Provider of Bioinformatics and software training, plus informatics services and resource management support.
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
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...
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
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
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
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 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...
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...
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....
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...
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
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,...
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 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...
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
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...
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
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
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
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
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
- 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: RNA-Seq
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...
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
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
The morning session will give you an overview of the possibilities of Genevestigator, a search engine of curated and normalized publicly available gene expression data. The interface allows you to visualize spatio-temporal (tissue - developmental stage) and perturbational gene expression...
Scientific topics: Gene expression analysis, Gene expression, Biomarkers
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...
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...
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
Data Carpentry June 2018
12 - 13 June 2018
Brussels, BelgiumData Carpentry June 2018 http://www.vib.be/en/training/research-training/courses/Pages/Data-Carpentry-June-2018.aspx https://tess.elixir-europe.org/events/data-carpentry-june-2018 2018-06-12 09:30:00 UTC 2018-06-13 17:00:00 UTC ELIXIR Belgium Brussels, Belgium Brussels Belgium 1050      
Electronic Lab Notebook Introduction - Ghent
23 May 2018
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 2018-05-23 10:00:00 UTC 2018-05-23 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      
Git for Humans
20 June 2018
Heverlee, BelgiumGit for Humans http://www.vib.be/en/training/research-training/courses/Pages/Elixir-git_versioncontrol_Leuven.aspx https://tess.elixir-europe.org/events/git-for-humans-ef1cd0f7-1779-4f7f-9db5-b57336debc0a 2018-06-20 13:00:00 UTC 2018-06-20 16:30:00 UTC ELIXIR Belgium Heverlee Campus. Dept. of Electrical Engineering (ESAT), room B01.35, Heverlee, Belgium Heverlee Campus. Dept. of Electrical Engineering (ESAT), room B01.35 Heverlee Belgium 3001      
Git for humans
25 June 2018
Gent, BelgiumGit for humans http://www.vib.be/en/training/research-training/courses/Pages/Elixir-git_versioncontrol_June_Ghent.aspx https://tess.elixir-europe.org/events/git-for-humans 2018-06-25 09:30:00 UTC 2018-06-25 12:30:00 UTC ELIXIR Belgium Campus: Boekentoren/Book Tower Room: Didacticum, Gent, Belgium Campus: Boekentoren/Book Tower Room: Didacticum Gent Belgium 9000      
qPCR analysis using qbasePLUS
10 September 2018
Gent, BelgiumqPCR analysis using qbasePLUS http://www.vib.be/en/training/research-training/courses/Pages/qPCR-analysis-using-qbasePLUS.aspx https://tess.elixir-europe.org/events/qpcr-analysis-using-qbaseplus 2018-09-10 09:30:00 UTC 2018-09-10 16:30:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052      
Basic statistics in R, part II
25 - 1 June 2018
Gent, BelgiumBasic statistics in R, part II http://www.vib.be/en/training/research-training/courses/Pages/Basic-statistics-in-R,-part-II.aspx https://tess.elixir-europe.org/events/basic-statistics-in-r-part-ii 2018-06-25 09:30:00 UTC 2018-06-01 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052      
Basic statistics theory
29 May 2018
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 2018-05-29 09:30:00 UTC 2018-05-29 16:30:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010      
Electronic Lab Notebook Introduction - Leuven
24 May 2018
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 researchers 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://storefront.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! 2018-05-24 09:30:00 UTC 2018-05-24 11:30:00 UTC VIB Bioinformatics Core O&N4 room 06.239 Campus Gasthuisberg, Leuven, Belgium O&N4 room 06.239 Campus Gasthuisberg Leuven Belgium 3000      
A tour of machine learning - classification
12 June 2018
Ghent, BelgiumA tour of machine learning - classification http://www.vib.be/en/training/research-training/courses/Pages/A-tour-of-machine-learning---classification.aspx https://tess.elixir-europe.org/events/a-tour-of-machine-learning-classification ok Python Numpy/Pandas 2018-06-12 09:30:00 UTC 2018-06-12 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Ghent, Belgium Bio-Accelerator Ghent Belgium 9052      
Transcriptomics and Single Cell RNA-Seq Analysis
26 - 31 August 2018
Leuven, BelgiumTranscriptomics and Single Cell RNA-Seq Analysis http://www.vib.be/en/training/research-training/courses/Pages/Transcrptomics-and-Single-Cell-RNA-Seq-Analysis.aspx https://tess.elixir-europe.org/events/transcriptomics-and-single-cell-rna-seq-analysis-c68d0326-09c8-41a4-90d9-c38feeab6d45 2018-08-26 09:30:00 UTC 2018-08-31 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
4 - 18 June 2018
Gent, 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) During this 3-day introduction to bioinformatics, we 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 any basic bioinformatics problem: how to obtain relevant information about your gene, you know where to get the required sequence data, manipulate the sequences, and how basic software and algorithms function so you can fine-tune them in order the get the most out of your analysis. 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, ToppGene, EnrichR, WebGestalt, Cytoscape GEO, GEO2R, GEO DataSet Browser OMIM, Variant reporter, Genomic variation server Biomart 2018-06-04 09:30:00 UTC 2018-06-18 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052      
Introduction to Galaxy
26 June 2018
Gent, BelgiumIntroduction to Galaxy http://www.vib.be/en/training/research-training/courses/Pages/ELIXIR-Introduction-to-Galaxy.aspx https://tess.elixir-europe.org/events/introduction-to-galaxy-16bfecc7-80c1-4541-897d-3bb9528ced2d 2018-06-26 09:30:00 UTC 2018-06-26 13:00:00 UTC ELIXIR Belgium Campus: Boekentoren/Book Tower Room: Didacticum, Gent, Belgium Campus: Boekentoren/Book Tower Room: Didacticum Gent Belgium 9000      
Public proteomics data reprocessing and the Tabloid Proteome
10 October 2018
Ghent, BelgiumPublic proteomics data reprocessing and the Tabloid Proteome http://www.vib.be/en/training/research-training/courses/Pages/Elixir-Tabloid-Proteome-Ghent.aspx https://tess.elixir-europe.org/events/public-proteomics-data-reprocessing-and-the-tabloid-proteome 2018-10-10 09:30:00 UTC 2018-10-10 17:00:00 UTC ELIXIR Belgium VIB-UGent Research Building LEAF room (E124) right side of the building, first floor, Ghent, Belgium VIB-UGent Research Building LEAF room (E124) right side of the building, first floor Ghent Belgium 9052      
ELIXIR-EXCELERATE Train the Trainer
20 - 21 August 2018
Antwerp, BelgiumELIXIR-EXCELERATE Train the Trainer https://www.eventbrite.com/e/elixir-excelerate-train-the-trainer-tickets-45758467809 https://tess.elixir-europe.org/events/elixir-excelerate-train-the-trainer-7d8246fe-4e5a-46bb-9144-62bfe8a56aa8 ELIXIR-EXCELERATE Train the Trainer (TtT) workshop 2018-08-20 09:00:00 UTC 2018-08-21 17:00:00 UTC ELIXIR Belgium University of Antwerp Building: G Room: G.004, Antwerp, Belgium University of Antwerp Building: G Room: G.004 Antwerp Belgium 2020