VIB Bioinformatics Core

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

VIB Bioinformatics Core https://tess.elixir-europe.org/content_providers/bitsvib Provider of Bioinformatics and software training, plus informatics services and resource management support. /system/content_providers/images/000/000/042/original/bioinformatics_core_rgb_pos.png?1492856095
Showing 30 materials out of 48. View all results.

This training will give you an overview of what GEO has to offer. Several experiments will be analyzed using simple tools to obtain differential gene lists. An introduction to downstream tools dedicated to functional enrichment will close the session.

Scientific topics: Expression data visualisation

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. Expression data visualisation Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09

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

Introductory statistics in GraphPad Prism https://tess.elixir-europe.org/materials/introductory-statistics-in-graphpad-prism This training gives an introduction to the use of statistics for basic analyses of life sciences data. The theoretical background obtained in the Basic statistics theory training  will be applied in a hands-on session on real-life data using the statistical software GraphPad Prism. BITS distributes the software for free to VIB scientists, for more information you can visit the GraphPad Prism page on the BITS web site. This is the reason why the training is limited to VIB scientists. Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09

We will investigate the following items: Quality control of the sequence reads to detect biases or contaminating adapters Mapping of the reads to the reference genome with use of a transcript database model Quality control of the mapping results Adjusting the mapping data to...

Scientific topics: RNA-Seq, Gene expression

RNA-Seq analysis for differential expression in GenePattern https://tess.elixir-europe.org/materials/rna-seq-analysis-for-differential-expression-in-genepattern We will investigate the following items: Quality control of the sequence reads to detect biases or contaminating adapters Mapping of the reads to the reference genome with use of a transcript database model Quality control of the mapping results Adjusting the mapping data to compensate for artefacts like duplicates Calculate transcript counts usable for differential expression and merging of count tables Computing differential expression using EdgeR and DESeq2 The code pieces used during the training are made available through our Wiki as well as detailed results and can be copied and adapted for own user needs with minimal edits. Key results have been saved to our server and can be downloaded to fully reproduce the training. RNA-Seq Gene expression post-docs PhD students Life Science Researchers beginner bioinformaticians 2016-04-22 2017-10-09

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 Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09

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

Scientific topics: Molecular biology, Gene regulation, Gene expression

Introduction to gene regulation https://tess.elixir-europe.org/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 regulation Gene expression Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The Training consists of two parts: Introduction Access ways to your notebook, ELN installation instructions and house rules, where to find documentation and get support Hands-on-demo Creating notebooks/experiments, importing and exporting (MS Office) files, sharing data, using templates,...

Electronic Lab Notebook Introduction - Leuven https://tess.elixir-europe.org/materials/electronic-lab-notebook-introduction-leuven The Training consists of two parts: Introduction Access ways to your notebook, ELN installation instructions and house rules, where to find documentation and get support Hands-on-demo Creating notebooks/experiments, importing and exporting (MS Office) files, sharing data, using templates, advanced searching, printing, tips and tricks Life Science Researchers PhD students post-docs 2016-04-22 2016-06-15

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 Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09

Introduction Bitmap vs vector images Image resolution PPI and DPI File formats VIB guidelines on image editing GIMP prepare images for publication Installation and documentation User Interface Import image files Image Properties Selection tools and options Transforming...

Initiation GIMP and Inkscape - Leuven https://tess.elixir-europe.org/materials/initiation-gimp-and-inkscape-leuven Introduction Bitmap vs vector images Image resolution PPI and DPI File formats VIB guidelines on image editing GIMP prepare images for publication Installation and documentation User Interface Import image files Image Properties Selection tools and options Transforming options Scaling and cropping Using Layers Contrast and brightness Undo/redo Image print size Saving/Exporting images Exercises Inkscape annotate plots and images, create figures (diagrams, schemes, ...), design posters Installation and documentation User interface Import image/vector files Drawing lines Creating paths Drawing objects Fill and stroke Aligning and distributing objects/nodes Z-order Adding text and text options Path effects Live path effects Diagrams Exporting images Exercises Life Science Researchers PhD students post-docs 2016-04-22 2016-06-15

The aim of this training is to teach you how to use Ingenuity Pathway Analysis (IPA) software on your own data. This can be for various applications: Creating and modifying biological networks e.g. which genes are involved in a certain disease Mapping data to biological processes,...

Scientific topics: Microarray experiment, Proteomics, Protein interactions, Metabolomics

Custom training: Ingenuity Pathway Analysis https://tess.elixir-europe.org/materials/custom-training-ingenuity-pathway-analysis The aim of this training is to teach you how to use Ingenuity Pathway Analysis (IPA) software on your own data. This can be for various applications: Creating and modifying biological networks e.g. which genes are involved in a certain disease Mapping data to biological processes, networks and pathways mapping a list of genes/proteins/chemicals mapping quantitative data e.g. microarray/proteomics/metabolomics data High quality visualisation of biological networks and pathways Assessing the biological significance of pathways in certain physiological conditions e.g. detecting overrepresented pathways in diseases Microarray experiment Proteomics Protein interactions Metabolomics Life Science Researchers post-docs PhD students 2016-04-22 2016-09-26

This training will start with the presentation of a 16S pipeline (psbweb05.psb.ugent.be/lotus/) in a linux environment, using a minimal amount of linux commands. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees. The 2nd part of the...

Metagenomics https://tess.elixir-europe.org/materials/metagenomics This training will start with the presentation of a 16S pipeline (psbweb05.psb.ugent.be/lotus/) in a linux environment, using a minimal amount of linux commands. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees. The 2nd part of the training will give an overview of numerical ecology and takes part entierly in R. post-docs PhD students beginner bioinformaticians Life Science Researchers 2016-04-22 2016-08-31

In this hands-on training you will learn how to use the CLC Bio Main Workbench for basic and advanced sequence analysis. The software supports a large number of DNA, RNA, and protein sequence analyses and microarray analysis. Since BITS provides a VIB-wide license to CLC Bio Main Workbench, this...

Scientific topics: Expression data visualisation, Local alignment, Global alignment

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. Expression data visualisation Local alignment Global alignment Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09

During this 3-day introduction to bioinformatics, BITS will take you along a guided tour that covers all basic aspects of biological sequence analysis. This workshop is an ideal opportunity to get familiar with bioinformatics and its many faces! At the end, you should be able to start tackling...

Scientific topics: Sequence analysis

Basic bioinformatics concepts, databases and tools https://tess.elixir-europe.org/materials/basic-bioinformatics-concepts-databases-and-tools During this 3-day introduction to bioinformatics, BITS will take you along a guided tour that covers all basic aspects of biological sequence analysis. This workshop is an ideal opportunity to get familiar with bioinformatics and its many faces! At the end, you should be able to start tackling any basic bioinformatics problem: how to obtain relevant information about your gene, you know where to get the required sequence data, manipulate the sequences, and how basic software and algorithms function so you can fine-tune it in order the get the most out of your analysis. Sequence analysis Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09

The aim of this training is to help you use OpenRefine on your own data. This can contain subjects like: load data files, import and parse data files from a URL clean data files: rename columns, transform and edit cells, split multivalue cells... transform data from one format to another:...

Scientific topics: Data quality management

Custom training: OpenRefine https://tess.elixir-europe.org/materials/custom-training-openrefine The aim of this training is to help you use OpenRefine on your own data. This can contain subjects like: load data files, import and parse data files from a URL clean data files: rename columns, transform and edit cells, split multivalue cells... transform data from one format to another: e.g. merge data from two files using  a column that is common to both data files, create new rows based on columns and vice versa... export cleaned, transformed data data manipulation pipelines data dashboards Data quality management Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09

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

Scientific topics: Protein structure analysis

Protein Structure Analysis https://tess.elixir-europe.org/materials/protein-structure-analysis This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure. Different hands-on exercises will allow you to compare the structure of homologues, to predict a structural model of proteins without any structure information and to find homologuous structures. We will use the FoldX program to quantify various interactions in the structures. Protein structure analysis Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09

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.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. Gene expression analysis Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09

- Run RNA-seq downstream processing analyses in GenePattern, such as clustering, classification, GSEA... - Use GenePattern to save workflows, ensure reproducibility and share methodologies with colleagues and reviewers - Use the GenePattern Notebook environment to create documents that...

Scientific topics: RNA-Seq

Downstream processing of RNA-Seq data in GenePattern https://tess.elixir-europe.org/materials/downstream-processing-of-rna-seq-data-in-genepattern - Run RNA-seq downstream processing analyses in GenePattern, such as clustering, classification, GSEA... - Use GenePattern to save workflows, ensure reproducibility and share methodologies with colleagues and reviewers - Use the GenePattern Notebook environment to create documents that interleave formatted text, graphics and other multimedia, executable code, and GenePattern analyses, creating a single "research narrative" that puts scientific discussion and analyses in the same place Summary The workshop will cover the use of GenePattern for downstream processing of high-throughput mRNA sequencing (RNA-Seq) data produced by Illumina sequencing machines.  This workshop is intended for non-programming biologists. 1. Running Analyses in GenePattern 2. Clustering 3. Prediction and Clasification 4. Working with analysis workflows: GenePattern pipelines 5. Working with Samples and Features 6. The GenePattern Notebook environment 7. Related tools: IGV, GSEA 8. Open Q&A The data files, slides and exercises will be made available after the workshop.   RNA-Seq Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09

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

UCSC Genome Browser https://tess.elixir-europe.org/materials/ucsc-genome-browser The UCSC Genome Browser provides a way to examine data from many genomes and includes extensive annotation tracks for various data types such as known UCSC (and Ensembl) genes, predicted genes, SNPs, miRNAs, comparative multi-species analysis and much more. During this training you will learn how to navigate this vital tool for your research. Required skills No specific prior knowledge is required.  BITS provides 15 laptops for their training sessions. Depending on the number of participants (max 20), it is possible that you have to share the laptop with one other participant but you can also choose to bring your own laptop for this training session. Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09

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.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 Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09

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.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 Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09

The morning session will give you an overview of the possibilities of Genevestigator, a search engine of curated and normalized publicly available gene expression data. The interface allows you to visualize spatio-temporal (tissue - developmental stage) and perturbational gene expression...

Scientific topics: Gene expression analysis, Gene expression, Biomarkers

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 analysis Gene expression Biomarkers Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09

This training gives an introduction to the use of the statistical software language R. R is a language for data analysis and graphics. This introduction to R is aimed at beginners. The training covers data handling, graphics, mathematical functions and some statistical techniques. R is for free...

Basic statistics in R https://tess.elixir-europe.org/materials/basic-statistics-in-r This training gives an introduction to the use of the statistical software language R. R is a language for data analysis and graphics. This introduction to R is aimed at beginners. The training covers data handling, graphics, mathematical functions and some statistical techniques. R is for free and for more information you can visit the site at the CRAN web site. This training is an introduction to the use of R and RStudio and stops at very basic analyses (t-tests and non-parametric equivalents). A full overview of statistical analyses in R including regression, ANOVA will be given in the follow-up training Basic statistics in R, part II Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09

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

Gentle hands-on introduction to Perl programming https://tess.elixir-europe.org/materials/gentle-hands-on-introduction-to-perl-programming This course is organised over two full days. With this extensive hands-on session, we introduce you Perl. The first day,we will cover the basics of Perl programming: what is a variable, different types, how to assign values to variable, what can you do with them, strings, arrays and hashes. Logic statements will be discussed, Everything will be demonstrated with step by step exercises. At the end of the day, you will be send home with some challenges to do yourself and additional learning material. As a homework, you may write a program to analyze your own data. On the second day of the training, we will look to the solutions of the homework and explain the results of the tasks. We will dig a little deeper in good programming hygiene, and create some more complex scripts using regexes and reading in files. By the end of the day, a firm basis for perl programming should be established to allow further self-study. Life Science Researchers PhD students post-docs beginner bioinformaticians 2016-04-22 2017-10-09

Probabilistic models describe how the observed data was generated, and what structure the signal and noise from potentially multiple sources may have. Many classical statistical models are special cases of probabilistic models with special modeling assumptions. Probabilistic models can be...

Scientific topics: Statistics and probability

Probabilistic programming with (R)Stan https://tess.elixir-europe.org/materials/probabilistic-programming-with-r-stan Probabilistic models describe how the observed data was generated, and what structure the signal and noise from potentially multiple sources may have. Many classical statistical models are special cases of probabilistic models with special modeling assumptions. Probabilistic models can be implemented, improved, and critizised in a flexible, explicit and transparent manner, and the analysis can be supported with prior information about the data. This 1-day course provides an introduction to Bayesian/probabilistic models. We will implement standard linear models based on the rstanarm package of the R statistical programming environment and readily available example data sets. The workshop is an ideal opportunity to familiarize yourself with the basic ideas in probabilistic modeling such as prior information, likelihood, model criticism and validation, as well as some of the available tools. At the end, you should be able to implement basic probabilistic models yourself, and understand their relative advantages and pitfalls compared to their classical alternatives. Statistics and probability Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22
Showing 14 upcoming events. Found 44 past events. View all results.
  • Data Carpentry June 2018

    12 - 13 June 2018

    Brussels, Belgium

    Elixir node event
    Data Carpentry June 2018 https://tess.elixir-europe.org/events/data-carpentry-june-2018 2018-06-12 09:30:00 UTC 2018-06-13 17:00:00 UTC ELIXIR Belgium Brussels, Belgium Brussels Belgium 1050 [] [] [] [] [] []
  • Electronic Lab Notebook Introduction - Ghent

    23 May 2018

    Ghent, Belgium

    Elixir node event
    Electronic Lab Notebook Introduction - Ghent https://tess.elixir-europe.org/events/electronic-lab-notebook-introduction-ghent 2018-05-23 10:00:00 UTC 2018-05-23 12:00:00 UTC VIB Bioinformatics Core PC room V114 - 1st floor front building VIB-UGent Research Building, Ghent, Belgium PC room V114 - 1st floor front building VIB-UGent Research Building Ghent Belgium 9052 [] [] [] [] [] []
  • Git for Humans

    20 June 2018

    Heverlee, Belgium

    Elixir node event
    Git for Humans https://tess.elixir-europe.org/events/git-for-humans-ef1cd0f7-1779-4f7f-9db5-b57336debc0a 2018-06-20 13:00:00 UTC 2018-06-20 16:30:00 UTC ELIXIR Belgium Heverlee Campus. Dept. of Electrical Engineering (ESAT), room B01.35, Heverlee, Belgium Heverlee Campus. Dept. of Electrical Engineering (ESAT), room B01.35 Heverlee Belgium 3001 [] [] [] [] [] []
  • Git for humans

    25 June 2018

    Gent, Belgium

    Elixir node event
    Git for humans https://tess.elixir-europe.org/events/git-for-humans 2018-06-25 09:30:00 UTC 2018-06-25 12:30:00 UTC ELIXIR Belgium Campus: Boekentoren/Book Tower Room: Didacticum, Gent, Belgium Campus: Boekentoren/Book Tower Room: Didacticum Gent Belgium 9000 [] [] [] [] [] []
  • qPCR analysis using qbasePLUS

    10 September 2018

    Gent, Belgium

    Elixir node event
    qPCR analysis using qbasePLUS https://tess.elixir-europe.org/events/qpcr-analysis-using-qbaseplus 2018-09-10 09:30:00 UTC 2018-09-10 16:30:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052 [] [] [] [] [] []
  • Basic statistics in R, part II

    25 - 1 June 2018

    Gent, Belgium

    Elixir node event
    Basic statistics in R, part II https://tess.elixir-europe.org/events/basic-statistics-in-r-part-ii 2018-06-25 09:30:00 UTC 2018-06-01 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052 [] [] [] [] [] []
  • Basic statistics theory

    29 May 2018

    Leuven, Belgium

    Elixir node event
    Basic statistics theory https://tess.elixir-europe.org/events/basic-statistics-theory After this basic statistics theory session, you should be able to: Understand basic statistical concepts and methods for statistical analysis of life sciences data Choose the correct statistical test for analyzing your data This training gives an introduction to the use of statistics for basic analyses of life sciences data. This training is a prerequisite introduction to a series of hands-on trainings on the statistical analysis of life sciences data: 'Basic statistics in R' and 'Basic statistics in Graphpad Prism'. If you want to follow one of these trainings, you have to follow this introduction. Ít will give you all the theoretical background that you need. Those that already have a strong statistical background may register directly for the 'Basic statistics in R, part II' training. No skills required.  9h30-12h30: Theoretical background 2018-05-29 09:30:00 UTC 2018-05-29 16:30:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Electronic Lab Notebook Introduction - Leuven

    24 May 2018

    Leuven, Belgium

    Elixir node event
    Electronic Lab Notebook Introduction - Leuven https://tess.elixir-europe.org/events/electronic-lab-notebook-introduction-leuven This training is an introduction to the Electronic Laboratory Notebook (ELN) implemented at VIB. This training is intended for all new VIB researchers and will teach you the basic knowledge required to successfully document in ELN. The training consists of two parts: Introduction: Access​ ways to your notebook, ELN installation instructions and house rules, where to find documentation and get support Hands-on-demo: Creating notebooks/experiments, importing and exporting (MS Office) files, sharing data, using templates, advanced searching, printing, tips and tricks This training is mandatory for all new VIB co-workers and requires an active VIB account. In order to check your username and password, go to https://storefront.vib.be, if login fails send an e-mail to eln*Replace*With*At*Sign*vib.be. People who want to join this training can register here! 2018-05-24 09:30:00 UTC 2018-05-24 11:30:00 UTC VIB Bioinformatics Core O&N4 room 06.239 Campus Gasthuisberg, Leuven, Belgium O&N4 room 06.239 Campus Gasthuisberg Leuven Belgium 3000 [] [] [] [] [] []
  • A tour of machine learning - classification

    12 June 2018

    Ghent, Belgium

    Elixir node event
    A tour of machine learning - classification https://tess.elixir-europe.org/events/a-tour-of-machine-learning-classification ok Python Numpy/Pandas 2018-06-12 09:30:00 UTC 2018-06-12 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Ghent, Belgium Bio-Accelerator Ghent Belgium 9052 [] [] [] [] [] []
  • Transcriptomics and Single Cell RNA-Seq Analysis

    26 - 31 August 2018

    Leuven, Belgium

    Elixir node event
    Transcriptomics and Single Cell RNA-Seq Analysis https://tess.elixir-europe.org/events/transcriptomics-and-single-cell-rna-seq-analysis-c68d0326-09c8-41a4-90d9-c38feeab6d45 2018-08-26 09:30:00 UTC 2018-08-31 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Basic bioinformatics concepts, databases and tools

    4 - 18 June 2018

    Gent, Belgium

    Elixir node event
    Basic bioinformatics concepts, databases and tools https://tess.elixir-europe.org/events/basic-bioinformatics-concepts-databases-and-tools Understand the capabilities and pitfalls of bioinformatics. Functioning of the most used bioinformatics algorithms and terms for reliable interpretation of the results. Navigate with confidence to numerous online data repositories. Know where to search for them. Basic analyses of single genes as well as groups of genes (gene lists) During this 3-day introduction to bioinformatics, we will take you along a guided tour that covers all basic aspects of biological sequence analysis. This workshop is an ideal opportunity to get familiar with bioinformatics and its many faces! At the end, you should be able to start tackling any basic bioinformatics problem: how to obtain relevant information about your gene, you know where to get the required sequence data, manipulate the sequences, and how basic software and algorithms function so you can fine-tune them in order the get the most out of your analysis. GenBank, SwissProt, RefSeq, Gene GQuery Ensembl Ugene BLAST, OrthoMCL, EMBOSS Needle, EMBOSS Water, Muscle, WebLogo, iceLogo HMMER, PSIBLAST, PROSITE, SMART, InterPro miRWalk, Pscan, Motiflab Primer3 PLUS, Primer BLAST, OligoAnalyzer, Ambion siRNA finder EMBOSS, Mobyle, Expasy PDB, Yasara GO, AmiGO, QuickGO, KEGG, STRING, DAVID, ToppGene, EnrichR, WebGestalt, Cytoscape GEO, GEO2R, GEO DataSet Browser OMIM, Variant reporter, Genomic variation server Biomart ​​​​​​​​ 2018-06-04 09:30:00 UTC 2018-06-18 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052 [] [] [] [] [] []
  • Introduction to Galaxy

    26 June 2018

    Gent, Belgium

    Elixir node event
    Introduction to Galaxy https://tess.elixir-europe.org/events/introduction-to-galaxy-16bfecc7-80c1-4541-897d-3bb9528ced2d 2018-06-26 09:30:00 UTC 2018-06-26 13:00:00 UTC ELIXIR Belgium Campus: Boekentoren/Book Tower Room: Didacticum, Gent, Belgium Campus: Boekentoren/Book Tower Room: Didacticum Gent Belgium 9000 [] [] [] [] [] []
  • Public proteomics data reprocessing and the Tabloid Proteome

    10 October 2018

    Ghent, Belgium

    Elixir node event
    Public proteomics data reprocessing and the Tabloid Proteome https://tess.elixir-europe.org/events/public-proteomics-data-reprocessing-and-the-tabloid-proteome 2018-10-10 09:30:00 UTC 2018-10-10 17:00:00 UTC ELIXIR Belgium VIB-UGent Research Building LEAF room (E124) right side of the building, first floor, Ghent, Belgium VIB-UGent Research Building LEAF room (E124) right side of the building, first floor Ghent Belgium 9052 [] [] [] [] [] []
  • ELIXIR-EXCELERATE Train the Trainer

    20 - 21 August 2018

    Antwerp, Belgium

    Elixir node event
    ELIXIR-EXCELERATE Train the Trainer https://tess.elixir-europe.org/events/elixir-excelerate-train-the-trainer-7d8246fe-4e5a-46bb-9144-62bfe8a56aa8 ELIXIR-EXCELERATE Train the Trainer (TtT) workshop 2018-08-20 09:00:00 UTC 2018-08-21 17:00:00 UTC ELIXIR Belgium University of Antwerp Building: G Room: G.004, Antwerp, Belgium University of Antwerp Building: G Room: G.004 Antwerp Belgium 2020 [] [] [] [] [] []
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