Previous courses at NBIS

Epigenomics Data Analysis: from Bulk to Single Cell

2023-09-18 to 2023-09-22 (5 days)
Deadline 2023-09-04
Online
More infoThis workshop aims to introduce the best practice bioinformatics methods for processing, analyses, visualisation and integration of epigenomics and functional genomics data.

ELIXIR-GOBLET Train-the-Trainer

2023-09-13 to 2023-09-15 (3 days)
Deadline 2023-08-21
Uppsala
More infoThis course offers guidance, ideas and tips for designing training/teaching, development and delivery on training activities, all based on research-driven educational principles. This course will cover 4 main topics: - Learning principles and how they apply to training and teaching - Design and plan session, course, materials - Teaching techniques to enhance learner engagement and participation - Assessment and feedback in training and teaching Note! The course is highly interactive and hence it is important that you, as a participant, actively contribute to all sessions and elements of the course.

RaukR, Advanced R for bioinformatics workshop

2023-06-11 to 2023-06-22 (12 days)
Visby
More infoThis course aims to help researchers who are already using R for basic bioinformatics analyses and who would like to start using R at a more advanced level.

NBIS/ELIXIR-SE Tools for Reproducible research

2023-04-24 to 2023-04-28 (5 days)
Online
More infoThis course aims to help researchers make their computational analysis more reproducible.

Introduction to Biostatistics and Machine Learning

2023-04-24 to 2023-04-28 (5 days)
Uppsala
More infoThe course is geared towards life scientists wanting to be able to understand and use basic statistical methods.

Introduction to Data Management Practices

2023-04-18 to 2023-04-20 (3 days)
Uppsala
More infoThis course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises.

Workshop on Data visualization in R

2023-04-17 to 2023-04-19 (3 days)
Lund
More infoThis course aims to help researchers to visualize their data in different ways using R.

Neural Networks and Deep Learning

2023-03-20 to 2023-03-24 (5 days)
Uppsala
More infoThis course will give an introduction to the concept of Neural Networks (NN) and Deep Learning. Topics covered will include: NN building blocks, including concepts such as neurons, activation functions, loss functions, gradient descent and back-propagation; Convolutional Neural Networks; Recursive Neural Networks; Autoencoders; and best practices when designing NNs,

RNAseq data analysis

2023-03-13 to 2023-03-16 (4 days)
Uppsala
More infoThis workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of lectures and computer practicals.

Omics Integration and Systems Biology

2023-02-08 to 2023-02-10 (3 days)
Online
More infoThe aim of this course is to provide an integrated view of data-driven hypothesis generation through machine learning integration methods, biological graph / network analysis and genome-scale metabolic models. A general description of different methods for analyzing different omics data (e.g. transcriptomics and genomics) will be presented with some of the lectures discussing key methods and pitfalls in their integration.

Introduction to bioinformatics using NGS data

2023-02-06 to 2023-02-10 (5 days)
Uppsala
More infoThis intense one-week workshop provides an introduction to the analysis of next generation sequencing data.

Single cell RNAseq data analysis

2023-01-30 to 2023-02-03 (5 days)
Solna
More infoThis workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of online lectures and computer practicals. The total course duration is 5 days, including the lectures and practical exercises

Tools for Reproducible Research

2022-11-21 to 2022-11-25 (5 days)
Online
More infoOne of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis, e.g. bioinformatics or computational biology, have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete, undocumented and/or unavailable code. This essentially prevents any possibility of attempting to reproduce the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication based on computational analysis should be distributed along with all the raw data and metadata used in the study, all the code and/or computational notebooks needed to produce results from the raw data, and the computational environment or a complete description thereof. Reproducible research not only leads to proper scientific conduct but also provides other researchers the access to build upon previous work. Most importantly, the person setting up a reproducible research project will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self!

UPPMAX Programming Formalisms

2022-10-24 to 2022-10-28 (5 days)
Online
More infoThis course aims to give life scientists, bioinformaticians, and other scientists with some experience in programming and scripting an understanding of the underlying principles of software development, design, and programming. The course aims to strengthen the understanding of more advanced programming concepts, ability to produce more reusable scripts through modular programming and to enable a better understanding of how to evaluate a script or programs performance. We will cover an introduction to Algorithms and Data structures, Programming Paradigms especially structured and object oriented programming and to give a overview of other paradigms like functional programming. Modular development and (code) reusability, testing and optimisation. The modules will cover theory with bridging practical examples and applications to enhance the theoretical understanding of the principles.

Epigenomics Data Analysis: from Bulk to Single Cell

2022-10-24 to 2022-10-28 (5 days)
Online
More infoThis workshop aims to introduce the best practice bioinformatics methods for processing, analyses, visualisation and integration of epigenomics and functional genomics data.

Introduction to Data Management Practices

2022-10-11 to 2022-10-13 (3 days)
Solna
More infoThis course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data.

Python programming with applications to bioinformatics

2022-10-10 to 2022-10-14 (5 days)
Online
More infoThis course provides a practical introduction to the writing of Python programs for the complete novice. Participants are led through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs.

Introduction to bioinformatics using NGS data

2022-09-26 to 2022-09-30 (5 days)
Uppsala
More infoThis intense one-week workshop provides an introduction to the analysis of next generation sequencing data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures.

Introduction to Biostatistics and Machine Learning

2022-09-12 to 2022-09-16 (5 days)
Uppsala
More infoThe course is geared towards life scientists wanting to be able to understand and use basic statistical methods. It would also suit those already applying biostatistical methods but have never got a chance to reflect on and truly grasp the basic statistical concepts, such as the commonly misinterpreted p-value.

Snakemake BYOC (bring-your-own-code) workshop

2022-08-31 to 2022-09-02 (3 days)
Online
More infoThe NBIS Tools for reproducible research course is held twice a year and provides an introduction into Snakemake and a tutorial to learn how to use Snakemake. This Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash, R or python into a Snakemake workflow, or B) apply more advanced techniques to their existing Snakemake workflows.

Spatial omics data analysis

2022-08-29 to 2022-09-02 (5 days)
Online
More infoThis workshop provides resources to advanced tools for analysis of spatial datasets via a series of online lectures and computer practicals.

RaukR, Advanced R for Bioinformatics

2022-06-13 to 2022-06-17 (5 days)
Online
More infoIn Life Science and Bioinformatics, R is increasingly being used to transform and analyse data, perform statistical analysis and produce publication-ready visualisations. This workshop will focus on advanced R functionality, to increase the participants skillset and understanding of what is possible to do today.

Nordic ELIXIR-GOBLET Train-the-Trainer

2022-05-10 to 2022-05-13 (4 days)
Online
More infoThis course offers guidance, ideas and tips for designing training/teaching, development and delivery on training activities, all based on research-driven educational principles.

Workshop on Data Visualization in R

2022-04-27 to 2022-04-29 (3 days)
Lund
More infoThis course aims to help researchers to visualize their data in different ways using R. This course will also aim to show researchers how they can make publication grade figures using R. A part of this course is also about making interactive plots that the researchers can view and share in a web-server to make interactive visualizations of the data.

NBIS/ELIXIR-SE Tools for Reproducible Research

2022-04-25 to 2022-04-29 (5 days)
Online
More infoOne of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis, e.g. bioinformatics or computational biology, have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete, undocumented and/or unavailable code. This essentially prevents any possibility of attempting to reproduce the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication based on computational analysis should be distributed along with all the raw data and metadata used in the study, all the code and/or computational notebooks needed to produce results from the raw data, and the computational environment or a complete description thereof. Reproducible research not only leads to proper scientific conduct but also provides other researchers the access to build upon previous work. Most importantly, the person setting up a reproducible research project will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self!

Introduction to Data Management Practices

2022-04-05 to 2022-04-07 (3 days)
Uppsala
More infoThis course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data.

Introduction to Bioinformatics using NGS data

2022-03-28 to 2022-04-01 (5 days)
Online
More infoThis course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data.s

Single cell RNA-seq data analysis

2022-02-02 to 2022-02-04 (3 days)
Solna
More infoThis workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of online lectures and computer practicals. The total course duration is 45 hours, including the online lectures (15 hours) to be watched in advance and practical workshop that will be held on site in Stockholm (30 hours). The practical session is divided into both analysis overview and a Bring-Your-Own-Data (BYOD) day.

NBIS workshop in Neural Nets and Deep Learning

2022-01-17 to 2022-01-21 (5 days)
Uppsala
More infoThis course will give an introduction to the concept of Neural Networks (NN) and Deep Learning.

FAIR principles in life science research practice

2021-12-09 to 2021-12-09 (1 days)
Online
More infoThis online workshop will showcase how to put the FAIR principles into practice and is specifically designed to cater to life science researchers at all career stages. It is organised by SciLifeLab Data Centre and NBIS and include international speakers, presenters from the SciLifeLab community and optional hands-on exercises guided by experts from NBIS and SciLifeLab Data Centre.

Introduction to bioinformatics using NGS data

2021-11-22 to 2021-11-26 (5 days)
Online
More infoThis intense one-week workshop provides an introduction to the analysis of next generation sequencing data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures.

ELIXIR Tools for Reproducible Research

2021-11-15 to 2021-11-19 (5 days)
Online
More infoOne of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis, e.g. bioinformatics or computational biology, have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete, undocumented and/or unavailable code. This essentially prevents any possibility of attempting to reproduce the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication based on computational analysis should be distributed along with all the raw data and metadata used in the study, all the code and/or computational notebooks needed to produce results from the raw data, and the computational environment or a complete description thereof. Reproducible research not only leads to proper scientific conduct but also provides other researchers the access to build upon previous work. Most importantly, the person setting up a reproducible research project will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self!

RNA-seq data analysis

2021-11-15 to 2021-11-19 (5 days)
Online
More infoThis workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of online lectures and computer practicals.

Epigenomics Data Analysis: from Bulk to Single Cell

2021-10-25 to 2021-10-29 (5 days)
Online
More infoThis workshop aims to introduce the best practice bioinformatics methods for processing, analyses and integration of epigenomics and functional genomics data.

Python programming with applications to bioinformatics

2021-10-18 to 2021-10-22 (5 days)
Online
More infoThis course provides a practical introduction to the writing of Python programs for the complete novice. Participants are led through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs.

Introduction to Data Management practices

2021-10-12 to 2021-10-14 (3 days)
Online
More infoThis course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data.

Introduction to biostatistics and machine learning

2021-10-04 to 2021-10-08 (5 days)
Online
More infoThe course is geared towards life scientists wanting to be able to understand and use basic statistical methods. It would also suit those already applying biostatistical methods but have never got a chance to reflect on and truly grasp the basic statistical concepts, such as the commonly misinterpreted p-value.

Snakemake BYOC (bring-your-own-code) workshop

2021-09-29 to 2021-10-01 (3 days)
Online
More infoAs data analysis projects grow and change over time, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake can be used to set up, perform and monitor defined sequences of computational tasks (“workflows”), thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well suited for bioinformatics workflows. The NBIS Tools for reproducible research course is held twice a year and provides an introduction into Snakemake and a tutorial to learn how to use Snakemake. This Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash, R or python into a Snakemake workflow, or B) apply more advanced techniques to their existing Snakemake workflows.

BiG Talks – Metabolic Atlas: genome-scale metabolic models for easy browsing and analysis

2021-09-10 to 2021-09-10 (1 days)
More info

BiG Talks – Network-based integration and visualization of large-scale data

2021-09-10 to 2021-09-10 (1 days)
More info

BiG Talks – Network based analysis of 1002 GWAS study defines a pleiotropy map of human cell biology

2021-09-08 to 2021-09-08 (1 days)
More info

Workshop on Plotting in R

2021-09-08 to 2021-09-09 (2 days)
Online
More infoThis course aims to help researchers to visualize their data in different ways using R. This course will also aim to show researchers how they can make publication grade figures using R. A part of this course is also about making interactive plots that the researchers can view and share in a web-server to make interactive visualizations of the data.

ELIXIR Omics Integration and Systems Biology

2021-09-06 to 2021-09-10 (5 days)
Online
More infoThe aim of this workshop is to provide an integrated view of data-driven hypothesis generation through biological network analysis, constraint-based modelling, and supervised and unsupervised integration methods. A general description of different methods for analysing different omics data (e.g. transcriptomics and genomics) will be presented with some of the lectures discussing key methods and pitfalls in their integration. The techniques will be discussed in terms of their rationale and applicability. The course will also include hands-on sessions and several seminars by invited speakers.