europe.org/materials/mass-spectrometry-data-processing In this training session we start by reviewing the types of mass spectrometer, and what the properties of their output data are. Out of our understanding of the data, we learn to extract meaningful interpretations. Proteomics Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
    Analysis of public microarray data sets

    This training will give you an overview of what GEO has to offer. Several experiments will be analyzed using simple tools to obtain differential gene lists. An introduction to downstream tools dedicated to functional enrichment will close the session.

    Scientific topics: Expression data visualisation

    Analysis of public microarray data sets https://tess.elixir-europe.org/materials/analysis-of-public-microarray-data-sets This training will give you an overview of what GEO has to offer. Several experiments will be analyzed using simple tools to obtain differential gene lists. An introduction to downstream tools dedicated to functional enrichment will close the session. Expression data visualisation Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
    Analysis of public microarray data using Genevestigator

    The morning session will give you an overview of the possibilities of Genevestigator, a search engine of curated and normalized publicly available gene expression data. The interface allows you to visualize spatio-temporal (tissue - developmental stage) and perturbational gene expression...

    Scientific topics: Gene expression analysis, Gene expression, Biomarkers

    Analysis of public microarray data using Genevestigator https://tess.elixir-europe.org/materials/analysis-of-public-microarray-data-using-genevestigator The morning session will give you an overview of the possibilities of Genevestigator, a search engine of curated and normalized publicly available gene expression data. The interface allows you to visualize spatio-temporal (tissue - developmental stage) and perturbational gene expression information of many species in a user-friendly graphical way. The afternoon session will focus on the practical applications in a hands-on tutorial on Genevestigator followed by concrete examples of software that can be used to further interpret the results of your Genevestigator searches, like Ingenuity Pathway Analysis and DAVID. Finally, you will be able to work on the questions that you want to answer in your own research under the supervision of the trainer. Participants are therefore encouraged to submit a description of the objectives of the analysis they want to perform. Gene expression analysis Gene expression Biomarkers 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
    Analyzing biological networks with Ingenuity Pathway Analysis

    IPA is software that allows researchers to analyze, integrate and understand data derived from experiments that generate a list of relevant genes, proteins or chemicals. The software relies on the Ingenuity Knowledge Base, a thoroughly curated database of high quality information on biological...

    Analyzing biological networks with Ingenuity Pathway Analysis https://tess.elixir-europe.org/materials/analyzing-biological-networks-with-ingenuity-pathway-analysis IPA is software that allows researchers to analyze, integrate and understand data derived from experiments that generate a list of relevant genes, proteins or chemicals. The software relies on the Ingenuity Knowledge Base, a thoroughly curated database of high quality information on biological interactions and functional annotation. The database is limited to information on human, mouse and rat. Life Science Researchers PhD students post-docs 2016-04-22 2016-06-15
    Basic statistics in R, part II

    This training builds further on the Basic statistics in R training, showing you how to do statistical analyses in R. Where the Basic statistics in R training is an introduction to the use of R and RStudio and stops at very basic analyses (t-tests and non-parametric equivalents), this training...

    Basic statistics in R, part II https://tess.elixir-europe.org/materials/basic-statistics-in-r-part-ii This training builds further on the Basic statistics in R training, showing you how to do statistical analyses in R. Where the Basic statistics in R training is an introduction to the use of R and RStudio and stops at very basic analyses (t-tests and non-parametric equivalents), this training gives you a full overview of statistical analyses in R including regression, ANOVA... Emphasis will be placed on practical applications. To this end, theory will be complemented with hands-on exercises in R, a free software environment for statistical computing and graphics. Topics include distributions, plots, confidence intervals, hypothesis testing... Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09
    Basics of databases and MySQL

    This hands-on training provides a comprehensive introduction to relational databases and the use of the MySQL relational database management system. MySQL is the leading free management system for relational databases. The training shows you how to use MySQL to efficiently store your data in...

    Basics of databases and MySQL https://tess.elixir-europe.org/materials/basics-of-databases-and-mysql This hands-on training provides a comprehensive introduction to relational databases and the use of the MySQL relational database management system. MySQL is the leading free management system for relational databases. The training shows you how to use MySQL to efficiently store your data in databases and manage both data and access to the data. The training gives an overview of the SQL syntax that allows you to access and manipulate the data. Additionally, the use of Python to automatically access MySQL databases is explained. Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09
    Building bioinformatics workflows

    This course presents a comprehensive overview of the principles and applications of scientific workflow systems. The course combines lectures with hands-on exercises in which the participants learn to apply these principles to real biomedical datasets. The course will be based on freely available...

    Building bioinformatics workflows https://tess.elixir-europe.org/materials/building-bioinformatics-workflows This course presents a comprehensive overview of the principles and applications of scientific workflow systems. The course combines lectures with hands-on exercises in which the participants learn to apply these principles to real biomedical datasets. The course will be based on freely available open source software and more specifically on Galaxy and KNIME. Life Science Researchers PhD students post-docs beginner bioinformaticians 2016-04-22 2016-06-15
    Cloning with SnapGene

    You will acquire the basic techniques that are used in recombinant DNA technology, particularly restriction enzymes, modification enzymes, polymerase chain reaction (PCR), plasmids (different vectors, mechanism to select and detect), site directed mutagenesis, heterologous gene expression in...

    Scientific topics: Gene expression analysis

    Cloning with SnapGene https://tess.elixir-europe.org/materials/cloning-with-snapgene You will acquire the basic techniques that are used in recombinant DNA technology, particularly restriction enzymes, modification enzymes, polymerase chain reaction (PCR), plasmids (different vectors, mechanism to select and detect), site directed mutagenesis, heterologous gene expression in prokaryotes/eukaryotes. You will be able to use a cloning program like CLC Bio Main Workbench or SnapGene. Gene expression analysis Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
    Comparative genomics in eukaryotes

    This course presents a comprehensive overview of the principles and applications of comparative genomics in eukaryotes. The course combines lectures with hands-on exercises.

    Comparative genomics in eukaryotes https://tess.elixir-europe.org/materials/comparative-genomics-in-eukaryotes This course presents a comprehensive overview of the principles and applications of comparative genomics in eukaryotes. The course combines lectures with hands-on exercises. Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
    Data Carpentry Workshop - Data Management beyond Excel

    The main ambition of this workshop is that researchers will be able to handle their data in a more reproducible and efficient way. They should be able to retrieve, view, manipulate, process and manage their own and other one's data. The following topics will be covered during the workshop: ...

    Data Carpentry Workshop - Data Management beyond Excel https://tess.elixir-europe.org/materials/data-carpentry-workshop-data-management-beyond-excel The main ambition of this workshop is that researchers will be able to handle their data in a more reproducible and efficient way. They should be able to retrieve, view, manipulate, process and manage their own and other one's data. The following topics will be covered during the workshop: How to use spreadsheet programs (e.g. Excel) more efficiently: what you can and can't do Getting data out of spreadsheets and into more powerful tools (e.g. R) Using databases, managing and querying data in SQL Workflows and automating repetitive tasks, including using command line PhD students post-docs Life Science Researchers 2016-04-22 2016-09-13
    Data manipulation in OpenRefine

    Most statistical and data mining tools assume that the data files are in a specific format, often completely different from the format that is created by the instrument that generates the data. Moreover, most of these tools only provide limited functionality for getting the raw data files in the...

    Data manipulation in OpenRefine https://tess.elixir-europe.org/materials/data-manipulation-in-openrefine Most statistical and data mining tools assume that the data files are in a specific format, often completely different from the format that is created by the instrument that generates the data. Moreover, most of these tools only provide limited functionality for getting the raw data files in the correct format. OpenRefine is a powerful tool for cleaning up messy data and transforming it in the required format.  Life Science Researchers PhD students post-docs 2016-04-22 2016-06-15
    Downstream processing of RNA-Seq data in GenePattern

    - Run RNA-seq downstream processing analyses in GenePattern, such as clustering, classification, GSEA... - Use GenePattern to save workflows, ensure reproducibility and share methodologies with colleagues and reviewers - Use the GenePattern Notebook environment to create documents that interleave...

    Scientific topics: RNA-Seq

    Downstream processing of RNA-Seq data in GenePattern https://tess.elixir-europe.org/materials/downstream-processing-of-rna-seq-data-in-genepattern - Run RNA-seq downstream processing analyses in GenePattern, such as clustering, classification, GSEA... - Use GenePattern to save workflows, ensure reproducibility and share methodologies with colleagues and reviewers - Use the GenePattern Notebook environment to create documents that interleave formatted text, graphics and other multimedia, executable code, and GenePattern analyses, creating a single "research narrative" that puts scientific discussion and analyses in the same place Summary The workshop will cover the use of GenePattern for downstream processing of high-throughput mRNA sequencing (RNA-Seq) data produced by Illumina sequencing machines.  This workshop is intended for non-programming biologists. 1. Running Analyses in GenePattern 2. Clustering 3. Prediction and Clasification 4. Working with analysis workflows: GenePattern pipelines 5. Working with Samples and Features 6. The GenePattern Notebook environment 7. Related tools: IGV, GSEA 8. Open Q&A The data files, slides and exercises will be made available after the workshop.   RNA-Seq Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
    GATK Best practices for variant discovery

    ÔÇïIn the course of this workshop, we highlight key functionalities such as  GVCF workflow for joint variant discovery in cohorts RNAseq-specific processing somatic variant discovery using MuTect2.  capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery the use...

    Scientific topics: RNA-Seq

    GATK Best practices for variant discovery https://tess.elixir-europe.org/materials/gatk-best-practices-for-variant-discovery ÔÇïIn the course of this workshop, we highlight key functionalities such as  GVCF workflow for joint variant discovery in cohorts RNAseq-specific processing somatic variant discovery using MuTect2.  capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery the use of pipelining tools to assemble and execute GATK workflows. RNA-Seq Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09
    Gentle hands-on introduction to Perl programming

    This course is organised over two full days. With this extensive hands-on session, we introduce you Perl. The first day,we will cover the basics of Perl programming: what is a variable, different types, how to assign values to variable, what can you do with them, strings, arrays and hashes. Logic...

    Gentle hands-on introduction to Perl programming https://tess.elixir-europe.org/materials/gentle-hands-on-introduction-to-perl-programming This course is organised over two full days. With this extensive hands-on session, we introduce you Perl. The first day,we will cover the basics of Perl programming: what is a variable, different types, how to assign values to variable, what can you do with them, strings, arrays and hashes. Logic statements will be discussed, Everything will be demonstrated with step by step exercises. At the end of the day, you will be send home with some challenges to do yourself and additional learning material. As a homework, you may write a program to analyze your own data. On the second day of the training, we will look to the solutions of the homework and explain the results of the tasks. We will dig a little deeper in good programming hygiene, and create some more complex scripts using regexes and reading in files. By the end of the day, a firm basis for perl programming should be established to allow further self-study. 2016-04-22 2017-10-09
    Gentle hands-on introduction to Python programming

    This course is organised over two full days. With the help of plenty hands-on exercises, you will get introduced into the different types of variables in python, the peculiarities of python and good programming habits. This course will provide you an ideal stepping stone for further developing...

    Scientific topics: Software engineering

    Gentle hands-on introduction to Python programming https://tess.elixir-europe.org/materials/gentle-hands-on-introduction-to-python-programming This course is organised over two full days. With the help of plenty hands-on exercises, you will get introduced into the different types of variables in python, the peculiarities of python and good programming habits. This course will provide you an ideal stepping stone for further developing programming skills in Python. Software engineering Life Science Researchers PhD students beginner bioinformaticians 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
    Introduction to CLC Bio Main Workbench

    In this hands-on training you will learn how to use the CLC Bio Main Workbench for basic and advanced sequence analysis. The software supports a large number of DNA, RNA, and protein sequence analyses and microarray analysis. Since BITS provides a VIB-wide license to CLC Bio Main Workbench, this...

    Scientific topics: Expression data visualisation, Local alignment, Global alignment

    Introduction to CLC Bio Main Workbench https://tess.elixir-europe.org/materials/introduction-to-clc-bio-main-workbench In this hands-on training you will learn how to use the CLC Bio Main Workbench for basic and advanced sequence analysis. The software supports a large number of DNA, RNA, and protein sequence analyses and microarray analysis. Since BITS provides a VIB-wide license to CLC Bio Main Workbench, this training is targeted specifically to VIB scientists. Expression data visualisation Local alignment Global alignment Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
    Introduction to network biology

    This course presents a comprehensive overview of the principles and applications of studying molecular networks. The course combines lectures with hands-on exercises in which the participants learn to apply these principles to real data. The course will be based on freely available data and...

    Introduction to network biology https://tess.elixir-europe.org/materials/introduction-to-network-biology This course presents a comprehensive overview of the principles and applications of studying molecular networks. The course combines lectures with hands-on exercises in which the participants learn to apply these principles to real data. The course will be based on freely available data and software. In particular, special attention will go to the use of Cytoscape and its extensions. PhD students Life Science Researchers post-docs 2016-04-22 2017-04-14
    Introductory session on programming with Bioperl

    On the first day, we will refresh Perl syntax and types of variables. This basic knowledge will serve as a starting point to explain the use of subroutines, and how to make a module of your subroutine. On the second day we will prepare for Bioperl by explaining how you can reuse Perl code....

    Introductory session on programming with Bioperl https://tess.elixir-europe.org/materials/introductory-session-on-programming-with-bioperl On the first day, we will refresh Perl syntax and types of variables. This basic knowledge will serve as a starting point to explain the use of subroutines, and how to make a module of your subroutine. On the second day we will prepare for Bioperl by explaining how you can reuse Perl code. Object-oriented programming will only be explained to the extent necessary for using Bioperl. We will write our first simple program in Bioperl and explore places where you can find information on the Bioperl modules. On the third day we will practice Bioperl further in real-life examples like sequence processing and applications that are defined by the participants. By the end of the session, you will understand Bioperl, and have already some first programming skills in Bioperl, which will allow you to practice further at an accelerated speed in order to becoming proficient in Bioperl. Life Science Researchers PhD students post-docs beginner bioinformaticians 2016-04-22 2016-06-15
    Protein Structure Analysis

    This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure....

    Scientific topics: Protein structure analysis

    Protein Structure Analysis https://tess.elixir-europe.org/materials/protein-structure-analysis This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure. Different hands-on exercises will allow you to compare the structure of homologues, to predict a structural model of proteins without any structure information and to find homologuous structures. We will use the FoldX program to quantify various interactions in the structures. Protein structure analysis Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
    RNA-Seq analysis for differential expression

    We first perform quality control of the sequence reads to detect biases or leftover adaptors. We then map the reads to the reference genome with use of a transcript database model. We perform a detailed QC analysis of the mapping results to again detect potential problems. The mapping data is...

    Scientific topics: RNA-Seq, Gene expression

    RNA-Seq analysis for differential expression https://tess.elixir-europe.org/materials/rna-seq-analysis-for-differential-expression We first perform quality control of the sequence reads to detect biases or leftover adaptors. We then map the reads to the reference genome with use of a transcript database model. We perform a detailed QC analysis of the mapping results to again detect potential problems. The mapping data is adjusted to compensate for artifacts like duplicates. The mappings are used to obtain transcript counts usable for differential expression. The count tables are merged and used to compute differential expression using several programs. We START a typical functional analysis of the obtained results similar to what is done for microarray data in order to exemplify handy tools and commercial alternatives. The code pieces used during the training are made available through our Wiki as well as detailed results and can be copied and adapted for own user needs with minimal edits. Key results have been saved to our server and can be downloaded to fully reproduce the training. RNA-Seq Gene expression Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09
    Text mining and curation

    This training will explain the basics of text mining, presenting the opportunities as well as the challenges of automatically extracting information from the literature. Further, the course will demonstrate how text mining data can be incorporated into a variety of applications and research...

    Scientific topics: Data submission, annotation and curation, Natural language processing

    Text mining and curation https://tess.elixir-europe.org/materials/text-mining-and-curation This training will explain the basics of text mining, presenting the opportunities as well as the challenges of automatically extracting information from the literature. Further, the course will demonstrate how text mining data can be incorporated into a variety of applications and research projects, covering not only human biology but also (other) animals, plants, bacteria, fungi and viruses. To ensure high quality of the textual data, the second day of the workshop will focus on manual evaluation and curation of the automatically retrieved information. Data submission, annotation and curation Natural language processing Life Science Researchers PhD students post-docs 2016-04-22 2017-04-14
    UCSC Genome Browser

    The UCSC Genome Browser provides a way to examine data from many genomes and includes extensive annotation tracks for various data types such as known UCSC (and Ensembl) genes, predicted genes, SNPs, miRNAs, comparative multi-species analysis and much more. During this training you will learn how...

    UCSC Genome Browser https://tess.elixir-europe.org/materials/ucsc-genome-browser The UCSC Genome Browser provides a way to examine data from many genomes and includes extensive annotation tracks for various data types such as known UCSC (and Ensembl) genes, predicted genes, SNPs, miRNAs, comparative multi-species analysis and much more. During this training you will learn how to navigate this vital tool for your research. Required skills No specific prior knowledge is required.  BITS provides 15 laptops for their training sessions. Depending on the number of participants (max 20), it is possible that you have to share the laptop with one other participant but you can also choose to bring your own laptop for this training session. 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
    Hands-on introduction to ChIP-Seq analysis

    This training gives an introduction to ChIP-seq data analysis, covering the processing steps starting from the reads to the peaks. Among all possible downstream analyses, the practical aspect will focus on motif analyses. A particular emphasis will be put on deciding which downstream analyses to...

    Scientific topics: Mapping, ChIP-seq

    Hands-on introduction to ChIP-Seq analysis https://tess.elixir-europe.org/materials/hands-on-introduction-to-chip-seq-analysis This training gives an introduction to ChIP-seq data analysis, covering the processing steps starting from the reads to the peaks. Among all possible downstream analyses, the practical aspect will focus on motif analyses. A particular emphasis will be put on deciding which downstream analyses to perform depending on the biological question. This training does not cover all methods available today. It does not aim at bringing users to a professional NGS analyst level but provides enough information to allow biologists understand what DNA sequencing practically is and to communicate with NGS experts for more in-depth needs. Mapping ChIP-seq Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09
    Introduction to Linux for bioinformatics

    This training is intended for all Linux novices who want to learn the basics of Linux without getting too much technical details. This hands-on training will show you how to effectively use Linux, a free operating system. Bioinformatics depends heavily on Linux-based computers and software. A lot...

    Introduction to Linux for bioinformatics https://tess.elixir-europe.org/materials/introduction-to-linux-for-bioinformatics This training is intended for all Linux novices who want to learn the basics of Linux without getting too much technical details. This hands-on training will show you how to effectively use Linux, a free operating system. Bioinformatics depends heavily on Linux-based computers and software. A lot of good scientific software is written specifically for Linux/Unix. Additionally, Linux has most popular programming languages (e.g.Python, Perl, C) already installed and ready to use! Data management happens swiftly with the dedicated text manipulation tools and file system properties. This training will teach you all you need to know to swiftly start using Linux, be it on the server of your department, or on your own computer (even if you're already running Windows or Mac OS). Prior to the training session, you will receive a poll to ask you your personal goals by following this training sesion. Depending on the outcome, the schedule will be adjusted. Life Science Researchers PhD students beginner bioinformaticians 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
    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
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    • Using MOFA for integration of omics data, online

      15 - 16 October 2020

      Gent, Belgium

      Elixir node event
      Using MOFA for integration of omics data, online https://tess.elixir-europe.org/events/using-mofa-for-integration-of-omics-data-autumn-session Participants can analyze their own data in the course. What kind of preprocessing of the data is required for MOFA? How to train MOFA on a multi-omic data set? How to interpret the MOFA factors by their loadings, using gene set enrichment or sample ordination? How to use MOFA for downstream analyses including regression, classification or clustering? How to impute missing values with MOFA? How to select the number of factors and compare different MOFA fits? 2020-10-15 09:00:00 UTC 2020-10-16 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []
    • Basic statistics in R, online

      23 October - 20 November 2020

      Elixir node event
      Basic statistics in R, online https://tess.elixir-europe.org/events/basic-statistics-in-r-autumn-session This training gives an introduction to the use of the free statistical software language R. This introduction is aimed at beginners.  The training covers data handling, graphics, and basic statistical techniques (t-tests, one-way ANOVA and non-parametric equivalents). A full overview of statistical analyses in R including regression, two-way ANOVA... will be given in follow-up trainings. By following this training you will: get an idea of what R and Rstudio is use R to handle data: creating, reading, reformatting and writing data use R to create graphics use basic statistical techniques in R : t-tests, wilcoxon tests, one-way ANOVA, Kruskal Wallis tests, chi square tests, correlations, survival analysis... write and use R scripts 2020-10-23 09:00:00 UTC 2020-11-20 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
    • Factorial design and analysis

      14 - 15 December 2020

      Elixir node event
      Factorial design and analysis https://tess.elixir-europe.org/events/factorial-design-and-analysis After attending this course, you will be able to reason about you experiment and come up with a design and analysis that fits your situations best, rather than to settle for a suboptimal textbook solution. 2020-12-14 09:00:00 UTC 2020-12-15 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
    • Liquid-Liquid Phase Separation

      14 - 15 December 2020

      Elixir node event
      Liquid-Liquid Phase Separation https://tess.elixir-europe.org/events/liquid-liquid-phase-separation-09e3b786-957d-4d94-9513-3bcfeb0269b7 The aim of this training day is – after a brief introduction – to provide guidelines for accurate experimental characterization of LLPS processes in vitro and in cells. We will end the day with a discussion on the implications of dysregulation of liquid-liquid phase separation for human disease. We have invited top-notch speakers on this topic to inform you on the latest developments.   2020-12-14 09:00:00 UTC 2020-12-15 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
    • Challenges in Omics Data Integration

      8 - 9 October 2020

      Elixir node event
      Challenges in Omics Data Integration https://tess.elixir-europe.org/events/challenges-in-omics-data-integration 2020-10-08 09:00:00 UTC 2020-10-09 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
    • Introduction to Protein Structure Analysis, autumn session

      29 October 2020

      Ghent, Belgium

      Elixir node event
      Introduction to Protein Structure Analysis, autumn session https://tess.elixir-europe.org/events/introduction-to-protein-structure-analysis-autumn-session Get to know the data generated from protein structure determination experiments (high-resolution NMR spectroscopy, X-ray crystallography, electron microscopy, ...) and where to get it. Display protein structure data and compare structures, through the use of Yasara. Create high-quality graphical representations of the structures. Calculate the effect of mutations on the stability of your protein. 2020-10-29 09:00:00 UTC 2020-10-29 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
    • Genome Engineering and Synthetic Biology (4th edition)

      23 - 24 September 2021

      Gent, Belgium

      Elixir node event
      Genome Engineering and Synthetic Biology (4th edition) https://tess.elixir-europe.org/events/genome-engineering-and-synthetic-biology-4th-edition Genome Engineering and Synthetic Biology are revolutionizing Life Sciences. Driven by advances in the CRISPR-toolbox for rapid, cheap, multiplex modification of genomes and breakthroughs in DNA synthesis technologies, the pace of progress enabled by these tools in the last years has been breathtaking. The first three editions (September 2013, January 2016, January 2018) were a roaring success and we are pleased to announce the 4th edition of GESB in beautiful Ghent in September, 2020. Travel Grants We offer 5 travel grants to international attendees, which will reimburse travel costs up to 400 Euros. Are you interested in attending GESB20 and want to have a chance on a travel grant? Submit your motivation below by clicking on the 'Apply for a grant' button before 24 June 2021. The organizing committee will notify you of your travel grant acceptance by the end of June. No registration is needed before submitting a travel grant proposal. When you’re awarded with a travel grant you will receive a practical email containing the next steps. Note that being awarded a travel grant does not mean being registered for the conference. Poster information: Format: A0 (841 x 1189 mm / 33.1 x 46.8 in), portrait orientation Deadlines: • Early Bird: 30 July 2020 • Late Registration: 26 August 2020 • Abstract deadline: 2 July 2020 Speakers: • Edward Lemke - Institute of Molecular Biology (IMB), DE, Johannes Gutenberg University (JGU), DE & EMBL, DE • Sarah Christine Heilshorn - Stanford University, US • Jane Langdale - University of Oxford, UK • George Guo-Qiang Chen - Tsinghua University, CN • Jason Gammack - Inscripta, US • Janice Chen - Mammoth Biosciences, US • Dan Voytas - University of Minnesota, US & Co-Founder & CSO, Calyxt, US • Alexis Komor - University of California, US • Fred Van Ex - Inari Agriculture, BE • Ross Sozzani - NC State Univeristy, US • Bruno Correia - EPFL, CH • Patrick Yizhi Cai - Manchester Institute of Biotechnology, University of Manchester, UK • Tilmann Buerckstuemmer - Aelian Biotechnology, AT • Peter Smibert - New York Genome Center, Techn Innovation lab, US • Tara Deans - University of Utah, US • Jonathan Gootenberg - McGovern Institute, MIT, US • Steve Harvey - CEO Camena Biosciences, UK • Rob Marchmont - VP Sphere Fluidics, UK • Charlie Silver - CEO Mission Bio, US • Bryan Dickinson - The University of Chicago, US • Holger Puchta - Botanical Institute, Karlsruhe Institute of Technology (KIT), DE • Ping-Wei Ho - VIB-KU Leuven Center for Microbiology, BE • And more to come! 2021-09-23 08:00:00 UTC 2021-09-24 18:00:00 UTC VIB De Bijloke, Bijlokekaai 7, 7, Bijlokekaai, Gent, Belgium De Bijloke, Bijlokekaai 7, 7, Bijlokekaai Gent Oost-Vlaanderen Belgium 9000 [] VIB Conferences team - +32(0)92446611 - conferences@vib.be TakaraTwist Bioscience IndustryPhD studentsAcademics 400 meetings_and_conferences [] genome engineeringSynthetic biologycrisprdna synthetistechnologies
    • Image processing for correlated and multimodal imaging techniques

      19 October 2020 - 9 March 2021

      Elixir node event
      Image processing for correlated and multimodal imaging techniques https://tess.elixir-europe.org/events/image-processing-for-correlated-and-multimodal-imaging-techniques The purpose of this event is to dedicate three days of intense training to an audience with little or basic expertise. The program will first cover a full day of online lectures (19 October 2020), followed by two days of hands-on training (8 & 9 March 2021, Ghent). 2020-10-19 09:00:00 UTC 2021-03-09 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
    • Bulk RNASeq: from counts to differential expression, autumn session

      12 - 19 October 2020

      Elixir node event
      Bulk RNASeq: from counts to differential expression, autumn session https://tess.elixir-europe.org/events/bulk-rnaseq-from-counts-to-differential-expression-autumn-session The course will show: R tools to generate count files like featureCounts, and summarizeOverlaps are demonstrated Count files from HTSeq-Count, FeatureCounts, Salmon or Kallisto are used to identify differentially expressed genes After the live session participants can analyze their own count files. Issues can be handled during the Q&A session. 2020-10-12 09:00:00 UTC 2020-10-19 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
    • Research Data Management in Life Sciences

      9 - 10 November 2020

      Elixir node event
      Research Data Management in Life Sciences https://tess.elixir-europe.org/events/research-data-management-in-life-sciences Upon completion of this course, participants should have an understanding of what Research Data Management is, and why it is important in academic research.  They should have an understanding of the FAIR data principles, and how they can make data more FAIR. They should be able to successfully manage all types of research data and to document both the research itself, as well as the data in a comprehensive way.  2020-11-09 09:00:00 UTC 2020-11-10 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] publish and share datacreate preservation documentationMigrate data to best mediaMigrate data to best formatcreate user documentationEstablish copyrightcite data sourcesmanage and store datadescribe and document datacapture data with metadataexplore existing data resourcesplan consent for sharingplan data management design research
    • ReproHack - A hackaton on reproducible data analysis

      20 October 2020

      Elixir node event
      ReproHack - A hackaton on reproducible data analysis https://tess.elixir-europe.org/events/reprohack-a-hackaton-on-reproducible-data-analysis During a ReproHack, participants attempt to reproduce published research of their choice from a list of proposed papers with publicly available associated code and data. This approach should provide a low-pressure environment to actually get working with other people's code and data. Besides evaluating the analysis of papers, this hackaton is also about working together, networking and learning from each other!  Disclaimer: It’s imperative to note that this event is by no means an attempt to criticize or discredit work. We see reproduction as beneficial scientific activity in itself, with useful outcomes for authors and valuable learning experiences for the participants and the research community as a whole. Nominate a paper We accept nominations from anyone. Both researchers that have submitted a paper and would like to test whether one of your own papers is reproducible, and researchers that want to dig into the code of another paper! Either way, we encourage proponents to seek consent from the original authors for their nominations. Nominate a paper via this link. The papers will be assembled and showcased before selection via this link.  Register as participant Join us at the hack to dig into exciting science, learn more about reproducibility, working with other people's code and data and more. 2020-10-20 09:00:00 UTC 2020-10-20 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
    • Python for downstream data analysis

      21 - 22 September 2020

      Leuven, Belgium

      Elixir node event
      Python for downstream data analysis https://tess.elixir-europe.org/events/python-for-data-science Use libraries for advanced data manipulation and visualization Working with biological data using Biopython Being able to write scripts and functions from scratch for specific bioinformatics problems 2020-09-21 09:00:00 UTC 2020-09-22 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
    • Label-free Proteomics data analysis in Galaxy

      3 - 4 December 2020

      Ghent, Belgium

      Elixir node event
      Label-free Proteomics data analysis in Galaxy https://tess.elixir-europe.org/events/label-free-proteomics-data-analysis-in-galaxy In the first part we will introduce you to the Galaxy platform. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work. The proteomics data analysis part comprises label-free data dependent analysis with MaxQuant and label-free data independent acquisition analysis (DIA) with i.a. OpenSwath. A detailed program will be provided shortly.  2020-12-03 09:00:00 UTC 2020-12-04 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
    • Containers and Workflow Pipelines for reproducible and automated data analysis

      26 - 27 October 2020

      Elixir node event
      Containers and Workflow Pipelines for reproducible and automated data analysis https://tess.elixir-europe.org/events/containers-and-workflow-pipelines-for-reproducible-and-automated-data-analysis-7a613826-6388-464d-858a-b4dce0da9e43 Containers Learn the concept of and the difference between Docker & Singularity containers  Write a Docker recipe, build and run a Docker image and containers Pull and push Docker container to / from Docker hub Docker files and layers; Docker cashing Working with volumes Pull Docker containers as a Singularity image Pipelines Understand Nextflow's basic concepts: processes, channels, ... Write and run a Nextflow pipeline (using a Singularity containers) 2020-10-26 09:00:00 UTC 2020-10-27 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
    • Introduction to Git & GitHub

      10 December 2020

      Ghent, Belgium

      Elixir node event
      Introduction to Git & GitHub https://tess.elixir-europe.org/events/introduction-to-git-github-tbc-autumn Get you started with Git from zero (note that if you already use Git, this workshop will be too basic for you). We'll work with GitHub (Desktop) and have a look into git on a command-line level.  Introduction, set-up & configurations Working locally: Create a repository, clone, edit, staging commits, commit & push Working with your history & logs Working in a project: Forking, branching & pull requests How to version control your code in Rstudio with GitHub 2020-12-10 09:00:00 UTC 2020-12-10 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
    • Research Software Developers Day

      3 December 2020

      Elixir node event
      Research Software Developers Day https://tess.elixir-europe.org/events/research-software-engineers-conference The aim of this conference is to foster a community of research software developers and to collectively improve the standard of software used for scientific research. For this, our first edition, we focus on three main themes: reproducibility, software quality and infrastructure. ​If you have something to say, whether broadly related to the topics mentioned above or not, we kindly request you to submit a talk or workshop proposal via this link. If you miss out, you'll have another opportunity to give a lightning talk on the day.   The schedule is accessible at www.be-rse.org/.  2020-12-03 09:00:00 UTC 2020-12-03 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
    • Deep learning in biology, autumn session

      30 September - 18 December 2020

      Elixir node event
      Deep learning in biology, autumn session https://tess.elixir-europe.org/events/deep-learning-in-biology-autumn-session Large amounts of data and compute resources have enabled the development of high-performance machine learning models. This is particularly due to deep learning techniques. By looking at many data samples, these models can find structure in the data that is useful for predictive and explorative analysis: e.g. classification, clustering, data generation, dimensionality reduction, etc. The most popular applications within biotechnology are concerned with image segmentation, diagnostics, sequence analysis, etc. However, deep learning models are far from straightforward to implement correctly due to the many different hyperparameter settings, optimization procedures, architecture choices, etc. In this course, we will make use of Jupyter Notebok and Keras, which are both based on Python, to apply deep learning techniques on both bio informatics and bio image informatics data. We aim to work towards applications that participants would like to study. 2020-09-30 09:00:00 UTC 2020-12-18 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
    • Gentle hands-on introduction to Python programming

      16 - 30 November 2020

      Leuven, Belgium

      Elixir node event
      Gentle hands-on introduction to Python programming https://tess.elixir-europe.org/events/gentle-hands-on-introduction-to-python-programming-tbc-autumn Learning the basics of Python programming: different variables, reading files, writing files, conditional statements Being able to write a basic Python script from scratch 2020-11-16 09:00:00 UTC 2020-11-30 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []