Provider of Bioinformatics and software training, plus informatics services and resource management support.
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, Biomarkers
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
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
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...
- 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...
Scientific topics: Gene finding, RNA-Seq
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
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...
Scientific topics: DNA
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
Keywords: Mass spectrometry data, Proteomics, Spectral analysis
This training will teach you how to choose the appropriate statistical test for analyzing your data. Attention will be paid to the correct interpretation of the results of statistical tests. The training is intended for scientists who want to get an introduction in statistics without getting too...
This training is aimed at researchers who are applying or planning to use Affymetrix microarrays in their research. The aim of this training is to familiarise the participants with microarray data analysis methodologies and provide hands-on training on the use of Bioconductor for Affymetrix...
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.
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
Keywords: Gene expression data analysis, Gene expression, PCR experiment
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...
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...
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...
Scientific topics: Information retrieval
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...
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...
This course presents a comprehensive overview of the principles and applications of comparative genomics in eukaryotes. The course combines lectures with hands-on exercises.
LaTeX is free high-quality publishing software. Life science researchers can benefit from the software because it includes features designed for the production of professional quality publications (papers, posters and presentations). Additionally, LaTeX allows automating many of the repetitive...
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: ...
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...
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: Mapping, RNA-Seq
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...
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
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: Gene expression
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: Sequence annotation
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...
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....
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...
Scientific topics: RNA-Seq, Gene expression
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, Text mining
Protein Structure Analysis
12 May 2017
Genth, BelgiumProtein Structure Analysis http://www.vib.be/en/training/research-training/courses/Pages/Protein-Structure-Analysis-Training.aspx https://tess.elixir-europe.org/events/protein-structure-analysis-f095d4f5-e03b-4b1d-9f38-38dff017174a 2017-05-12 09:30:00 UTC 2017-05-12 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Genth, Belgium BioAccelerator Genth Belgium 9052
Introduction to Biopython
13 - 14 Apr 2017
Ghent, BelgiumIntroduction to Biopython http://www.vib.be/en/training/research-training/courses/Pages/Introduction-to-Biopython.aspx https://tess.elixir-europe.org/events/introduction-to-biopython Understand what Biopython is and what it can do. Learn how to get Biopython running. Learn how to retrieve data records from NCBI. Learn how to read and write sequence files. Learn how to run BLAST from Python and read the results. Learn how to read and write phylogenetic tree files. Learn how to read and write 3D structure files. Learn how to use the Biopython documentation, examples, and where to find help. Understand what alternatives to Biopython exist and what they can do. 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 command line. Afterwards, you will take a tour of the most important components: sequences, NCBI queries, BLAST, trees, and 3D structures. You will try each of these modules on practical examples. Please don't hesitate to ask questions about Python basics or particular data formats (e.g. XML or NGS data). The second day of the training is to broaden your perspective: What other features does the library have? How can you use the documentation effectively? What is Biopython not capable of? What can I do to visualize my data? Are there alternatives? If you have your own data that you would like to work on with Biopython in more detail, there is room for that. For me, the most important thing is to identify concrete Python modules and functions that help you to get your research done. Participants are encouraged to submit a description of their research topic and/or the questions they would like to answer with Biopython. Additionally, participants can bring their own data that they would like to process in Python to the training. 2017-04-13 09:30:00 UTC 2017-04-14 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Ghent, Belgium BioAccelerator Ghent Belgium 9052
VIB Community Meeting - Bioinformatics and Computational Biology
27 Feb 2017
Brussels, BelgiumVIB Community Meeting - Bioinformatics and Computational Biology http://www.vib.be/en/training/research-training/courses/Pages/VIB-Community-Meeting---Bioinformatics-and-Computational-Biology.aspx https://tess.elixir-europe.org/events/vib-community-meeting-bioinformatics-and-computational-biology Lennart Martens (VIB-UGent CompOmics) and Alexander Botzki (VIB Bioinformatics Core) organise an interactive VIB Community Meeting on Bioinformatics and Computational Biology on the 27th of February 2017 in Brussels. In order to foster the VIB-wide collaboration among bioinformaticians, we would like to organise open discussion sessions around several field-related topics. The idea is to organize 3 short presentations (max. 15 min.) on innovative matter per topic, followed by 30 min. discussions each. The day will be closed by a plenary brainstorm session on ideas which have been put forward to pursue in the parallel sessions. A preliminary agenda for the meeting can be found below. Program: VIB Community Meeting: Bioinformatics and Computational Biology.pdf 2017-02-27 09:00:00 UTC 2017-02-27 16:30:00 UTC VIB Bioinformatics Core U-Residence, Brussels, Belgium U-Residence Brussels Belgium 1050
Electronic Lab Notebook Introduction - Leuven
23 Mar 2017
Leuven, BelgiumElectronic Lab Notebook Introduction - Leuven http://www.vib.be/en/training/research-training/courses/Pages/Electronic-Lab-Notebook-Introduction---Leuven.aspx https://tess.elixir-europe.org/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! 2017-03-23 10:00:00 UTC 2017-03-23 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
Basic statistics theory
18 Apr 2017
Leuven, BelgiumBasic statistics theory http://www.vib.be/en/training/research-training/courses/Pages/Basic-statistics-theory.aspx https://tess.elixir-europe.org/events/basic-statistics-theory After this basic statistics theory session, you should be able to: Understand basic statistical concepts and methods for statistical analysis of life sciences data Choose the correct statistical test for analyzing your data 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. No skills required. 9h30-12h30: Theoretical background 2017-04-18 09:30:00 UTC 2017-04-18 16:30:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010
Analyzing flow cytometry data using FlowJo
24 Apr 2017
Gent (Sint-Denijs-Westrem), BelgiumAnalyzing flow cytometry data using FlowJo http://www.vib.be/en/training/research-training/courses/Pages/Analyzing-flow-cytometry-data-using-FlowJo.aspx https://tess.elixir-europe.org/events/analyzing-flow-cytometry-data-using-flowjo Learn researchers how to analyze flow cytometry data in an efficient way using Flowjo X,the world’s nr.1 analysis software tool for flow cytometry data. 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. 2017-04-24 09:30:00 UTC 2017-04-24 17:00:00 UTC VIB Bioinformatics Core Holiday Inn Gent Expo, Gent (Sint-Denijs-Westrem), Belgium Holiday Inn Gent Expo Gent (Sint-Denijs-Westrem) Belgium 9051
Hands-on introduction to Perl programming
6 - 13 Mar 2017
Leuven, BelgiumHands-on introduction to Perl programming http://www.vib.be/en/training/research-training/courses/Pages/Gentle-hands-on-introduction-to-perl-programming.aspx https://tess.elixir-europe.org/events/hands-on-introduction-to-perl-programming Learning the basics of Perl programming: different variables, reading files, writing files, regex. Being able to write small scripts to parse text files Using Perl in windows. Day 2 9:30 - 10:30 Recapitulation of learned concepts by correcting the homework 10:30 - 12:30 More Perl programming: pseudo code, conditional statements, routines, best practices 13:00 - 17:00 Exercise session combining all the skills we have gathered. 2017-03-06 09:30:00 UTC 2017-03-13 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
02 May 2017
Ghent, BelgiumInitiation GIMP and Inkscape Ghent http://www.vib.be/en/training/research-training/courses/Pages/Initiation-GIMP-and-Inkscape--Ghent.aspx https://tess.elixir-europe.org/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
Introductory statistics in GraphPad Prism
06 Jun 2017
Leuven, BelgiumIntroductory statistics in GraphPad Prism http://www.vib.be/en/training/research-training/courses/Pages/Introductory-statistics-in-GraphPad-Prism.aspx https://tess.elixir-europe.org/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
Basic bioinformatics concepts, databases and tools
10 - 24 Mar 2017
Leuven, BelgiumBasic bioinformatics concepts, databases and tools http://www.vib.be/en/training/research-training/courses/Pages/Basic-bioinformatics-concepts,-databases-and-tools.aspx https://tess.elixir-europe.org/events/basic-bioinformatics-concepts-databases-and-tools Understand the capabilities and pitfalls of bioinformatics. Functioning of the most used bioinformatics algorithms and terms for reliable interpretation of the results. Navigate with confidence to numerous online data repositories. Know where to search for them. Basic analyses of single genes as well as groups of genes (gene lists) GenBank, SwissProt, RefSeq, Gene GQuery Ensembl Ugene BLAST, OrthoMCL, EMBOSS Needle, EMBOSS Water, Muscle, WebLogo, iceLogo HMMER, PSIBLAST, PROSITE, SMART, InterPro miRWalk, Pscan, Motiflab Primer3 PLUS, Primer BLAST, OligoAnalyzer, Ambion siRNA finder EMBOSS, Mobyle, Expasy PDB, Yasara GO, AmiGO, QuickGO, KEGG, STRING, DAVID, TopGene, EnrichR, WebGestalt, Cytoscape GEO, GEO2R, GEO DataSet Browser OMIM, Variant reporter, Genomic variation server BioGPS and Biomart 2017-03-10 09:30:00 UTC 2017-03-24 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010
Basic statistics in R
19 - 26 May 2017
Leuven, BelgiumBasic statistics in R http://www.vib.be/en/training/research-training/courses/Pages/Introduction-to-R.aspx https://tess.elixir-europe.org/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 2017-05-26 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010
Electronic Lab Notebook Introduction - Ghent
16 Mar 2017
Ghent, BelgiumElectronic Lab Notebook Introduction - Ghent http://www.vib.be/en/training/research-training/courses/Pages/Electronic-Lab-Notebook-Introduction---Ghent.aspx https://tess.elixir-europe.org/events/electronic-lab-notebook-introduction-ghent 2017-03-16 14:00:00 UTC 2017-03-16 16:00:00 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
RNA-Seq analysis for differential expression in Genepattern
08 May 2017
Leuven, BelgiumRNA-Seq analysis for differential expression in Genepattern http://www.vib.be/en/training/research-training/courses/Pages/RNA-Seq-analysis-for-differential-expression.aspx https://tess.elixir-europe.org/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
Introduction to the analysis of NGS data
21 Apr 2017
Leuven, BelgiumIntroduction to the analysis of NGS data http://www.vib.be/en/training/research-training/courses/Pages/Introduction-to-the-analysis-of-NGS-data.aspx https://tess.elixir-europe.org/events/introduction-to-the-analysis-of-ngs-data This training is an introduction to a series of trainings on the analysis of Next Generation Sequencing data. This training is intended for newbies to the field and will teach them all background knowledge required to successfully complete the advanced NGS analysis trainings. To this end the training will give an overview of: - The Illumina platform - NGS data formats and file handling - Quality control of NGS data - Assembly and mapping of NGS data - Supporting IT: Galaxy and GenePattern platform This training is an introduction to 'Hands on introduction to ChIP-Seq analysis', Hands-on introduction to NGS variant analysis', 'GATK training', and 'RNA-Seq analysis for differential expression in GenePattern'. If you want to follow one of these trainings but you have no experience with NGS data you should follow this introduction. 2017-04-21 09:30:00 UTC 2017-04-21 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010
Prep course for Biopython
31 Mar 2017
Leuven, BelgiumPrep course for Biopython http://www.vib.be/en/training/research-training/courses/Pages/Prep-course-for-Biopython.aspx https://tess.elixir-europe.org/events/prep-course-for-biopython This training is an introduction to the Biopython training. This training is intended for people who have no experience with Linux and will teach them all knowledge of Linux command line that is required to successfully follow the Biopython training. If you want to follow the Biopython training and you have no experience with Linux command line, you have to follow this introduction. 2017-03-31 09:30:00 UTC 2017-03-31 17:00:00 UTC VIB Bioinformatics Core O&N4 room 06.239 Gasthuisberg, Leuven, Belgium O&N4 room 06.239 Gasthuisberg Leuven Belgium 3000