VIB Bioinformatics Core

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

Showing 30 materials out of 43. View all results.

- 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

Downstream processing of RNA-Seq data in GenePattern https://tess.elixir-europe.org/materials/downstream-processing-of-rna-seq-data-in-genepattern - Run RNA-seq downstream processing analyses in GenePattern, such as clustering, classification, GSEA... - Use GenePattern to save workflows, ensure reproducibility and share methodologies with colleagues and reviewers - Use the GenePattern Notebook environment to create documents that interleave formatted text, graphics and other multimedia, executable code, and GenePattern analyses, creating a single "research narrative" that puts scientific discussion and analyses in the same place Summary The workshop will cover the use of GenePattern for downstream processing of high-throughput mRNA sequencing (RNA-Seq) data produced by Illumina sequencing machines.  This workshop is intended for non-programming biologists. 1. Running Analyses in GenePattern 2. Clustering 3. Prediction and Clasification 4. Working with analysis workflows: GenePattern pipelines 5. Working with Samples and Features 6. The GenePattern Notebook environment 7. Related tools: IGV, GSEA 8. Open Q&A The data files, slides and exercises will be made available after the workshop.   RNA-Seq PhD students Life Science Researchers post-docs 2016-04-22 2017-07-27

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

UCSC Genome Browser https://tess.elixir-europe.org/materials/ucsc-genome-browser The UCSC Genome Browser provides a way to examine data from many genomes and includes extensive annotation tracks for various data types such as known UCSC (and Ensembl) genes, predicted genes, SNPs, miRNAs, comparative multi-species analysis and much more. During this training you will learn how to navigate this vital tool for your research. Required skills No specific prior knowledge is required.  BITS provides 15 laptops for their training sessions. Depending on the number of participants (max 20), it is possible that you have to share the laptop with one other participant but you can also choose to bring your own laptop for this training session. PhD students Life Science Researchers post-docs 2016-04-22 2017-07-27

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.elixir-europe.org/materials/analysis-of-public-microarray-data-sets This training will give you an overview of what GEO has to offer. Several experiments will be analyzed using simple tools to obtain differential gene lists. An introduction to downstream tools dedicated to functional enrichment will close the session. post-docs Life Science Researchers PhD students 2016-04-22 2017-07-27

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.elixir-europe.org/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 2017-07-27

This training gives an introduction to the use of statistics for basic analyses of life sciences data. The theoretical background obtained in the Basic statistics theory training  will be applied in a hands-on session on real-life data using the statistical software GraphPad...

Introductory statistics in GraphPad Prism https://tess.elixir-europe.org/materials/introductory-statistics-in-graphpad-prism This training gives an introduction to the use of statistics for basic analyses of life sciences data. The theoretical background obtained in the Basic statistics theory training  will be applied in a hands-on session on real-life data using the statistical software GraphPad Prism. BITS distributes the software for free to VIB scientists, for more information you can visit the GraphPad Prism page on the BITS web site. This is the reason why the training is limited to VIB scientists. post-docs Life Science Researchers PhD students 2016-04-22 2017-07-27

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

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

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

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

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

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

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

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

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.elixir-europe.org/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. Life Science Researchers PhD students post-docs 2016-04-22 2017-07-27

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

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

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

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

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

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

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

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 - Leuven https://tess.elixir-europe.org/materials/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, advanced searching, printing, tips and tricks Life Science Researchers PhD students post-docs 2016-04-22 2016-06-15

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...

Initiation GIMP and Inkscape - Leuven https://tess.elixir-europe.org/materials/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 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 Life Science Researchers PhD students post-docs 2016-04-22 2016-06-15

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

Custom training: Ingenuity Pathway Analysis https://tess.elixir-europe.org/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 Proteomics Protein interactions Metabolomics Life Science Researchers post-docs PhD students 2016-04-22 2016-09-26

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.elixir-europe.org/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 SVG Life Science Researchers post-docs 2017-07-27

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.elixir-europe.org/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. post-docs PhD students beginner bioinformaticians Life Science Researchers 2016-04-22 2016-08-31

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.elixir-europe.org/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 post-docs Life Science Researchers PhD students 2016-04-22 2017-07-27

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

Introduction to Biopython https://tess.elixir-europe.org/materials/introduction-to-biopython-8ccf2441-bd7d-46f2-84f8-c2b123844a23 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 us, 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. Software engineering Life Science Researchers post-docs PhD students beginner bioinformaticians 2016-04-22 2017-07-27

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

Keywords: Workflows, Sequence trace format, Sequence feature annotation format, Sequence assembly

Introduction to the analysis of NGS data https://tess.elixir-europe.org/materials/introduction-to-the-analysis-of-ngs-data This training is a prerequisite introduction to a series of trainings on the analysis of NGS data for different applications: 'Hands-on introduction to NGS variant analysis', 'RNA-Seq analysis for differential expression', and 'Hands-on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings, you have to follow this introduction. The training will give you all the background that you will need in the later NGS trainings. Workflows Sequence assembly Workflows, Sequence trace format, Sequence feature annotation format, Sequence assembly Life Science Researchers PhD students post-docs 2016-04-22 2017-07-27

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.elixir-europe.org/materials/basic-statistics-in-r This training gives an introduction to the use of the statistical software language R. R is a language for data analysis and graphics. This introduction to R is aimed at beginners. The training covers data handling, graphics, mathematical functions and some statistical techniques. R is for free and for more information you can visit the site at the CRAN web site. This training is an introduction to the use of R and RStudio and stops at very basic analyses (t-tests and non-parametric equivalents). A full overview of statistical analyses in R including regression, ANOVA will be given in the follow-up training Basic statistics in R, part II Life Science Researchers PhD students post-docs 2016-04-22 2017-07-27

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

Basics of databases and MySQL https://tess.elixir-europe.org/materials/basics-of-databases-and-mysql This hands-on training provides a comprehensive introduction to relational databases and the use of the MySQL relational database management system. MySQL is the leading free management system for relational databases. The training shows you how to use MySQL to efficiently store your data in databases and manage both data and access to the data. The training gives an overview of the SQL syntax that allows you to access and manipulate the data. Additionally, the use of Python to automatically access MySQL databases is explained. beginner bioinformaticians Life Science Researchers post-docs PhD students 2016-04-22 2017-07-27

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

Gentle hands-on introduction to Perl programming https://tess.elixir-europe.org/materials/gentle-hands-on-introduction-to-perl-programming This course is organised over two full days. With this extensive hands-on session, we introduce you Perl. The first day,we will cover the basics of Perl programming: what is a variable, different types, how to assign values to variable, what can you do with them, strings, arrays and hashes. Logic statements will be discussed, Everything will be demonstrated with step by step exercises. At the end of the day, you will be send home with some challenges to do yourself and additional learning material. As a homework, you may write a program to analyze your own data. On the second day of the training, we will look to the solutions of the homework and explain the results of the tasks. We will dig a little deeper in good programming hygiene, and create some more complex scripts using regexes and reading in files. By the end of the day, a firm basis for perl programming should be established to allow further self-study. Life Science Researchers PhD students post-docs beginner bioinformaticians 2016-04-22 2017-07-27

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

Scientific topics: Protein structure analysis

Protein Structure Analysis https://tess.elixir-europe.org/materials/protein-structure-analysis This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure. Different hands-on exercises will allow you to compare the structure of homologues, to predict a structural model of proteins without any structure information and to find homologuous structures. We will use the FoldX program to quantify various interactions in the structures. Protein structure analysis Life Science Researchers post-docs PhD students 2016-04-22 2017-07-27

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: Biomarkers, Gene expression, Gene expression analysis

Analysis of public microarray data using Genevestigator https://tess.elixir-europe.org/materials/analysis-of-public-microarray-data-using-genevestigator The morning session will give you an overview of the possibilities of Genevestigator, a search engine of curated and normalized publicly available gene expression data. The interface allows you to visualize spatio-temporal (tissue - developmental stage) and perturbational gene expression information of many species in a user-friendly graphical way. The afternoon session will focus on the practical applications in a hands-on tutorial on Genevestigator followed by concrete examples of software that can be used to further interpret the results of your Genevestigator searches, like Ingenuity Pathway Analysis and DAVID. Finally, you will be able to work on the questions that you want to answer in your own research under the supervision of the trainer. Participants are therefore encouraged to submit a description of the objectives of the analysis they want to perform. Biomarkers Gene expression Gene expression analysis post-docs PhD students Life Science Researchers 2016-04-22 2017-07-27

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

Basic bioinformatics concepts, databases and tools https://tess.elixir-europe.org/materials/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 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 it in order the get the most out of your analysis. Sequence analysis PhD students post-docs Life Science Researchers 2016-04-22 2017-07-27

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.elixir-europe.org/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 2017-07-27

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

Introduction to CLC Bio Main Workbench https://tess.elixir-europe.org/materials/introduction-to-clc-bio-main-workbench In this hands-on training you will learn how to use the CLC Bio Main Workbench for basic and advanced sequence analysis. The software supports a large number of DNA, RNA, and protein sequence analyses and microarray analysis. Since BITS provides a VIB-wide license to CLC Bio Main Workbench, this training is targeted specifically to VIB scientists. Local alignment Global alignment post-docs Life Science Researchers PhD students 2016-04-22 2017-07-27

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

Scientific topics: Software engineering

Gentle hands-on introduction to Python programming https://tess.elixir-europe.org/materials/gentle-hands-on-introduction-to-python-programming This course is organised over two full days. With the help of plenty hands-on exercises, you will get introduced into the different types of variables in python, the peculiarities of python and good programming habits. This course will provide you an ideal stepping stone for further developing programming skills in Python. Software engineering PhD students Life Science Researchers post-docs beginner bioinformaticians 2016-04-22 2017-07-27
Showing 17 upcoming events. Found 21 past events. View all results.
  • Basic statistics theory

    22 September 2017

    Leuven, Belgium

    Elixir node event
    Basic statistics theory 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 2017-09-22 09:30:00 UTC 2017-09-22 16:30:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] []
  • Introduction to gene regulation

    9 October 2017

    Gent, Belgium

    Elixir node event
    Introduction to gene regulation https://tess.elixir-europe.org/events/introduction-to-gene-regulation 2017-10-09 09:30:00 UTC 2017-10-09 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Gent, Belgium Bio-Accelerator Gent Belgium 9052 [] [] [] [] []
  • Analysis of public microarray data using Genevestigator

    24 November 2017

    Gent, Belgium

    Elixir node event
    Analysis of public microarray data using Genevestigator https://tess.elixir-europe.org/events/analysis-of-public-microarray-data-using-genevestigator 2017-11-24 09:30:00 UTC 2017-11-24 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Gent, Belgium Bio-Accelerator Gent Belgium 9052 [] [] [] [] []
  • Linux for bioinformatics

    20 - 27 November 2017

    Gent, Belgium

    Elixir node event
    Linux for bioinformatics https://tess.elixir-europe.org/events/linux-for-bioinformatics 2017-11-20 09:30:00 UTC 2017-11-27 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Gent, Belgium Bio-Accelerator Gent Belgium 9052 [] [] [] [] []
  • Advanced FlowJo training

    21 November 2017

    Gent (Sint-Denijs-Westrem), Belgium

    Elixir node event
    Advanced FlowJo training https://tess.elixir-europe.org/events/advanced-flowjo-training 2017-11-21 09:30:00 UTC 2017-11-21 17:00:00 UTC VIB Bioinformatics Core Holiday Inn Ghent Expo, Gent (Sint-Denijs-Westrem), Belgium Holiday Inn Ghent Expo Gent (Sint-Denijs-Westrem) Belgium 9051 [] [] [] [] []
  • Electronic Lab Notebook Introduction - Ghent

    27 September 2017

    Ghent, Belgium

    Elixir node event
    Electronic Lab Notebook Introduction - Ghent https://tess.elixir-europe.org/events/electronic-lab-notebook-introduction-ghent 2017-09-27 10:00:00 UTC 2017-09-27 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 [] [] [] [] []
  • Analyzing flow cytometry data using FlowJo

    16 October 2017

    Gent (Sint-Denijs-Westrem), Belgium

    Elixir node event
    Analyzing flow cytometry data using FlowJo 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 v10,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. 2017-10-16 09:30:00 UTC 2017-10-16 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 NGS variant analysis

    20 October 2017

    Leuven, Belgium

    Elixir node event
    Hands-On introduction to NGS variant analysis https://tess.elixir-europe.org/events/hands-on-introduction-to-ngs-variant-analysis Using a full publicly available chromosome read-set from one of the 1000 genome sample: 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. Skills required to follow this training include basic knowledge of Illumina NGS read structure. People who lack knowledge of Illumina reads should follow the 'Introduction to the analysis of NGS data' training. 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.​ ​similar workflow(s) using commercial products like the 'CLC genomics workbench' similar workflow(s) using the free Galaxy GUI (although perfectly doable using the acquired knowledge) variant analysis at multi-genome level & GWAS (<- advanced computing and statistical expertise required). structural variant analysis (large indels, translocations, CNV) as being too complex with no all-in-one tool available. ​​​​​​​​​​​​​ 2017-10-20 09:30:00 UTC 2017-10-20 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 - Leuven

    28 September 2017

    Leuven, Belgium

    Elixir node event
    Electronic Lab Notebook Introduction - Leuven 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! 2017-09-28 10:00:00 UTC 2017-09-28 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 [] [] [] [] []
  • Python for Data Processing

    5 - 6 October 2017

    Heverlee, Belgium

    Elixir node event
    Python for Data Processing https://tess.elixir-europe.org/events/python-for-data-processing 2017-10-05 09:30:00 UTC 2017-10-06 17:00:00 UTC VIB Bioinformatics Core ICTS Education Center KUL, Heverlee, Belgium ICTS Education Center KUL Heverlee Belgium 3001 [] [] [] [] []
  • Biomolecular data mining: a hands-on training

    11 - 13 September 2017

    Antwerpen, Belgium

    Elixir node event
    Biomolecular data mining: a hands-on training https://tess.elixir-europe.org/events/biomolecular-data-mining-a-hands-on-training This course aims to introduce the core principles and biomedical applications of different data mining and machine learning techniques in a hands-on manner. It will tackle both unsupervised (clustering, frequent pattern mining, data projection) and supervised (classification) techniques. The methods that will be seen include hierarchical clustering, k- means clustering, item set mining, association rule mining, principle component analysis, support vector machines, random forests, bayesian networks and artificial neural networks. Attendees will be introduced to the basic operations of these data mining techniques, with a focus on the practical use and interpretation of these procedures rather than the mathematical formulas. In addition, attendants will be introduced to some important data processing and performance evaluation methods related to these data mining techniques. The software used in this course will be R. The course itself will consist of 50% theory lessons, 40% hands-on practicals and 10% application case studies. Organised by biomina: Dr. Pieter Meysman Prof. dr. Kris Laukens 2017-09-11 09:00:00 UTC 2017-09-13 17:00:00 UTC biomina Antwerpen Groenenborgerlaan, Antwerpen, Belgium Antwerpen Groenenborgerlaan Antwerpen Antwerpen Belgium 2020 Biomedical science Machine learning Data mining University of Antwerp Dr. Pieter Meysman Prof. dr. Kris Laukens ELIXIR Belgium and Flemish Region PhD studentsPostDocs 30 workshops_and_courses registration_of_interest []
  • Gentle hands-on introduction to Python programming

    18 - 25 September 2017

    Leuven, Belgium

    Elixir node event
    Gentle hands-on introduction to Python programming https://tess.elixir-europe.org/events/gentle-hands-on-introduction-to-python-programming 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 [] [] [] [] []
  • Protein Structure Analysis

    17 November 2017

    Genth, Belgium

    Elixir node event
    Protein Structure Analysis https://tess.elixir-europe.org/events/protein-structure-analysis-f095d4f5-e03b-4b1d-9f38-38dff017174a 2017-11-17 09:30:00 UTC 2017-11-17 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Genth, Belgium BioAccelerator Genth Belgium 9052 [] [] [] [] []
  • Functional Plant Bioinformatics - PLAZA

    14 - 15 September 2017

    Ghent, Belgium

    Elixir node event
    Functional Plant Bioinformatics - PLAZA https://tess.elixir-europe.org/events/functional-plant-bioinformatics-plaza 2017-09-14 10:00:00 UTC 2017-09-15 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator Meeting Center, Ghent, Belgium Bio-Accelerator Meeting Center Ghent Belgium 9052 [] [] [] [] []
  • VIB Community Meeting - Bioinformatics and Computational Biology

    12 December 2017

    Brussels, Belgium

    Elixir node event
    VIB Community Meeting - Bioinformatics and Computational Biology 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 the second VIB Community Meeting on Bioinformatics and Computational Biology on 4 December 2017 in Brussels. In order to create a strong bioinformatician community, we would like to organise flash presentations of all PhD students and postdocs in the field of computational biology and bioinformatics. In those presentation (2 minutes) they would present themselves (who they are and what they do). The afternoon will be covered by two parallel sessions, 'NGS/single-cell' on the one hand and 'Developed@VIB' on the other hand. The day will be closed by a reception. A preliminary agenda for the meeting has to be confirmed yet. Program: TBD ​​​​​​ 2017-12-12 09:30:00 UTC 2017-12-12 16:00:00 UTC VIB Bioinformatics Core U-Residence, Brussels, Belgium U-Residence Brussels Belgium 1050 [] [] [] [] []
  • Introduction to the analysis of NGS data

    8 September 2017

    Leuven, Belgium

    Elixir node event
    Introduction to the analysis of NGS data 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.  2017-09-08 09:30:00 UTC 2017-09-08 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 September 2017

    Gent, Belgium

    Elixir node event
    Mass spectrometry data processing https://tess.elixir-europe.org/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 [] [] [] [] []
alexander.botzki@vib.be updated VIB Bioinformatics Core at 2017-04-22 10:14:55 UTC.
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alexander.botzki@vib.be updated VIB Bioinformatics Core at 2017-04-22 10:11:55 UTC.
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alexander.botzki@vib.be updated VIB Bioinformatics Core at 2017-04-22 10:10:35 UTC.
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scraper updated VIB Bioinformatics Core at 2016-10-18 08:55:47 UTC.
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niall updated VIB Bioinformatics Core at 2016-10-05 03:00:22 UTC.
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niall updated VIB Bioinformatics Core at 2016-09-22 16:45:23 UTC.
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niall updated VIB Bioinformatics Core at 2016-09-20 03:00:17 UTC.
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niall updated VIB Bioinformatics Core at 2016-09-18 03:00:21 UTC.
niall updated VIB Bioinformatics Core at 2016-09-17 03:00:16 UTC.
niall updated VIB Bioinformatics Core at 2016-09-16 03:00:17 UTC.
niall updated VIB Bioinformatics Core at 2016-09-15 03:00:18 UTC.
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niall updated VIB Bioinformatics Core at 2016-09-13 14:22:55 UTC.
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niall updated VIB Bioinformatics Core at 2016-09-12 14:54:47 UTC.
niall updated VIB Bioinformatics Core at 2016-09-12 03:00:16 UTC.
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niall updated VIB Bioinformatics Core at 2016-09-05 03:00:15 UTC.
niall updated VIB Bioinformatics Core at 2016-09-04 03:00:15 UTC.
niall updated VIB Bioinformatics Core at 2016-09-03 03:00:16 UTC.
niall updated VIB Bioinformatics Core at 2016-09-02 03:00:16 UTC.
niall updated VIB Bioinformatics Core at 2016-09-01 03:00:17 UTC.
niall updated VIB Bioinformatics Core at 2016-08-31 14:19:56 UTC.
niall updated VIB Bioinformatics Core at 2016-08-31 03:00:16 UTC.
niall updated VIB Bioinformatics Core at 2016-08-30 03:00:15 UTC.
niall updated VIB Bioinformatics Core at 2016-08-29 03:00:21 UTC.
niall updated VIB Bioinformatics Core at 2016-08-28 03:00:15 UTC.
niall updated VIB Bioinformatics Core at 2016-08-27 03:00:15 UTC.
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niall updated VIB Bioinformatics Core at 2016-08-20 03:00:11 UTC.
niall updated VIB Bioinformatics Core at 2016-08-19 03:00:11 UTC.
niall updated VIB Bioinformatics Core at 2016-08-18 13:51:16 UTC.
niall updated VIB Bioinformatics Core at 2016-08-18 03:00:11 UTC.
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niall updated VIB Bioinformatics Core at 2016-08-10 03:00:10 UTC.
niall updated VIB Bioinformatics Core at 2016-08-09 03:00:10 UTC.
niall updated VIB Bioinformatics Core at 2016-08-08 03:00:12 UTC.
niall updated VIB Bioinformatics Core at 2016-08-07 03:00:11 UTC.
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niall updated VIB Bioinformatics Core at 2016-08-05 03:00:13 UTC.
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niall updated VIB Bioinformatics Core at 2016-08-03 03:00:11 UTC.
niall updated VIB Bioinformatics Core at 2016-08-02 03:00:11 UTC.
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niall updated VIB Bioinformatics Core at 2016-07-31 03:00:11 UTC.
niall updated VIB Bioinformatics Core at 2016-07-30 03:00:10 UTC.
niall updated VIB Bioinformatics Core at 2016-07-29 03:00:11 UTC.
niall updated VIB Bioinformatics Core at 2016-07-28 03:00:13 UTC.
niall updated VIB Bioinformatics Core at 2016-07-27 03:00:10 UTC.
niall updated VIB Bioinformatics Core at 2016-07-26 03:00:12 UTC.
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niall updated VIB Bioinformatics Core at 2016-07-03 03:00:04 UTC.
niall updated VIB Bioinformatics Core at 2016-07-02 03:00:04 UTC.
niall updated VIB Bioinformatics Core at 2016-07-01 03:00:04 UTC.
niall updated VIB Bioinformatics Core at 2016-06-30 03:00:04 UTC.
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niall updated VIB Bioinformatics Core at 2016-06-28 03:00:04 UTC.
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niall updated VIB Bioinformatics Core at 2016-06-24 03:00:04 UTC.
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niall updated VIB Bioinformatics Core at 2016-06-21 03:00:04 UTC.
niall updated VIB Bioinformatics Core at 2016-06-20 16:24:17 UTC.
niall updated VIB Bioinformatics Core at 2016-06-15 17:01:13 UTC.
niall updated VIB Bioinformatics Core at 2016-06-15 17:00:12 UTC.
niall updated VIB Bioinformatics Core at 2016-06-15 16:59:56 UTC.
niall updated VIB Bioinformatics Core at 2016-06-15 16:59:25 UTC.
scraper updated VIB Bioinformatics Core at 2016-06-15 07:09:35 UTC.
niall updated VIB Bioinformatics Core at 2016-06-14 17:43:25 UTC.
milo updated VIB Bioinformatics Core at 2016-06-13 10:46:03 UTC.
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niall updated VIB Bioinformatics Core at 2016-05-10 12:45:20 UTC.
niall created VIB Bioinformatics Core at 2016-05-10 12:42:49 UTC.