VIB Bioinformatics Core

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

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
Showing 58 materials out of 58. View all results.
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: Expression analysis, Gene expression, Biomarkers

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...

Probabilistic programming with (R)Stan

Probabilistic models describe how the observed data was generated, and what structure the signal and noise from potentially multiple sources may have. Many classical statistical models are special cases of probabilistic models with special modeling assumptions. Probabilistic models can be...

Scientific topics: Statistics and probability

Introduction to Nextflow workshop

workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available...

Scientific topics: Workflows

Keywords: Nextflow, DSL2

Resource type: Presentation, course 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...

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...

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 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...

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....

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...

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

Electronic Lab Notebook Introduction - Leuven

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,...

Initiation GIMP and Inkscape - Leuven

Introduction

Bitmap vs vector images
Image resolution
PPI and DPI
File formats
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...

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,...

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

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...

Custom training: OpenRefine

The aim of this training is to help you use OpenRefine on your own data. This can contain subjects like:

load data files, import and parse data files from a URL
clean data files: rename columns, transform and edit cells, split multivalue cells...
transform data from one format to another:...

Scientific topics: Data quality management

Introduction to Biopython

Biopython is the best-known Python library to process biological data. This training is aimed to empower you to use Biopython to make your research more efficient.
The first day of the training is to give an overview of Biopython. You are going to start with your first steps in Biopython on the...

Scientific topics: Software engineering

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.

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...

Analysis of metabolome data

This training will focus on the processing of raw data obtained via either Gas Chromatography- (GC) or Liquid Chromatography- (LC) mass spectrometry (MS). In addition, based on the comparative analysis between two sample sets (e.g. control vs treatment), the subsequent identification of...

Scientific topics: Metabolomics

Initiation GIMP and Inkscape

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...

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

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, 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...

Electronic Lab Notebook Introduction - Ghent

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,...

Scop3P

Scop3P is available as a web-interface for PTM visualisation and can be accessed at https://iomics.ugent.be/scop3p
Search Scop3P with Swiss-Prot accession/ID, protein name, PDB ID, ProteomeXchange ID or by keywords

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

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

Advanced FlowJo training

The training will start with an introduction to FlowJo v10 but there will be enough details and features to make it worth even for advanced users. In the afternoon, advanced tools in FlowJo and new plugins (tSNE, SPADE) will be presented showing you how to work in high...

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...

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...

Research Data Management in Life Sciences

The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences.

Scientific topics: Data management

Resource type: Presentation, Vignette, Video

Containers & Workflow pipelines workshop

The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify...

Keywords: Containers, Nextflow

Resource type: Training materials

A tour of machine learning - classification

Machine learning has become ubiquitous in biotechnology (as in many other fields), fueled largely by the increasing availability and amount of data. Learning algorithms can figure out how to perform important tasks by generalizing examples. Typical applications are diagnoses/prognoses,...

Scientific topics: Machine learning

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

Reusing existing data

  • how to find existing data (OmicsDI, pubmed, BioStudies, Google Data search, Data Management Hub)
  • licenses
  • datasets as first-class research products
  • research software as first-class research products
  • data citations

Scientific topics: Data management

Keywords: data licenses, software licenses, data journal

Resource type: Presentation

Preserve, publish and share your data

  • why preserve data
  • what data should be preserved
  • how share data
  • where to deposit your data
  • Fairsharing, re3data
  • ELIXIR Core Resources
  • Data Formats
  • Generic archives

Scientific topics: Data management, Data submission, annotation, and curation

Keywords: data formats, ELIXIR Core resources, FAIR data submission

Resource type: Presentation

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

Reproducible data analysis with RStudio, github and Rmarkdown

Best practices for writing reproducible data-analysis
Creating a reproducible and re-usable data-analysis environment with Rstudio
Input: https://github.com/vibbits/RDM-LS
Output: https://github.com/vibbits/RDM-LS-solution

Scientific topics: Data management, Data architecture, analysis and design

Keywords: Data analysis

Resource type: Presentation

Valorisation and intellectual properties in research data management

Valorisation and IP

  • Basics of Tech Transfer and IPR from an academic perspective
  • Insights as to:
    • Why is it important when handling and managing research data?
    • How do IP rights fit in FAIR data principles
    • When to safeguard data for proprietary protection?
    • Where/how...

Scientific topics: Data management

Keywords: intellectual property protection

Resource type: Presentation

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

Introduction to 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....

Keywords: Protein structure visualisation

Resource type: e-learning

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...

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

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

Basic bioinformatics concepts, databases and tools

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

Scientific topics: Sequence analysis

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, Expression analysis, Gene expression

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...

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

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...

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: Expression analysis

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 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...

Scientific topics: Molecular biology, Gene regulation, Gene expression

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, Differential gene expression profiling

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

Data Management and Writing a Data Management Plan

Writing a Data Management Plan

A good data management plan is crucial for any scientist and researcher. In this course, you will learn how to write one. You will find out how you can prepare, handle and share your research data.

Scientific topics: Data management

Resource type: e-learning

Image Ethics and Poster Design

The image ethics part handles on the theoretical aspects of image manipulation, the mistakes people make and how to avoid image fraud. VIB has guidelines for acceptable scientific image manipulations. Not all manipulations are scientifically correct. There are manipulations that fall within the...

Scientific topics: Image

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...

Found 0 upcoming events. Found 202 past events. View all results.