Training
18
July
2016
This workshop (18 July 2016) is organised by the ULB Machine Learning Group and aims to present the current and future perspectives of former and current ULB MLG researchers in data science and bioinformatics. More information.
7-8
November
2016
This two-day workshop (7-8 November 2016) will get researchers more familiar with genomics data. The focus is on Linux, command line tools and visualisation in R. The workshop is aimed at researchers in the life sciences at all career stages and is designed for learners with little to no prior knowledge of Linux and command line tools, programming in R or biological networks in Cytoscape. More…
14-17
November
2016
This workshop and conference (14-17 November 2016) is organised by the Interuniversity Institute of Bioinformatics in Brussels - (IB)² and Genome Diagnostics Nijmegen.
6-8
December
2016
This two-day hands-on training (6-7 December 2016) is organised by Biopark Formation and the Interuniversity Institute of Bioinformatics in Brussels - (IB)².
30-1
May/Jun
2017
This three-day workshop (30 May - 1 June 2017) will showcase the potential of FAIR data in the context of plant research and will host a hackathon to make the interoperability platform within the plant domain (BrAPI) FAIR reusing the general accepted MIAPPE standards and assessing data validation with ISA-TOOLS.
Organised by ELIXIR Belgium and ELIXIR The Netherlands.
11-13
September
2017
Three days training (11-13 September 2017) for life scientists. Aims to introduce the concepts as well as hands-on skills to the data mining and machine learning techniques that are able to analyse biomedical data.
Target audience: doctoral students and postdoctoral researchers in life sciences.
Number of places: limited to 30; for half of the places, priority is given to UAntwerpen PhD…
14-15
September
2017
Using PLAZA to get more out of your plant omics data
This two-day workshop (14-15 September 2017) will introduce the basic concepts of comparative and functional -omics data analysis in plants through lectures and practical hands-on sessions. Both plant biologists and geneticists with an interest in bioinformatics, data analysis, and comparative & regulatory genomics should attend this…
5-6
October
2017
Two-day data processing course (5-6 October 2017). This course starts with an introduction to the language, its simple datatypes and control structures, moving on to its more complex data structures, and classes. The emphasis is on how to use Python to solve real world problems in the domain of data transformation relevant to scientific computing. Subjects such as regular expressions, various…
23
January
2018
This short course “Quick introduction to RStudio” (23 January 2018) aims at introducing the basic features in RStudio to get started with R. It will follow-up with a workshop in data manipulation using tidyverse.
The course is open to PhD students, researchers and industry staff in life-sciences; no prior programming knowledge is needed. The trainer for this course is Paula Andrea, ELIXIR…
19
February
2018
Short hands-on workshop (19 February 2018) aimed at people who wish to start learning R from scratch. No previous experience with R or other programming languages is expected.
The trainer for this course is Paula Andrea, ELIXIR Belgium’s Bioinformatics and Data Skills trainer. The workshop is organised by ELIXIR Belgium together with VUB. More information and registration on this link.
21
February
2018
Tidyverse is a collection of R-packages used for data manipulation, exploration and visualisation. This half-day course “Introduction to tidyverse” (21 February 2018) aims at introducing the tidyverse packages in order to increase productivity of data handling.
The course is open to PhD students, researchers and industry staff in life-sciences. A basic knowledge of the R programming…
5
March
2018
Tidyverse is a collection of R-packages used for data manipulation, exploration and visualisation. This half-day course “Introduction to tidyverse” (5 March 2018) aims at introducing the tidyverse packages in order to increase productivity of data handling.
The course is open to PhD students, researchers and industry staff in life-sciences. A basic knowledge of the R programming language…
7
March
2018
Tidyverse is a collection of R-packages used for data manipulation, exploration and visualisation. This half-day course “Introduction to tidyverse” (7 March 2018) aims at introducing the tidyverse packages in order to increase productivity of data handling.
The course is open to PhD students, researchers and industry staff in life-sciences. A basic knowledge of the R programming language…
13
March
2018
Tidyverse is a collection of R-packages used for data manipulation, exploration and visualisation. This half-day course “Introduction to tidyverse” (13 March 2018) aims at introducing the tidyverse packages in order to increase productivity of data handling.
The course is open to PhD students, researchers and industry staff in life-sciences. A basic knowledge of the R programming language…
24
April
2018
This short workshop gets you started with Git from zero and is intended for life scientists who have an existing project with code (in any language) or text files that need track of changes.
This workshop is organised by ELIXIR Belgium; the trainer is Paula Andrea Martinez.
More information and registration on this link.
12-13
June
2018
Workshops on the fundamental data skills for data-driven research. This workshop is aimed at researchers and graduate students who want to be introduced to the following topics: R for reproducible analysis, introduction to databases and data organisation using spreadsheets. If you have a bit of exposure to R, this workshop is for you, we will use packages from tidyverse like ggplot2 and ddplyr…
15
June
2018
This training is organised in the framework of the ELIXIR Implementation study “Using clouds and VMs for bioinformatics training”.
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…
25
June
2018
This short workshop gets you started with Git from zero and is intended for life scientists who have an existing project with code (in any language) or text files that need track of changes.
This workshop is organised by ELIXIR Belgium; the trainer is Paula Andrea Martinez.
More information and registration on this link.
26
June
2018
Galaxy is an open software framework that enables researchers without informatics expertise to perform computational biology analyses through the web. This training aims to familiarise you with the Galaxy user interface. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work.
The course is aimed at…
20-21
August
2018
Two-day workshop for individuals involved in teaching and training in bioinformatics and related fields. The workshop covers learning principles and how they apply to training, training techniques that can be used to enhance the learner engagement and participation, assessment and feedback in training, course and materials design.
This ELIXIR Train the Trainer workshop is organised by ELIXIR…
26-31
August
2018
The Summer School is an unmissable learning opportunity for all life scientists analysing transcriptomics data. The aim of the course is to keep up with recent developments in transcriptome data analysis and bring own data along to analyse during the course under the supervision of expert trainers. This will provide the ultimate hands-on experience in Next Generation Sequencing data processing…
1-6
Oct/May
2018
This course is currently only offered in Dutch
Deze navormingscyclus is gericht op medewerkers die werkzaam zijn in de medische moleculaire diagnostiek en wordt georganiseerd door AZ Sint-Jan campus Brugge, UZ Gent en Hogeschool West-Vlaanderen (Howest) campus Brugge.
Het doel van deze opleiding is om meer inzicht te verwerven in de bio-informatica processen die toegepast worden in de…
10
October
2018
One-day ELIXIR course on public proteomics data reprocessing and the Tabloid Proteome. Tabloid Proteome is a database of protein association network generated using publically available mass spectrometry based experiments in PRIDE. These associations represent a broad scala of biological associations between pairs of proteins that goes well beyond mere binary protein interactions.
Topics…
24-25
October
2018
Two-day workshop (24-25 October 2018) on good development practices that encourage efficient and reproducible research computing. This workshop is aimed at researchers in life -sciences who need to analyse data, even if not full time. The target participant has the need to read and use Python scripts, the interest to understand better how the code works and the will to pursue efficiency. …
6
November
2018
This one-day workshop will introduce you to the Galaxy user interface using NGS data. You will learn how to import data, run tools, work with histories, and create workflows. After this short course, you will be able to perform computational biology analyses through the web.
This workshop is organised by ELIXIR Belgium; the trainer for the workshop is Paula Andrea Martinez. Click here for…
13-14
May
2019
This Data Carpentry Workshop, with a special focus on sequence handling for variant calling using the cloud resources, will introduce you to Genomic concepts and scripting. For those unfamiliar with the concept, Data Carpentry aims at systematically delivering workshops on the fundamental data skills needed to conduct research. The instructors are Mateusz Kuzak, Toby Hodges and Christof De Bo…
15
May
2019
The 4 Open Software Recommendations are designed around Open Science values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. These recommendations recognise that not everyone can or want to make their software open from day one, but encourage to learn from the recommendations and adapt them as needed…
20-21
May
2019
The goal of this two-days workshop is to initiate wet-lab scientists to reproducible data analysis with R. The “Data organisation in spreadsheets” section will focus on tabular data structure and management. We will then introduce OpenRefine and how it can be used for initial data exploration and cleaning.
The biggest part of the workshop will focus on R. We will start with a general…
10
September
2019
In this workshop, we address how to predict features of proteins from their sequence only, using Python scripts to access APIs of web services available online. We will introduce single-sequence based predictions of biophysical characteristics of proteins (e.g. DynaMine for backbone dynamics), methods that use multiple sequence alignments (e.g. I-TASSER), and methods that determine the…
8
October
2019
This practical aims to familiarize you with the Galaxy user interface & execute a complete analysis of RNA-seq data.
It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work. In this tutorial, we will introduce you to bare basics of Galaxy:
Getting data from external databases such as UCSC…
21-22
October
2019
This two-day workshop (21-22 October 2019) will introduce the basic concepts of comparative and functional -omics data analysis in plants through lectures and practical hands-on sessions. Plant biologists and geneticists with an interest in bioinformatics and data analysis are encouraged to attend this training. After this workshop, you will have a good understanding of the organization of…
7
November
2019
This half-day workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers. This course is open to everyone for free, organized by ELIXIR Belgium. More info.
9-10
January
2020
During this 2-day course, you will - with the help of plenty hands-on exercises - 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. More info.
Course organized by VIB Bioinformatics core and ELIXIR Belgium.
6
March
2020
This practical aims to familiarize you with the Galaxy user interface & execute a complete analysis of RNA-seq data. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work. More info and registration.
Workshop organized by ELIXIR Belgium and the VIB Bioinformatics Core.
30-31
March
2020
This course is organised over two full days (30-31 March 2020). 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. More info and registration.
Organized by ELIXIR…
19
June
2020
This half-day workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers. More info and registration.
Workshop organized by ELIXIR Belgium and the VIB Bioinformatics Core.
22
June
2020
This course is organised over two full days (22 and 26 June 2020). 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. More info and registration.
Organized by…
16
September
2020
This 1-day course aims to introduce how to use the Galaxy platform using variant discovery as a use-case. The course is organised in the context of the “Connecting ESFRIs project”. Apart from the offered training, phylogenetic analysis tools are made available in Galaxy. Although initially set-up for Botanical Garden researchers, participants from other research institutes are welcome to attend.
21-22
September
2020
This course is organised over two full days (21 and 22 September 2020). By means of hands-on exercises, you will learn to fetch biological data and sequencing files from online databases, and be able to parse and analyse this data. There will be time to highlight specific requests of topics from participants.
Organized by ELIXIR Belgium and the VIB Bioinformatics Core.
More information…
20
October
2020
During this ReproHack – the first one organised in Belgium – participants will attempt to reproduce published research from a list of proposed papers with available code and data. The hackathon stimulates to start working with other people's code and data, and make your own data analysis reproducible. Participants will largely work together and learn from each other. More information and…
26-27
October
2020
This is two-day course will give you an insight in Docker & Singularity containers, and the Nextflow analysis pipeline. Containers allow you to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. This allows you to perform data analysis without conflicting package dependencies. With Nextflow, you can write…
9-10
November
2020
This two-day course will help researchers to develop their knowledge and practical skills in handling and managing their research data. The participants will be guided through the key aspects on how to document, store and safeguard research data. Planning and implementing good data management in research projects in accordance to current best practices will also be addressed. More information.…
13
November
2020
On request of and in collaboration with Janssen Pharmaceutica, ELIXIR Belgium and the VIB Bioinformatics core organized a workshop series on Docker, Singularity and Nextflow. In three afternoon sessions (13/11, 20/11, 4/12 2020), topics as version control, software containers and workflow pipeline tools were tackled. Participants of Janssen Pharmaceutica learned about containerization of…
16-30
November
2020
This course is organised over three full days (16, 23, 30 November 2020). 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.
Organised by ELIXIR Belgium and the VIB…
3
December
2020
Galaxy enables researchers without bioinformatics expertise to perform computational analyses through the web. This hands-on workshop aims to familiarize you with the Galaxy user interface & execute (label-free) proteomics data-analysis.
The first part of this hands-on workshop will introduce the participants to the Galaxy platform. Basic tasks such as importing data, running tools, working…
10
December
2020
This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers.
This course, organised by ELIXIR Belgium, is open to everyone for free.
More info and registration.
8-22
January
2021
This training is an introduction to 'Bulk RNA-Seq analysis for differential expression', Hands-on introduction to NGS variant analysis', and 'Hands on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings and you have no experience with NGS data you should follow this introduction first.
Objectives
This training is an introduction to a series of trainings on the…
11
January
2021
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be…
19-2
Jan/Feb
2021
This course gently introduces programming to new programmers. There are plenty of opportunities to apply and practice what you learn, and ask questions in a safe place. Furthermore, surprise yourself by building a substantial project over the 3 course weeks. We use the popular Python programming language to prepare you for real-world research application of what you learn.
Objectives
…
5-6
February
2021
This course consists of a live session on counting and differential expression analysis in R and a Q&A session to answer all the questions that arise when trying the analysis on your own data. The live session will demonstrate R tools to generate count files like featureCounts, and summarizeOverlaps are demonstrated, as well as how count files from HTSeq-Count, FeatureCounts, Salmon or…
25-4
Feb/Mar
2021
This course is organized over two full days. We will start with a brief recap of the basics of Python, followed by exploring several libraries for data manipulation and visualization. With the help of plenty of hands-on exercises, you will learn to fetch biological data and sequencing files from online databases, and be able to parse and analyze this data. There will be time to highlight…
19-2
Mar/Apr
2021
This training is an introduction to 'Bulk RNA-Seq analysis for differential expression', Hands-on introduction to NGS variant analysis', and 'Hands on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings and you have no experience with NGS data you should follow this introduction first.
Objectives
This training is an introduction to a series of trainings on the…
29-1
Mar/Apr
2021
The ELIXIR Train the Trainer programme aims to build a network of trainers to allow them to benefit from reciprocal support and discussion. ELIXIR TtT courses aim to give new instructors tools and tips for providing an enriching learning experience to trainees, irrespective of topic, and to include best-practice guidance on course and training material development.
A complete list of topics…
11
May
2021
This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers.
Objectives
To get you started with Git from zero, we'll work with GitHub (Desktop) and have a look into git on a command-line level.
Introduction,…
20-27
May
2021
This two-day course (20 and 27 May 2021) will give you an insight in Docker & Singularity containers, and the Nextflow analysis pipeline.
The first day is dedicated to containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others…
21-4
May/Jun
2021
This training is an introduction to 'Bulk RNA-Seq analysis for differential expression', Hands-on introduction to NGS variant analysis', and 'Hands on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings and you have no experience with NGS data you should follow this introduction first.
Objectives
This training is an introduction to a series of trainings on the…
25
May
2021
Metatranscriptomics analysis examines how the microbiome responds to the environment by studying the taxonomic composition and functional analysis of genes expressed by the microbiome, using microbial community RNASeq data and subsequent metatranscriptomics workflows. This workshop will introduce researchers to the basic concepts and tools from the ASaiM-MT workflow. ASaiM-MT provides a curated…
11-18
June
2021
This course consists of a live session on counting and differential expression analysis in R and a Q&A session to answer all the questions that arise when trying the analysis on your own data. The live session will demonstrate R tools to generate count files like featureCounts, and summarizeOverlaps are demonstrated, as well as how count files from HTSeq-Count, FeatureCounts, Salmon or…
14-16
June
2021
This training will start with the presentation of a 16S pipeline 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 second part of the training will give an overview of numerical ecology and takes part entirely in R.
Objectives
The main objective is to…
1-5
Jul/Aug
2021
In this course, realistic research cases form the starting point for which we will try to find practical solutions. We will tackle research questions by designing tailor-made factorial experiments within the budget and lab constraints. Power analysis will be key to achieve this goal. Finally, we will analyse the expected output in a statistical sound manner, interpret the results and propose…
27-10
Aug/Sep
2021
This course gently introduces programming to new programmers. There are plenty of opportunities to apply and practice what you learn, and ask questions in a safe place. Furthermore, surprise yourself by building a substantial project over the 3 course weeks. We use the popular Python programming language to prepare you for real-world research application of what you learn.
Objectives
…
30-7
Sep/Oct
2021
This training is an introduction to 'Bulk RNA-Seq analysis for differential expression', Hands-on introduction to NGS variant analysis', and 'Hands on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings and you have no experience with NGS data you should follow this introduction first.
Objectives
This training is an introduction to a series of trainings on the…
25-26
October
2021
This two-day workshop will introduce the basic concepts of comparative and functional -omics data analysis in plants through lectures and practical hands-on sessions. Plant biologists and geneticists with an interest in bioinformatics and data analysis are encouraged to attend this training. After this workshop, you will have a good understanding of the organization of plant genomes, the…
15
November
2021
This workshop will provide new knowledge and skills related to impact evaluation through hands-on learning and knowledge-exchange. Learning will be facilitated by impact evaluators from the European Future Innovation System Centre.
Objectives
Gain new knowledge and skills related to impact evaluation, through hands-on learning, complemented with knowledge-exchange.
Refine the case…
18-25
November
2021
This training is an introduction to 'Bulk RNA-Seq analysis for differential expression', Hands-on introduction to NGS variant analysis', and 'Hands on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings and you have no experience with NGS data you should follow this introduction first.
Objectives
This training is an introduction to a series of trainings on the…
2
December
2021
This workshop will show you the possibilities and the pitfalls of transferring software tools to the cloud using real-life examples. Four scientists will testify about their experiences with implementing the tool that was developed in their lab in the cloud. We will end the workshop with a panel discussion. More info and registration.
Talks:
Living on the edge: reproducible RNA-seq data…
9-16
December
2021
This training is an introduction to 'Bulk RNA-Seq analysis for differential expression', Hands-on introduction to NGS variant analysis', and 'Hands on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings and you have no experience with NGS data you should follow this introduction first.
Objectives
This training is an introduction to a series of trainings on the…
24-25
December
2021
With Dodona we provide an online learning environment for learning to code. It supports various programming languages and acts as an online co-teacher. The focus is on automatic corrections and giving meaningful feedback to students on submitted solutions. Teachers can create their own course, composed of different series of existing or custom made exercises. Built-in learning analytics and data visualisations allow easy monitoring of the progress of students. Watch the video trailer of the interactive course on Python to get a feel for working with Dodona, both as a student and as a teacher.
VIB’s e-learning platform offers online courses on a variety of topics including Alphafold on the HPC, Containers as a cornerstone of reproducible data analysis, Next generation sequencing analysis, Bulk and Single cell RNAseq analysis, and Protein structure analysis.
10
January
2022
The course will give an introduction to containers (Docker & Singularity) which are great components to achieve portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, Singularity will be…
14-28
January
2022
This course introduces Python programming and is organized online over three full days (14, 21, 28 January). With the help of plenty of hands-on exercises, you will get introduced to the different types of variables in Python, the peculiarities of Python and good programming habits. This course will provide you with an ideal stepping stone for further developing programming skills in Python.
…
17
January
2022
You will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language.
Objectives
Understand Nextflow's basic concepts: channels, processes, modules, workflows, etc…
4-6
February
2022
The course consists of two separate sessions on the 4th and 11th of February, feautring a youtube session on counting and differential expression analysis in R and an online Q&A session to solve the exercises and answer all the questions that arise when trying the analysis on your own data.
Objectives
The course will show:
Tools to generate count files like featureCounts, and htseq count…
10
March
2022
This is a repeat webinar for the fully subscribed Getting started with impact evaluation training event. This time, there is no limit to the number of attendees, and anyone interested in impact (of research infrastructures) is welcome to join. You do not need to be part of ELIXIR.
The event will be shorter (2.5h) and less hands-on (no group work using MURAL) than the original event, yet still…
31
March
2022
The webinar series will feature speakers actively engaged in developing novel applications of Artificial Intelligence and Deep Learning techniques to advance experimental and computational structural biology and other key research areas in biology. Each presentation will be followed by a 20 minutes Q/A session.
The goal of these series is to illustrate and critically appraise the advances made…
4-18
May
2022
This course gently introduces programming to new programmers. There are plenty of opportunuties to apply and practice what you learn, and ask questions in a safe place. Furthermore, surprise yourself by building a substantial project over the 3 course weeks. We use the popular Python programming language to prepare you for real-world research application of what you learn.
Objectives
After…
15
June
2022
In this workshop you will be introduced to the Galaxy platform and learn how to perform phylogenetic analysis using its tools and workflows. Phylogenetic analysis using sequence data involves many steps using various bioinformatic tools. This translates into a steep and long learning curve for researchers with little bioinformatic knowledge since the majority of these tools run on the command…
17
June
2022
This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers.
Get you started with Git from zero (note that if you already use Git, this workshop will be too basic for you). We'll explore Git on the command-line and…
3-17
August
2022
This course introduces Python programming and is organised online over three full days (3, 10, 17 August). 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. More info…
13
September
2022
This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers.
Get you started with Git from zero (note that if you already use Git, this workshop will be too basic for you). We'll explore Git on the command-line and…
15-22
September
2022
This training is an introduction to 'Bulk RNA-Seq analysis for differential expression', and 'Hands on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings and you have no experience with NGS data you should follow this introduction first.
Objectives
This training is an introduction to a series of trainings on the analysis of Next Generation Sequencing data.…
27
September
2022
Free hands-on introductions to research data management and publication
LifeWatch and ELIXIR Belgium invite you to a hands-on workshop to manage and publish research data. The workshop is organized in the context of the Empowering Biodiversity Research conference and will cover data management plans, data cleaning and GitHub. If this is jargon you always wanted to know about (but were…
29-4
Sep/Oct
2022
This 2-day course consists of e-learning on counting, showing tools to generate count files (e.g. FeatureCounts, HTSeq Count) and how these count files are used to identify differentially expressed genes. The course also offers two face-to-face sessions on differential expression analysis in R and all the questions that arise when analysing your own data.
Requirements:
Knowledge of NGS…
24-26
October
2022
The course will give an introduction to containers (Docker & Singularity) which are great components to achieve portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, Singularity will be…
3-17
November
2022
This course gently introduces programming to new programmers. There are plenty of opportunuties to apply and practice what you learn, and ask questions in a safe place. Furthermore, surprise yourself by building a substantial project over the 3 course weeks. We use the popular Python programming language to prepare you for real-world research application of what you learn.
Objectives
…
17-18
November
2022
You will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language.
Objectives
Understand Nextflow's basic concepts: channels, processes, modules, workflows,…
21-23
November
2022
This training will start with the presentation of a 16S pipeline in a Galaxy environment. 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 entirely in R (meaning that knowledge of R is mandatory).
Objectives
Processing and statistical…
12-13
December
2022
In this course you will learn how to use Research Data Management (RDM) in order to improve the writing of your publications and potentially increase its impact.
Starting from basic concepts together with hands-on activities and discussions, during two days you will learn how to standardise, document and submit your data in a repository and how all of this will help you to underpin your…
4-18
January
2023
This combined 3-day course gently introduces programming to new programmers. There are plenty of opportunities to apply and practice what you learn, and ask questions in a safe place. Furthermore, surprise yourself by building a substantial project over the 3 course weeks. We use the popular Python programming language to prepare you for real-world research application of what you learn.
…
8
February
2023
This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers.
Get you started with Git from zero (note that if you already use Git, this workshop will be too basic for you). We'll explore Git on the command-line and its…
13-14
March
2023
The course will give an introduction to containers (Docker & Singularity) which are great components to achieve portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, Singularity will be…
30-31
March
2023
You will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language.
Objectives
Understand Nextflow's basic concepts: channels, processes, modules, workflows,…
12-26
April
2023
This course gently introduces programming to new programmers. There are plenty of opportunities to apply and practice what you learn, and ask questions in a safe place. Furthermore, surprise yourself by building a substantial project over the 3 course weeks. We use the popular Python programming language to prepare you for real-world research application of what you learn. The course consists…
17-21
April
2023
The Galaxy Admin workshop will cover introductory and advanced topics you need to know to set up your own production, high-performance and multi-user Galaxy instance. Sessions will be intensive and hands-on, and taught by experienced instructors from the Galaxy Community. Participants will learn how to install, configure, customise, and extend their own Galaxy servers.
Topics include tool…
2
May
2023
The TCR analysis workshop is designed for researchers seeking to enhance their T-cell receptor (TCR) repertoire analysis skills. The 3-hour workshop will offer an intensive hands-on training on state-of-the-art TCR repertoire analysis tools. Participants will be guided through the TCR interpretation process, from annotated immunosequencing data to detailed insights, including exploratory…
16-17
May
2023
This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers.
Get you started with Git from zero (note that if you already use Git, this workshop will be too basic for you). We'll explore Git on the command-line and its…
2-9
June
2023
The course consists of introductory online material (e-learning) on counting and two face-to-face sessions on differential expression analysis in R and all the questions that arise when trying the analysis on your own data.
The course will show:
Tools to generate count files like featureCounts, and htseq count are demonstrated
Count files from HTSeq-Count, FeatureCounts, Salmon or…
14-15
June
2023
In this course, you will be guided how to use the different facets of research data management in order to improve the writing of your publications and potentially increase its impact.
Starting from basic concepts together with hands-on activities and discussions, you will learn how to standardise, document and submit your data in a repository and how this will help you to underpin your…