VIB Bioinformatics Training and Services

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

Showing 30 materials out of 43. View all results.

Initiation GIMP and Inkscape - Leuven from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/321-gimp-inkscape-leuven.

Initiation GIMP and Inkscape - Leuven https://tess.oerc.ox.ac.uk/materials/initiation-gimp-and-inkscape-leuven Initiation GIMP and Inkscape - Leuven from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/321-gimp-inkscape-leuven. 2016-04-19

Electronic Lab Notebook Introduction - Leuven from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/297-intro-eln-leuven.

Electronic Lab Notebook Introduction - Leuven https://tess.oerc.ox.ac.uk/materials/electronic-lab-notebook-introduction-leuven Electronic Lab Notebook Introduction - Leuven from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/297-intro-eln-leuven. 2016-04-14

Electronic Lab Notebook Introduction - Ghent from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/296-intro-eln-ghent.

Electronic Lab Notebook Introduction - Ghent https://tess.oerc.ox.ac.uk/materials/electronic-lab-notebook-introduction-ghent Electronic Lab Notebook Introduction - Ghent from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/296-intro-eln-ghent. 2016-04-19

This course presents a comprehensive overview of the principles and applications of studying eukaryotic gene regulation. 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...

Scientific topics: Gene expression, Gene regulation, Molecular biology, Molecular biology, Gene expression, Gene regulation, Molecular biology, Gene regulation, Gene expression, Gene regulation, Molecular biology, Gene expression, Gene expression, Gene regulation, Molecular biology, Gene regulation, Molecular biology, Gene expression, Gene expression, Gene regulation, Molecular biology, Gene regulation, Gene expression, Molecular biology, Molecular biology, Gene regulation, Gene expression, Gene expression, Gene regulation, Molecular biology, Gene regulation, Molecular biology, Gene expression, Gene regulation, Gene expression, Molecular biology, Molecular biology, Gene regulation, Gene expression, Molecular biology, Gene regulation, Gene expression, Gene regulation, Gene expression, Molecular biology, Gene expression, Molecular biology, Gene regulation

Introduction to gene regulation https://tess.oerc.ox.ac.uk/materials/introduction-to-gene-regulation This course presents a comprehensive overview of the principles and applications of studying eukaryotic gene regulation. 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. Gene expression Gene regulation Molecular biology Molecular biology Gene expression Gene regulation Molecular biology Gene regulation Gene expression Gene regulation Molecular biology Gene expression Gene expression Gene regulation Molecular biology Gene regulation Molecular biology Gene expression Gene expression Gene regulation Molecular biology Gene regulation Gene expression Molecular biology Molecular biology Gene regulation Gene expression Gene expression Gene regulation Molecular biology Gene regulation Molecular biology Gene expression Gene regulation Gene expression Molecular biology Molecular biology Gene regulation Gene expression Molecular biology Gene regulation Gene expression Gene regulation Gene expression Molecular biology Gene expression Molecular biology Gene regulation post-docs Life Science Researchers PhD students 2016-04-22 2017-04-26

Custom training: Spotfire from https://www.bits.vib.be/training/training/110-bits/training/custom-trainings/279-custom-training-spotfire.

Custom training: Spotfire https://tess.oerc.ox.ac.uk/materials/custom-training-spotfire Custom training: Spotfire from https://www.bits.vib.be/training/training/110-bits/training/custom-trainings/279-custom-training-spotfire. 2016-04-16

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, Gene expression analysis, Gene expression analysis, Gene expression analysis, Gene expression analysis, Gene expression analysis, Gene expression analysis, Gene expression analysis, Gene expression analysis, Gene expression analysis, Gene expression analysis, Gene expression analysis, Gene expression analysis, Gene expression analysis, Gene expression analysis

Cloning with SnapGene https://tess.oerc.ox.ac.uk/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 Gene expression analysis Gene expression analysis Gene expression analysis Gene expression analysis Gene expression analysis Gene expression analysis Gene expression analysis Gene expression analysis Gene expression analysis Gene expression analysis Gene expression analysis Gene expression analysis Gene expression analysis Gene expression analysis PhD students post-docs Life Science Researchers 2016-04-22 2017-04-26

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, Gene expression analysis, Gene expression, PCR experiment, Gene expression analysis, Gene expression analysis, Gene expression, PCR experiment, PCR experiment, Gene expression analysis, Gene expression, Gene expression, PCR experiment, Gene expression analysis, Gene expression analysis, Gene expression, PCR experiment, Gene expression analysis, PCR experiment, Gene expression, Gene expression, PCR experiment, Gene expression analysis, PCR experiment, Gene expression, Gene expression analysis, PCR experiment, Gene expression analysis, Gene expression, Gene expression analysis, Gene expression, PCR experiment, Gene expression analysis, Gene expression, PCR experiment, Gene expression, PCR experiment, Gene expression analysis, Gene expression analysis, Gene expression, PCR experiment, Gene expression analysis, Gene expression, PCR experiment, Gene expression, PCR experiment

Analysis of qPCR data using qbase+ https://tess.oerc.ox.ac.uk/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 Gene expression analysis Gene expression PCR experiment Gene expression analysis Gene expression analysis Gene expression PCR experiment PCR experiment Gene expression analysis Gene expression Gene expression PCR experiment Gene expression analysis Gene expression analysis Gene expression PCR experiment Gene expression analysis PCR experiment Gene expression Gene expression PCR experiment Gene expression analysis PCR experiment Gene expression Gene expression analysis PCR experiment Gene expression analysis Gene expression Gene expression analysis Gene expression PCR experiment Gene expression analysis Gene expression PCR experiment Gene expression PCR experiment Gene expression analysis Gene expression analysis Gene expression PCR experiment Gene expression analysis Gene expression PCR experiment Gene expression PCR experiment post-docs Life Science Researchers PhD students 2016-04-22 2017-04-26

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...

Basic statistics in R https://tess.oerc.ox.ac.uk/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 2017-04-26

The Training consists of two parts: Introduction Access ways to your notebook, ELN installation instructions and house rules, where to find documentation and get support Hands-on-demo Creating notebooks/experiments, importing and exporting (MS Office) files, sharing data, using templates,...

Electronic Lab Notebook Introduction - Ghent https://tess.oerc.ox.ac.uk/materials/electronic-lab-notebook-introduction The Training consists of two parts: Introduction Access ways to your notebook, ELN installation instructions and house rules, where to find documentation and get support Hands-on-demo Creating notebooks/experiments, importing and exporting (MS Office) files, sharing data, using templates, advanced searching, printing, tips and tricks Life Science Researchers PhD students post-docs 2016-04-22 2017-04-26

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, Software engineering, Software engineering, Software engineering, Software engineering, Software engineering, Software engineering, Software engineering, Software engineering, Software engineering, Software engineering, Software engineering, Software engineering, Software engineering, Software engineering, Software engineering

Gentle hands-on introduction to Python programming https://tess.oerc.ox.ac.uk/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 Software engineering Software engineering Software engineering Software engineering Software engineering Software engineering Software engineering Software engineering Software engineering Software engineering Software engineering Software engineering Software engineering Software engineering Software engineering PhD students beginner bioinformaticians Life Science Researchers post-docs 2016-04-22 2017-04-26

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...

Scientific topics: DNA, DNA, DNA, DNA, DNA, DNA, DNA, DNA, DNA, DNA, DNA, DNA, DNA, DNA, DNA, DNA

Hands-on introduction to NGS variant analysis https://tess.oerc.ox.ac.uk/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 DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA DNA Life Science Researchers post-docs beginner bioinformaticians PhD students 2016-04-22 2017-04-26

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.oerc.ox.ac.uk/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. Life Science Researchers post-docs PhD students 2016-04-22 2017-04-14

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, Proteomics, Proteomics, Proteomics, Proteomics, Proteomics, Proteomics, Proteomics, Proteomics, Proteomics, Proteomics, Proteomics, Proteomics, Proteomics, Proteomics, Proteomics

Mass spectrometry data processing https://tess.oerc.ox.ac.uk/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 Proteomics Proteomics Proteomics Proteomics Proteomics Proteomics Proteomics Proteomics Proteomics Proteomics Proteomics Proteomics Proteomics Proteomics Proteomics Life Science Researchers PhD students post-docs 2016-04-22 2017-04-26

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: Local alignment, Global alignment, Global alignment, Local alignment, Global alignment, Local alignment, Local alignment, Global alignment, Local alignment, Global alignment, Local alignment, Global alignment, Local alignment, Global alignment, Local alignment, Global alignment, Local alignment, Global alignment, Global alignment, Local alignment, Local alignment, Global alignment, Local alignment, Global alignment, Global alignment, Local alignment, Local alignment, Global alignment, Local alignment, Global alignment, Sequence annotation

Introduction to CLC Bio Main Workbench https://tess.oerc.ox.ac.uk/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. Local alignment Global alignment Global alignment Local alignment Global alignment Local alignment Local alignment Global alignment Local alignment Global alignment Local alignment Global alignment Local alignment Global alignment Local alignment Global alignment Local alignment Global alignment Global alignment Local alignment Local alignment Global alignment Local alignment Global alignment Global alignment Local alignment Local alignment Global alignment Local alignment Global alignment Sequence annotation post-docs PhD students Life Science Researchers 2016-04-22 2017-04-26

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.oerc.ox.ac.uk/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. PhD students Life Science Researchers post-docs 2016-04-22 2017-04-26

This training will start with the presentation of a 16S pipeline (psbweb05.psb.ugent.be/lotus/) in a linux environment, using a minimal amount of linux commands. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees. The 2nd part of the...

Metagenomics https://tess.oerc.ox.ac.uk/materials/metagenomics This training will start with the presentation of a 16S pipeline (psbweb05.psb.ugent.be/lotus/) in a linux environment, using a minimal amount of linux commands. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees. The 2nd part of the training will give an overview of numerical ecology and takes part entierly in R. Life Science Researchers beginner bioinformaticians PhD students post-docs 2016-04-22 2016-08-18

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: Gene expression, Gene expression, RNA-Seq, Gene expression, RNA-Seq, RNA-Seq, Gene expression, Gene expression, RNA-Seq, Gene expression, RNA-Seq, RNA-Seq, Gene expression, RNA-Seq, Gene expression, Gene expression, RNA-Seq, RNA-Seq, Gene expression, RNA-Seq, Gene expression, RNA-Seq, Gene expression, RNA-Seq, Gene expression, RNA-Seq, RNA-Seq, Gene expression, RNA-Seq, Gene expression, RNA-Seq, Gene expression

RNA-Seq analysis for differential expression https://tess.oerc.ox.ac.uk/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. Gene expression Gene expression RNA-Seq Gene expression RNA-Seq RNA-Seq Gene expression Gene expression RNA-Seq Gene expression RNA-Seq RNA-Seq Gene expression RNA-Seq Gene expression Gene expression RNA-Seq RNA-Seq Gene expression RNA-Seq Gene expression RNA-Seq Gene expression RNA-Seq Gene expression RNA-Seq RNA-Seq Gene expression RNA-Seq Gene expression RNA-Seq Gene expression Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-04-26

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...

Introduction to Linux for bioinformatics https://tess.oerc.ox.ac.uk/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. beginner bioinformaticians Life Science Researchers PhD students 2016-04-22 2017-04-26

Initiation GIMP and Inkscape from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/316-gimp-inkscape.

Scientific topics: Data governance, Data management

Initiation GIMP and Inkscape https://tess.oerc.ox.ac.uk/materials/initiation-gimp-and-inkscape Initiation GIMP and Inkscape from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/316-gimp-inkscape. Data governance Data management 2016-04-08

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.

Analysis of public microarray data sets https://tess.oerc.ox.ac.uk/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. Life Science Researchers PhD students post-docs 2016-04-22 2017-04-26

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.oerc.ox.ac.uk/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. PhD students post-docs Life Science Researchers 2016-04-22 2017-04-26

Flowjo version10 is a newly designed version of the famous Flowjo software. In contrast with previous versions (iOS only), version 10 is now a multi-platform software tool (Windows, iOS, Linux). It now has a very intuitive user interface designed to analyze your data in a very practical and fast...

Analyzing flow cytometry data using FlowJo https://tess.oerc.ox.ac.uk/materials/analyzing-flow-cytometry-data-using-flowjo Flowjo version10 is a newly designed version of the famous Flowjo software. In contrast with previous versions (iOS only), version 10 is now a multi-platform software tool (Windows, iOS, Linux). It now has a very intuitive user interface designed to analyze your data in a very practical and fast way. The training will be focused on getting familiar with all the tools available within the software. PhD students Life Science Researchers post-docs 2016-04-22 2017-04-26

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

Basic statistics theory https://tess.oerc.ox.ac.uk/materials/basic-statistics-theory This training gives an introduction to the use of statistics for basic analyses of life sciences data. This training is a prerequisite introduction to a series of hands-on trainings on the statistical analysis of life sciences data: 'Basic statistics in R' and 'Basic statistics in Graphpad Prism'. If you want to follow one of these trainings, you have to follow this introduction. Ít will give you all the theoretical background that you need. Those that already have a strong statistical background may register directly for the 'Basic statistics in R, part II' training. post-docs PhD students Life Science Researchers 2016-04-22 2017-04-26

The aim of this training is to teach you how to use Ingenuity Pathway Analysis (IPA) software on your own data. This can be for various applications: Creating and modifying biological networks e.g. which genes are involved in a certain disease Mapping data to biological processes,...

Scientific topics: Microarray experiment, Metabolomics, Protein interactions, Proteomics

Custom training: Ingenuity Pathway Analysis https://tess.oerc.ox.ac.uk/materials/custom-training-ingenuity-pathway-analysis The aim of this training is to teach you how to use Ingenuity Pathway Analysis (IPA) software on your own data. This can be for various applications: Creating and modifying biological networks e.g. which genes are involved in a certain disease Mapping data to biological processes, networks and pathways mapping a list of genes/proteins/chemicals mapping quantitative data e.g. microarray/proteomics/metabolomics data High quality visualisation of biological networks and pathways Assessing the biological significance of pathways in certain physiological conditions e.g. detecting overrepresented pathways in diseases Microarray experiment Metabolomics Protein interactions Proteomics post-docs Life Science Researchers PhD students 2016-04-22 2016-09-26

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: Sequence assembly, Workflows, Sequence assembly, Workflows, Sequence assembly, Workflows, Sequence assembly, Workflows, Sequence assembly, Workflows, Sequence assembly, Workflows, Workflows, Sequence assembly, Sequence assembly, Workflows, Workflows, Sequence assembly, Workflows, Sequence assembly, Sequence assembly, Workflows, Workflows, Sequence assembly, Sequence assembly, Workflows, Sequence assembly, Workflows, Workflows, Sequence assembly, Workflows, Sequence assembly

Introduction to the analysis of NGS data https://tess.oerc.ox.ac.uk/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. Sequence assembly Workflows Sequence assembly Workflows Sequence assembly Workflows Sequence assembly Workflows Sequence assembly Workflows Sequence assembly Workflows Workflows Sequence assembly Sequence assembly Workflows Workflows Sequence assembly Workflows Sequence assembly Sequence assembly Workflows Workflows Sequence assembly Sequence assembly Workflows Sequence assembly Workflows Workflows Sequence assembly Workflows Sequence assembly Life Science Researchers post-docs PhD students 2016-04-22 2017-04-26

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.oerc.ox.ac.uk/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 2017-04-26

Introduction Bitmap vs vector images Image resolution PPI and DPI File formats and compression VIB guidelines on image editing GIMP prepare images for publication Installation and documentation User Interface Import image files Image Properties Selection tools and...

Initiation GIMP and Inkscape https://tess.oerc.ox.ac.uk/materials/initiation-gimp-and-inkscape-ghent Introduction Bitmap vs vector images Image resolution PPI and DPI File formats and compression VIB guidelines on image editing GIMP prepare images for publication Installation and documentation User Interface Import image files Image Properties Selection tools and options Transforming options Scaling and cropping Using Layers Contrast and brightness Undo/redo Image print size Saving/Exporting images Exercises Inkscape annotate plots and images, create figures (diagrams, schemes, ...), design posters Installation and documentation User interface Import image/vector files Drawing lines Creating paths Drawing objects Fill and stroke Aligning and distributing objects/nodes Z-order Adding text and text options Path effects Live path effects Diagrams Exporting images Exercises Image format PhD students Life Science Researchers SVG post-docs 2017-04-26

​In 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...

Scientific topics: RNA-Seq, RNA-Seq, RNA-Seq, RNA-Seq, RNA-Seq, RNA-Seq, RNA-Seq, RNA-Seq, RNA-Seq, RNA-Seq, RNA-Seq, RNA-Seq, RNA-Seq, RNA-Seq, RNA-Seq, Mapping, RNA-Seq

GATK Best practices for variant discovery https://tess.oerc.ox.ac.uk/materials/gatk-best-practices-for-variant-discovery ​In 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 RNA-Seq RNA-Seq RNA-Seq RNA-Seq RNA-Seq RNA-Seq RNA-Seq RNA-Seq RNA-Seq RNA-Seq RNA-Seq RNA-Seq RNA-Seq RNA-Seq Mapping RNA-Seq post-docs PhD students Life Science Researchers beginner bioinformaticians 2016-04-22 2017-04-26

We will investigate the following items: Quality control of the sequence reads to detect biases or contaminating adapters Mapping of the reads to the reference genome with use of a transcript database model Quality control of the mapping results Adjusting the mapping data to...

Scientific topics: RNA-Seq, Gene expression

RNA-Seq analysis for differential expression in GenePattern https://tess.oerc.ox.ac.uk/materials/rna-seq-analysis-for-differential-expression-in-genepattern We will investigate the following items: Quality control of the sequence reads to detect biases or contaminating adapters Mapping of the reads to the reference genome with use of a transcript database model Quality control of the mapping results Adjusting the mapping data to compensate for artefacts like duplicates Calculate transcript counts usable for differential expression and merging of count tables Computing differential expression using EdgeR and DESeq2 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 post-docs PhD students Life Science Researchers beginner bioinformaticians 2016-04-22 2017-04-26

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, Protein structure analysis, Protein structure analysis, Protein structure analysis, Protein structure analysis, Protein structure analysis, Protein structure analysis, Protein structure analysis, Protein structure analysis, Protein structure analysis, Protein structure analysis, Protein structure analysis, Protein structure analysis, Protein structure analysis, Protein structure analysis

Protein Structure Analysis https://tess.oerc.ox.ac.uk/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 Protein structure analysis Protein structure analysis Protein structure analysis Protein structure analysis Protein structure analysis Protein structure analysis Protein structure analysis Protein structure analysis Protein structure analysis Protein structure analysis Protein structure analysis Protein structure analysis Protein structure analysis Protein structure analysis Protein structure analysis PhD students Life Science Researchers post-docs 2016-04-22 2017-04-26
Showing 13 upcoming events. Found 13 past events. View all results.
  • Initiation GIMP and Inkscape Ghent

    02 May 2017

    Ghent, Belgium

    Initiation GIMP and Inkscape Ghent https://tess.oerc.ox.ac.uk/events/initiation-gimp-and-inkscape-ghent 2017-05-02 09:00:00 UTC 2017-05-02 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Ghent, Belgium Bio-Accelerator Ghent Belgium 9052
  • Protein Structure Analysis

    12 May 2017

    Ghent, Belgium

    Protein Structure Analysis https://tess.oerc.ox.ac.uk/events/protein-structure-analysis-e2917b45-24e1-454f-92f8-1181f2189115 2017-05-12 09:30:00 UTC 2017-05-12 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Ghent, Belgium BioAccelerator Ghent Belgium 9052
  • Electronic Lab Notebook Introduction - Ghent

    10 May 2017

    Ghent, Belgium

    Electronic Lab Notebook Introduction - Ghent https://tess.oerc.ox.ac.uk/events/electronic-lab-notebook-introduction-ghent 2017-05-10 10:00:00 UTC 2017-05-10 12:00:00 UTC VIB Bioinformatics Core PC room V114 - 1st floor front building VIB-UGent Research Building, Ghent, Belgium PC room V114 - 1st floor front building VIB-UGent Research Building Ghent Belgium 9052
  • Electronic Lab Notebook Introduction - Leuven

    11 May 2017

    Leuven, Belgium

    Electronic Lab Notebook Introduction - Leuven https://tess.oerc.ox.ac.uk/events/electronic-lab-notebook-introduction-leuven This training is an introduction to the Electronic Laboratory Notebook (ELN) implemented at VIB. This training is intended for all new VIB co-workers (except administrative personnel) and will teach you the basic knowledge required to successfully document in ELN. The training consists of two parts: Introduction: Access​ ways to your notebook, ELN installation instructions and house rules, where to find documentation and get support Hands-on-demo: Creating notebooks/experiments, importing and exporting (MS Office) files, sharing data, using templates, advanced searching, printing, tips and tricks This training is mandatory for all new VIB co-workers and requires an active VIB account. In order to check your username and password, go to https://ctxportal.vib.be, if login fails send an e-mail to eln*Replace*With*At*Sign*vib.be. People who want to join this training can register here! 2017-05-11 10:00:00 UTC 2017-05-11 12:00:00 UTC VIB Bioinformatics Core O&N4 room 07.339 Campus Gasthuisberg, Leuven, Belgium O&N4 room 07.339 Campus Gasthuisberg Leuven Belgium 3000
  • Initiation GIMP and Inkscape Leuven

    04 May 2017

    Leuven, Belgium

    Initiation GIMP and Inkscape Leuven https://tess.oerc.ox.ac.uk/events/initiation-gimp-and-inkscape-leuven 2017-05-04 09:00:00 UTC 2017-05-04 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010
  • Gentle hands-on introduction to Python programming

    18 - 25 Sep 2017

    Leuven, Belgium

    Gentle hands-on introduction to Python programming https://tess.oerc.ox.ac.uk/events/gentle-hands-on-introduction-to-python-programming 2017-09-18 09:30:00 UTC 2017-09-25 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010
  • Introductory statistics in GraphPad Prism

    06 Jun 2017

    Leuven, Belgium

    Introductory statistics in GraphPad Prism https://tess.oerc.ox.ac.uk/events/introductory-statistics-in-graphpad-prism In this hands-on session, you will apply the theory that you learnt in the Basic statistics theory training in Prism. The following topics will be covered: What is Prism? Where to find more information? How to install and use it? How to use Prism to handle data: reading data How to use Prism to create graphics How to use basic statistical techniques in Prism: mean, variance, confidence intervals, correlations, hypothesis testing...     2017-06-06 09:30:00 UTC 2017-06-06 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010
  • RNA-Seq analysis for differential expression in Genepattern

    08 May 2017

    Leuven, Belgium

    RNA-Seq analysis for differential expression in Genepattern https://tess.oerc.ox.ac.uk/events/rna-seq-analysis-for-differential-expression-in-genepattern You will execute a complete analysis workflow in GenePattern and R to detect differential expression between two conditions We'll go through the different steps of the workflow: Quality control of the sequence reads to detect biases or contaminating adapters. Mapping of the reads to the reference genome with use of a transcript database model. Quality control  of the mapping results. Adjusting the mapping data to compensate for artefacts like duplicates. Calculate transcript counts usable for differential expression and merging of count tables  Computing differential expression using EdgeR and DESeq2. • fastQC • trimmomatic• Groomer • tophat2 • STAR• samtools• Picard • RSeQC• HTSeq• R - RStudio - Bioconductor - various packages    Familiarity with RNA-seq assembly RNA-seq analysis for isoform detection RNA-seq analysis for detection of short RNA species .Organised by the VIB Bioinformatics Core​ 2017-05-08 09:30:00 UTC 2017-05-08 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010
  • Initiation GIMP and Inkscape - Ghent

    09 May 2017

    Ghent, Belgium

    Initiation GIMP and Inkscape - Ghent https://tess.oerc.ox.ac.uk/events/initiation-gimp-and-inkscape-ghent-ea8add26-ae76-4c83-a280-5ba83c5b3066 2017-05-09 09:00:00 UTC 2017-05-09 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator Meeting Centre, Ghent, Belgium Bio-Accelerator Meeting Centre Ghent Belgium 9052
  • Basic statistics in R

    19 - 29 May 2017

    Leuven, Belgium

    Basic statistics in R https://tess.oerc.ox.ac.uk/events/basic-statistics-in-r Get an idea of what R and Rstudio is, where to find more information, how to install and use it Use R to handle data: data types, reading data Use R to create graphics Use mathematical functions and basic statistical techniques in R  Write and manage R scripts 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 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.   Requirements The training is intended for people who have no experience with R. However, understanding of basic statistical concepts is required, such as data types, normal distribution, descriptive statistics, tests for comparing groups... If you don't have sufficient statistical background you are strongly encouraged to attend the Basic statistics theory training.  This training is recommended for people with no experience in R who are planning to follow a training that requires some R background, like the metagenomics training and the RNA-Seq training. BITS provides 15 laptops for their training sessions. Depending on the number of participants (max 20), it might be 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. 2017-05-19 09:30:00 UTC 2017-05-29 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010
  • Mass spectrometry data processing

    11 - 12 Sep 2017

    Gent, Belgium

    Mass spectrometry data processing https://tess.oerc.ox.ac.uk/events/mass-spectrometry-data-processing 2017-09-11 09:30:00 UTC 2017-09-12 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052
  • qPCR analysis using qbasePLUS

    19 Jun 2017

    Ghent (Zwijnaarde), Belgium

    qPCR analysis using qbasePLUS https://tess.oerc.ox.ac.uk/events/qpcr-analysis-using-qbaseplus 2017-06-19 13:00:00 UTC 2017-06-19 17:00:00 UTC VIB Bioinformatics Core VIB Bioinformatics Core, Ghent (Zwijnaarde), Belgium VIB Bioinformatics Core Ghent (Zwijnaarde) Belgium 9052
  • Basic statistics in R, part II

    23 - 30 Jun 2017

    Gent, Belgium

    Basic statistics in R, part II https://tess.oerc.ox.ac.uk/events/basic-statistics-in-r-part-ii 2017-06-23 09:30:00 UTC 2017-06-30 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052
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scraper updated VIB Bioinformatics Training and Services at 2016-08-18 03:00:12 UTC.
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