VIB Bioinformatics Training and Services

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

VIB Bioinformatics Training and Services https://tess.oerc.ox.ac.uk/content_providers/vib-bioinformatics-training-and-services Provider of Bioinformatics and software training, plus informatics services and resource management support. /system/content_providers/images/000/000/015/original/BITS_website.jpg?1474561988
Showing 30 materials out of 43. View all results.

Initiation GIMP and Inkscape - Leuven from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/321-gimp-inkscape-leuven.

Initiation GIMP and Inkscape - Leuven https://tess.oerc.ox.ac.uk/materials/initiation-gimp-and-inkscape-leuven Initiation GIMP and Inkscape - Leuven from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/321-gimp-inkscape-leuven. 2016-04-19

Electronic Lab Notebook Introduction - Leuven from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/297-intro-eln-leuven.

Electronic Lab Notebook Introduction - Leuven https://tess.oerc.ox.ac.uk/materials/electronic-lab-notebook-introduction-leuven Electronic Lab Notebook Introduction - Leuven from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/297-intro-eln-leuven. 2016-04-14

Electronic Lab Notebook Introduction - Ghent from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/296-intro-eln-ghent.

Electronic Lab Notebook Introduction - Ghent https://tess.oerc.ox.ac.uk/materials/electronic-lab-notebook-introduction-ghent Electronic Lab Notebook Introduction - Ghent from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/296-intro-eln-ghent. 2016-04-19

Custom training: Spotfire from https://www.bits.vib.be/training/training/110-bits/training/custom-trainings/279-custom-training-spotfire.

Custom training: Spotfire https://tess.oerc.ox.ac.uk/materials/custom-training-spotfire Custom training: Spotfire from https://www.bits.vib.be/training/training/110-bits/training/custom-trainings/279-custom-training-spotfire. 2016-04-16

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: Gene expression analysis, Gene expression, PCR experiment

Analysis of qPCR data using qbase+ https://tess.oerc.ox.ac.uk/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. Gene expression analysis Gene expression PCR experiment Life Science Researchers post-docs PhD students 2016-04-22 2017-09-19

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.oerc.ox.ac.uk/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 2017-09-19

You will acquire the basic techniques that are used in recombinant DNA technology, particularly restriction enzymes, modification enzymes, polymerase chain reaction (PCR), plasmids (different vectors, mechanism to select and detect), site directed mutagenesis, heterologous gene expression in...

Scientific topics: Gene expression analysis

Cloning with SnapGene https://tess.oerc.ox.ac.uk/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. Gene expression analysis Life Science Researchers post-docs PhD students 2016-04-22 2017-09-19

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.oerc.ox.ac.uk/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 Life Science Researchers post-docs PhD students beginner bioinformaticians 2016-04-22 2017-09-19

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

Mass spectrometry data processing https://tess.oerc.ox.ac.uk/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 post-docs PhD students Life Science Researchers 2016-04-22 2017-09-19

This training gives an introduction to the use of popular NGS analysis software packages at the command line. It reviews several exchangeable tools and provide hints to evaluate quality and content of DNA-Seq data by a biologist.   This training does not cover all methods available today. It...

Scientific topics: DNA

Hands-on introduction to NGS variant analysis https://tess.oerc.ox.ac.uk/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 PhD students beginner bioinformaticians Life Science Researchers post-docs 2016-04-22 2017-09-19

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.oerc.ox.ac.uk/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. Life Science Researchers post-docs PhD students 2016-04-22 2017-04-14

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: Global alignment, Local alignment

Introduction to CLC Bio Main Workbench https://tess.oerc.ox.ac.uk/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. Global alignment Local alignment PhD students Life Science Researchers post-docs 2016-04-22 2017-09-19

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.oerc.ox.ac.uk/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. Life Science Researchers beginner bioinformaticians PhD students post-docs 2016-04-22 2016-08-18

Initiation GIMP and Inkscape from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/316-gimp-inkscape.

Scientific topics: Data governance, Data management

Initiation GIMP and Inkscape https://tess.oerc.ox.ac.uk/materials/initiation-gimp-and-inkscape Initiation GIMP and Inkscape from https://www.bits.vib.be/training/training/112-bits/training/upcoming-trainings/316-gimp-inkscape. Data governance Data management 2016-04-08

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.oerc.ox.ac.uk/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 2017-09-19

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.oerc.ox.ac.uk/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. post-docs PhD students Life Science Researchers 2016-04-22 2017-09-19

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, Metabolomics, Protein interactions, Proteomics

Custom training: Ingenuity Pathway Analysis https://tess.oerc.ox.ac.uk/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 Metabolomics Protein interactions Proteomics post-docs Life Science Researchers PhD students 2016-04-22 2016-09-26

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

Introduction to the analysis of NGS data https://tess.oerc.ox.ac.uk/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 Life Science Researchers PhD students post-docs 2016-04-22 2017-09-19

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.oerc.ox.ac.uk/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 PhD students post-docs Life Science Researchers 2016-04-22 2017-04-14

ÔÇïIn the course of this workshop, we highlight key functionalities such as  GVCF workflow for joint variant discovery in cohorts RNAseq-specific processing somatic variant discovery using MuTect2.  capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery the...

Scientific topics: RNA-Seq

GATK Best practices for variant discovery https://tess.oerc.ox.ac.uk/materials/gatk-best-practices-for-variant-discovery ÔÇïIn the course of this workshop, we highlight key functionalities such as  GVCF workflow for joint variant discovery in cohorts RNAseq-specific processing somatic variant discovery using MuTect2.  capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery the use of pipelining tools to assemble and execute GATK workflows. RNA-Seq Life Science Researchers PhD students post-docs beginner bioinformaticians 2016-04-22 2017-09-19

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.oerc.ox.ac.uk/materials/electronic-lab-notebook-introduction-ghent-769c35af-869d-4ace-b8aa-af6e0fc8c7b5 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 PhD students post-docs Life Science Researchers 2016-04-22 2017-01-05

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.oerc.ox.ac.uk/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 PhD students Life Science Researchers post-docs 2016-04-22 2017-09-19

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.oerc.ox.ac.uk/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... beginner bioinformaticians post-docs Life Science Researchers PhD students 2016-04-22 2017-09-19

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.oerc.ox.ac.uk/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 Life Science Researchers PhD students 2016-04-22 2017-03-02

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.oerc.ox.ac.uk/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. post-docs Life Science Researchers PhD students 2016-04-22 2017-09-19

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.oerc.ox.ac.uk/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 2017-09-19

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

Scientific topics: Molecular biology, Gene expression, Gene regulation

Introduction to gene regulation https://tess.oerc.ox.ac.uk/materials/introduction-to-gene-regulation This course presents a comprehensive overview of the principles and applications of studying eukaryotic gene regulation. The course combines lectures with hands-on exercises in which the participants learn to apply these principles to real data. The course will be based on freely available data and software. Molecular biology Gene expression Gene regulation Life Science Researchers PhD students post-docs 2016-04-22 2017-09-19

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.oerc.ox.ac.uk/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 PhD students post-docs Life Science Researchers 2016-04-22 2017-09-19

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.oerc.ox.ac.uk/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. 2017-09-19

We first perform quality control of the sequence reads to detect biases or leftover adaptors. We then map the reads to the reference genome with use of a transcript database model. We perform a detailed QC analysis of the mapping results to again detect potential problems. The mapping data is...

Scientific topics: RNA-Seq, Gene expression

RNA-Seq analysis for differential expression https://tess.oerc.ox.ac.uk/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 PhD students beginner bioinformaticians Life Science Researchers post-docs 2016-04-22 2017-09-19
Showing 17 upcoming events. Found 19 past events. View all results.
  • Protein Structure Analysis

    17 November 2017

    Genth, Belgium

    Elixir node event
    Protein Structure Analysis https://tess.oerc.ox.ac.uk/events/protein-structure-analysis-e2917b45-24e1-454f-92f8-1181f2189115 2017-11-17 09:30:00 UTC 2017-11-17 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Genth, Belgium BioAccelerator Genth 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.oerc.ox.ac.uk/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) Oost-Vlaanderen Belgium 9051 [] [] [] [] []
  • Electronic Lab Notebook Introduction - Ghent

    4 October 2017

    Ghent, Belgium

    Elixir node event
    Electronic Lab Notebook Introduction - Ghent https://tess.oerc.ox.ac.uk/events/electronic-lab-notebook-introduction-ghent 2017-10-04 10:00:00 UTC 2017-10-04 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 [] [] [] [] []
  • Introduction to Biopython

    29 - 30 March 2018

    Ghent, Belgium

    Elixir node event
    Introduction to Biopython https://tess.oerc.ox.ac.uk/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. 2018-03-29 09:30:00 UTC 2018-03-30 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Ghent, Belgium BioAccelerator Ghent Belgium 9052 [] [] [] [] []
  • Introductory statistics in GraphPad Prism

    12 January 2018

    Leuven, Belgium

    Elixir node event
    Introductory statistics in GraphPad Prism https://tess.oerc.ox.ac.uk/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...     2018-01-12 09:30:00 UTC 2018-01-12 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] []
  • Basic bioinformatics concepts, databases and tools

    9 - 23 February 2018

    Leuven, Belgium

    Elixir node event
    Basic bioinformatics concepts, databases and tools https://tess.oerc.ox.ac.uk/events/basic-bioinformatics-concepts-databases-and-tools Understand the capabilities and pitfalls of bioinformatics. Functioning of the most used bioinformatics algorithms and terms for reliable interpretation of the results. Navigate with confidence to numerous online data repositories. Know where to search for them. Basic analyses of single genes as well as groups of genes (gene lists) GenBank, SwissProt, RefSeq, Gene GQuery Ensembl Ugene BLAST, OrthoMCL, EMBOSS Needle, EMBOSS Water, Muscle, WebLogo, iceLogo HMMER, PSIBLAST, PROSITE, SMART, InterPro miRWalk, Pscan, Motiflab Primer3 PLUS, Primer BLAST, OligoAnalyzer, Ambion siRNA finder EMBOSS, Mobyle, Expasy PDB, Yasara GO, AmiGO, QuickGO, KEGG, STRING, DAVID, TopGene, EnrichR, WebGestalt, Cytoscape GEO, GEO2R, GEO DataSet Browser OMIM, Variant reporter, Genomic variation server BioGPS and Biomart ​​​​​​​​ 2018-02-09 09:30:00 UTC 2018-02-23 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] []
  • Advanced FlowJo training

    21 November 2017

    Gent (Sint-Denijs-Westrem), Belgium

    Elixir node event
    Advanced FlowJo training https://tess.oerc.ox.ac.uk/events/advanced-flowjo-training Participants must have experience with FlowJo. If you're new to the software you can attend our FlowJo introduction training​ first. ​ 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 [] [] [] [] []
  • Python for Data Processing

    5 - 6 October 2017

    Heverlee, Belgium

    Elixir node event
    Python for Data Processing https://tess.oerc.ox.ac.uk/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 [] [] [] [] []
  • VIB Community Meeting - Bioinformatics and Computational Biology

    12 December 2017

    Brussels, Belgium

    Elixir node event
    VIB Community Meeting - Bioinformatics and Computational Biology https://tess.oerc.ox.ac.uk/events/vib-community-meeting-bioinformatics-and-computational-biology Lennart Martens (VIB-UGent CompOmics) and Alexander Botzki (VIB Bioinformatics Core) are pleased to announce the second VIB Community Meeting on Bioinformatics and Computational Biology on Tuesday 12 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 presentations (max. 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 transcriptomics and Developed@VIB. The day will be closed by a reception. A preliminary agenda for the meeting can be found below. Program: Program_bioit_meeting.pdf ​​​​​​ 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 gene regulation

    9 October 2017

    Gent, Belgium

    Elixir node event
    Introduction to gene regulation https://tess.oerc.ox.ac.uk/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 [] [] [] [] []
  • Linux for bioinformatics

    20 - 27 November 2017

    Gent, Belgium

    Elixir node event
    Linux for bioinformatics https://tess.oerc.ox.ac.uk/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 [] [] [] [] []
  • Analysis of public microarray data using Genevestigator

    24 November 2017

    Gent, Belgium

    Elixir node event
    Analysis of public microarray data using Genevestigator https://tess.oerc.ox.ac.uk/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 [] [] [] [] []
  • Hands-On introduction to NGS variant analysis

    20 October 2017

    Leuven, Belgium

    Elixir node event
    Hands-On introduction to NGS variant analysis https://tess.oerc.ox.ac.uk/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 several popular NGS analysis software packages under the GenePattern Graphical interface. 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 unix operative system and the command-line approach.​ ​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 [] [] [] [] []
  • Basic statistics in R

    12 - 26 March 2018

    Leuven, Belgium

    Elixir node event
    Basic statistics in R https://tess.oerc.ox.ac.uk/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. 2018-03-12 09:30:00 UTC 2018-03-26 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] []
  • Fundamental data skills for data-driven research

    6 - 7 November 2017

    Brussels, Belgium

    Elixir node event
    Fundamental data skills for data-driven research https://tess.oerc.ox.ac.uk/events/fundamental-data-skills-for-data-driven-research 2017-11-06 09:30:00 UTC 2017-11-07 17:00:00 UTC VIB Bioinformatics Core Belgian Sciene Policy - BELSPO, Brussels, Belgium Belgian Sciene Policy - BELSPO Brussels Belgium 1050 [] [] [] [] []
  • Basic statistics theory

    22 September 2017

    Leuven, Belgium

    Elixir node event
    Basic statistics theory https://tess.oerc.ox.ac.uk/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 [] [] [] [] []
  • Electronic Lab Notebook Introduction - Leuven

    21 September 2017

    Leuven, Belgium

    Elixir node event
    Electronic Lab Notebook Introduction - Leuven https://tess.oerc.ox.ac.uk/events/electronic-lab-notebook-introduction-leuven This training is an introduction to the Electronic Laboratory Notebook (ELN) implemented at VIB. This training is intended for all new VIB researchers and will teach you the basic knowledge required to successfully document in ELN. The training consists of two parts: Introduction: Access​ ways to your notebook, ELN installation instructions and house rules, where to find documentation and get support Hands-on-demo: Creating notebooks/experiments, importing and exporting (MS Office) files, sharing data, using templates, advanced searching, printing, tips and tricks This training is mandatory for all new VIB co-workers and requires an active VIB account. In order to check your username and password, go to https://storefront.vib.be, if login fails send an e-mail to eln*Replace*With*At*Sign*vib.be. People who want to join this training can register here! 2017-09-21 10:00:00 UTC 2017-09-21 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 [] [] [] [] []
niall updated VIB Bioinformatics Training and Services at 2017-04-26 10:48:12 UTC.
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