VIB Bioinformatics Training and Services

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

Showing 30 materials out of 47. View all results.

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 PhD students post-docs beginner bioinformaticians 2016-04-22 2017-03-28

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

Hands-on introduction to ChIP-Seq analysis https://tess.elixir-europe.org/materials/hands-on-introduction-to-chip-seq-analysis This training gives an introduction to ChIP-seq data analysis, covering the processing steps starting from the reads to the peaks. Among all possible downstream analyses, the practical aspect will focus on motif analyses. A particular emphasis will be put on deciding which downstream analyses to perform depending on the biological question. This training does not cover all methods available today. It does not aim at bringing users to a professional NGS analyst level but provides enough information to allow biologists understand what DNA sequencing practically is and to communicate with NGS experts for more in-depth needs. Mapping ChIP-seq beginner bioinformaticians post-docs PhD students Life Science Researchers 2016-04-22 2017-03-28

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 2017-03-28

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

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. Gene expression Biomarkers post-docs Life Science Researchers PhD students 2016-04-22 2017-03-28

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 post-docs Life Science Researchers PhD students 2016-04-22 2017-03-28

- 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

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.   Gene finding RNA-Seq post-docs Life Science Researchers PhD students 2016-04-22 2017-03-28

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

Hands-on introduction to NGS variant analysis https://tess.elixir-europe.org/materials/hands-on-introduction-to-ngs-variant-analysis This training gives an introduction to the use of popular NGS analysis software packages at the command line. It reviews several exchangeable tools and provide hints to evaluate quality and content of DNA-Seq data by a biologist.   This training does not cover all methods available today. It does not aim at bringing users to a professional NGS analyst level but provides enough information to allow biologists understand what DNA sequencing practically is and to communicate with NGS experts for more in-depth needs. DNA post-docs PhD students beginner bioinformaticians Life Science Researchers 2016-04-22 2017-03-28

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

Mass spectrometry data processing https://tess.elixir-europe.org/materials/mass-spectrometry-data-processing In this training session we start by reviewing the types of mass spectrometer, and what the properties of their output data are. Out of our understanding of the data, we learn to extract meaningful interpretations. Proteomics Mass spectrometry data, Proteomics, Spectral analysis post-docs Life Science Researchers PhD students 2016-04-22 2017-03-28

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...

Advanced statistics in R https://tess.elixir-europe.org/materials/advanced-statistics-in-r 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 much mathematical details. Emphasis will be placed on practical applications. To this end, theory will be complemented with hands-on exercises in R, a free software environment for statistical computing and graphics. Topics include distributions, basic plots, confidence intervals, hypothesis testing... post-docs PhD students Life Science Researchers 2016-04-22 2017-03-02

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...

Analysis of Affymetrix microarray data using Bioconductor https://tess.elixir-europe.org/materials/analysis-of-affymetrix-microarray-data-using-bioconductor 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 microarray analysis. Participants can use their own data during the training as long as the design of the experiment is similar to those used in the training e.g. comparison of two or multiple groups of samples. Life Science Researchers PhD students post-docs beginner bioinformaticians 2016-04-22 2016-06-15

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. PhD students post-docs Life Science Researchers 2016-04-22 2017-03-28

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

Analysis of qPCR data using qbase+ https://tess.elixir-europe.org/materials/analysis-of-qpcr-data-using-qbase This hands-on training provides an introduction to the analysis of qPCR data using Biogazelle's qbase+ software. Although this software allows to do various types of analyses (gene expression, copy number analysis, miRNA profiling), we will focus in the training on gene expression analysis. qbase+ software is freely distributed by BITS to VIB scientists. Therefore the training will be limited to VIB scientists. PCR experiment Gene expression Gene expression data analysis, Gene expression, PCR experiment Life Science Researchers PhD students post-docs 2016-04-22 2017-03-28

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 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...

Basic statistics in R, part II https://tess.elixir-europe.org/materials/basic-statistics-in-r-part-ii This training builds further on the Basic statistics in R training, showing you how to do statistical analyses in R. Where the Basic statistics in R training is an introduction to the use of R and RStudio and stops at very basic analyses (t-tests and non-parametric equivalents), this training gives you a full overview of statistical analyses in R including regression, ANOVA... Emphasis will be placed on practical applications. To this end, theory will be complemented with hands-on exercises in R, a free software environment for statistical computing and graphics. Topics include distributions, plots, confidence intervals, hypothesis testing... Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-03-28

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

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. Information retrieval Life Science Researchers beginner bioinformaticians post-docs PhD students 2016-04-22 2017-03-28

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

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...

Cloning with SnapGene https://tess.elixir-europe.org/materials/cloning-with-snapgene You will acquire the basic techniques that are used in recombinant DNA technology, particularly restriction enzymes, modification enzymes, polymerase chain reaction (PCR), plasmids (different vectors, mechanism to select and detect), site directed mutagenesis, heterologous gene expression in prokaryotes/eukaryotes. You will be able to use a cloning program like CLC Bio Main Workbench or SnapGene. post-docs Life Science Researchers PhD students 2016-04-22 2017-03-28

This course presents a comprehensive overview of the principles and applications of comparative genomics in eukaryotes. The course combines lectures with hands-on exercises.

Comparative genomics in eukaryotes https://tess.elixir-europe.org/materials/comparative-genomics-in-eukaryotes This course presents a comprehensive overview of the principles and applications of comparative genomics in eukaryotes. The course combines lectures with hands-on exercises. PhD students post-docs Life Science Researchers 2016-04-22 2017-03-28

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...

Creating scientific publications in LaTeX https://tess.elixir-europe.org/materials/creating-scientific-publications-in-latex 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 and time-consuming steps in publishing e.g. manage and format references, figures, tables, equations... Many journals and conferences provide LaTeX style files for easy and correct submission. Life Science Researchers PhD students post-docs 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

​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

GATK Best practices for variant discovery https://tess.elixir-europe.org/materials/gatk-best-practices-for-variant-discovery ​In the course of this workshop, we highlight key functionalities such as  GVCF workflow for joint variant discovery in cohorts RNAseq-specific processing somatic variant discovery using MuTect2.  capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery the use of pipelining tools to assemble and execute GATK workflows. Mapping RNA-Seq Life Science Researchers post-docs beginner bioinformaticians PhD students 2016-04-22 2017-03-28

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 2016-06-15

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 post-docs Life Science Researchers PhD students beginner bioinformaticians 2016-04-22 2017-03-28

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

Introduction to Affymetrix microarray analysis https://tess.elixir-europe.org/materials/introduction-to-affymetrix-microarray-analysis Following this training is a prerequisite to the training on the analysis of Affymetrix microarray data using free Affymetrix software. If you want to follow this training, you have to follow this introduction first. If you want to follow the Genevestigator training or the training on the analysis of public microarray data sets and you have no experience with microarrays, you can also follow this introduction or consult the training material of this introduction. Gene expression Life Science Researchers PhD students post-docs 2016-04-22 2017-03-28

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

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. Sequence annotation PhD students Life Science Researchers post-docs 2016-04-22 2017-03-28

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 2017-03-28

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

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

RNA-Seq analysis for differential expression https://tess.elixir-europe.org/materials/rna-seq-analysis-for-differential-expression We first perform quality control of the sequence reads to detect biases or leftover adaptors. We then map the reads to the reference genome with use of a transcript database model. We perform a detailed QC analysis of the mapping results to again detect potential problems. The mapping data is adjusted to compensate for artifacts like duplicates. The mappings are used to obtain transcript counts usable for differential expression. The count tables are merged and used to compute differential expression using several programs. We START a typical functional analysis of the obtained results similar to what is done for microarray data in order to exemplify handy tools and commercial alternatives. The code pieces used during the training are made available through our Wiki as well as detailed results and can be copied and adapted for own user needs with minimal edits. Key results have been saved to our server and can be downloaded to fully reproduce the training. RNA-Seq Gene expression post-docs beginner bioinformaticians Life Science Researchers PhD students 2016-04-22 2017-03-28

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

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 Text mining post-docs Life Science Researchers PhD students 2016-04-22 2017-03-28
Showing 12 upcoming events. Found 9 past events. View all results.
  • Protein Structure Analysis

    12 May 2017

    Genth, Belgium

    Protein Structure Analysis 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
  • Basic statistics theory

    18 Apr 2017

    Leuven, Belgium

    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 2017-04-18 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
  • Initiation GIMP and Inkscape Leuven

    04 May 2017

    Leuven, Belgium

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

    18 - 25 Sep 2017

    Leuven, Belgium

    Gentle hands-on introduction to Python programming https://tess.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
  • Introduction to Biopython

    13 - 14 Apr 2017

    Ghent, Belgium

    Introduction to Biopython 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
  • Analyzing flow cytometry data using FlowJo

    24 Apr 2017

    Gent (Sint-Denijs-Westrem), Belgium

    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 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
  • Initiation GIMP and Inkscape Ghent

    02 May 2017

    Ghent, Belgium

    Initiation GIMP and Inkscape Ghent 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
  • Introduction to the analysis of NGS data

    21 Apr 2017

    Leuven, Belgium

    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.  2017-04-21 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
  • RNA-Seq analysis for differential expression in Genepattern

    08 May 2017

    Leuven, Belgium

    RNA-Seq analysis for differential expression in Genepattern 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
  • Prep course for Biopython

    31 Mar 2017

    Leuven, Belgium

    Prep course for Biopython 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
  • Basic statistics in R

    19 - 26 May 2017

    Leuven, Belgium

    Basic statistics in R 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
  • Introductory statistics in GraphPad Prism

    06 Jun 2017

    Leuven, Belgium

    Introductory statistics in GraphPad Prism 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
changed User to: 64
scraper updated VIB Bioinformatics Training and Services at 2016-10-18 08:55:47 UTC.
scraper updated VIB Bioinformatics Training and Services at 2016-10-14 03:00:21 UTC.
scraper updated VIB Bioinformatics Training and Services at 2016-10-13 03:00:21 UTC.
scraper updated VIB Bioinformatics Training and Services at 2016-10-12 03:00:20 UTC.
scraper updated VIB Bioinformatics Training and Services at 2016-10-11 03:00:14 UTC.
scraper updated VIB Bioinformatics Training and Services at 2016-10-10 12:19:53 UTC.
scraper updated VIB Bioinformatics Training and Services at 2016-10-10 09:47:09 UTC.
scraper updated VIB Bioinformatics Training and Services at 2016-10-10 09:44:36 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-10-05 03:00:22 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-10-04 03:00:20 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-10-03 03:00:18 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-10-02 03:00:22 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-10-01 03:00:15 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-30 03:00:14 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-29 03:00:22 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-28 03:00:20 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-27 03:00:17 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-26 03:00:22 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-25 03:00:17 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-24 03:00:16 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-23 03:00:21 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-22 16:45:23 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-22 03:00:22 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-21 03:00:17 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-20 03:00:17 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-19 03:00:22 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-18 03:00:21 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-17 03:00:16 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-16 03:00:17 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-15 03:00:18 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-14 03:00:16 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-13 14:22:55 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-13 03:00:15 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-12 14:54:47 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-12 03:00:16 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-11 03:00:15 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-10 03:00:16 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-09 03:00:15 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-08 03:00:21 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-07 03:00:19 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-06 03:00:16 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-05 03:00:15 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-04 03:00:15 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-03 03:00:16 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-02 03:00:16 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-09-01 03:00:17 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-31 14:19:56 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-31 03:00:16 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-30 03:00:15 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-29 03:00:21 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-28 03:00:15 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-27 03:00:15 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-26 03:00:16 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-25 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-24 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-23 03:00:12 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-22 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-21 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-20 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-19 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-18 13:51:16 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-18 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-17 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-16 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-15 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-14 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-13 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-12 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-11 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-10 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-09 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-08 03:00:12 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-07 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-06 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-05 03:00:13 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-04 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-03 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-02 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-08-01 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-31 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-30 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-29 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-28 03:00:13 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-27 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-26 03:00:12 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-25 03:00:11 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-24 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-23 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-22 03:00:10 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-21 16:13:30 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-21 15:58:42 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-21 15:58:17 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-18 16:00:07 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-11 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-10 03:00:05 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-09 03:00:05 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-08 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-07 03:00:05 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-06 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-05 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-04 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-03 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-02 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-07-01 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-30 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-29 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-28 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-27 03:00:05 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-26 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-25 03:00:05 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-24 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-23 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-22 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-21 03:00:04 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-20 16:24:17 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-15 17:01:13 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-15 17:00:12 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-15 16:59:56 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-15 16:59:25 UTC.
scraper updated VIB Bioinformatics Training and Services at 2016-06-15 07:09:35 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-14 17:43:25 UTC.
milo updated VIB Bioinformatics Training and Services at 2016-06-13 10:46:03 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-10 16:29:48 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-10 15:22:46 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-10 15:20:49 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-10 15:20:12 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-10 15:17:31 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-10 15:07:06 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-10 15:05:27 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-10 15:02:20 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-06-10 15:01:21 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-05-11 10:16:01 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-05-11 10:15:18 UTC.
niall updated VIB Bioinformatics Training and Services at 2016-05-10 12:45:20 UTC.
niall created VIB Bioinformatics Training and Services at 2016-05-10 12:42:49 UTC.