JIC Training in Bioinformatics and Scientific Computing

Course Directory

This page lists the courses that we run internally, as well as providing direct links to our online course materials. For more information, just e-mail us.

An introduction to HPC

Making use of the cluster

The HPC facilities at the NBI provide a fantastic resource for computational biology. This course will introduce you to these facilities and provide hands on experience in how to use them. You'll also get to know the people running the cluster.
Half day
Next session October 2020

RNA-Seq Part II

Studying the transcriptome.

RNA-Seq allows to study the transcriptoe of organisms. Several applications of RNA-Seq include measuring expression levels of genes, gene annotation or the interrogation of the gene space as a complexity. This course teaches to process RNA Seq data from receiving raw sequence files to getting expression values for genes.
Full day
Next session December 2020

Version Control with Git and GitHub

Managing your files and scripts

Version control systems are the lab notebook of the digital world. They let you record the history of your files and scripts, look at old versions and see who changed what, when. Online systems for sharing version control repositories, particularly GitHub, have become a standard for publishing scientific code.

Next session Discontinued

Machine Learning for beginners

Applying AI to biology

Machine learning is an exciting set of tools and techniques for classifying and analysing data. This course will introduce the state of the art in machine learning and provide some hand-on experience with data handling and analysis.

Next session Spring 2021

Introduction to Scientific Computing

What the JIC can offer

Research in biology is increasingly dependent on computational approaches. From bioinformatics and quantitative image analysis to data visualisation and numerical modelling, scientific computing underpins many aspects of modern science. This course will introduce you to the resources, support and training available at the JIC.
One hour
Next session Deprecated

Introduction to R

A software environment for statistical computing

R is a free software environment for statistical computing and graphics. It is widely used in scientific data analysis. R is a great tool for biologists, since it provides cutting edge statisical techniques, excellent graph and figure plotting capabilities and bioinformatics tools all in one package.
Two full days
Next session March 2021

Bioinformatics (and how to learn it)

Introducing the wonderful world of bioinformatics

Research in biology is increasingly dependent on computational approaches. However, the world of Computational Biology is big and confusing. This course aims to provide an introduction and map to that world, explaning what tools and techniques are out there and what you'll need to do to take advantage of them.
2 x half day
Next session December 2020

Quick Unix/Linux command line shell

The key to power bioinformatics

The command line shell is the main way to interact with most powerful computing systems and bioinformatics tools. This course provides what you need to get going with the shell.

Next session October 2020

Python for Biologists

Programming for Scientific Computing

Python is a flexible programming language that is becoming increasingly popular for scientific computing. This course will give you a basic introduciton in how to use Python. The course will work towards a script for parsing FASTA files and calculating the GC-content of DNA sequences.

Next session January 2021

Image Analysis with Fiji

From images to data

Bioimaging is a rich source of data in biology. However, quantifying those data requires a strong understanding of the correct computational techniques. This course provides an introduction to those techniques using Fiji (powerful and free image analysis software designed for biological applications). We'll also look at managing image data with OMERO and the ethics of image analysis.
Half day
Next session May 2021

Introduction to RNA-Seq

Studying the transcriptome.

RNA-Seq allows to study the transcriptoe of organisms. Several applications of RNA-Seq include measuring expression levels of genes, gene annotation or the interrogation of the gene space as a complexity. This course teaches to process RNA Seq data from receiving raw sequence files to getting expression values for genes.
Full day
Next session November 2020

Introduction to Linux

The operating system for bioinformatics

Linux is the operating system of high performance clusters and supercomputers all over the world. Learning to use Linux is a key part of making use of cutting edge bioinformatics tools. This course provides an extensive introduction to Linux, covering both basic and advanced use.
Two half days
Next session November 2020

Introduction to Phylogenetics

Aligning sequences and building trees

The course aims to provide the basics of building and interpreting phylogenetic trees. It will provide lectures on the principle of phylogenetics and hands-on practice of using various freely-available programs used in phylogenetics studies.

Next session Spring 2021

A Quick Introduction to R

Getting familiar with R

This course provides a quick introduction to R for those who are interested in exploring its capabilities before committing to a longer course.
Half day.
Next session Discontinued

Advanced image analysis

Automating your image processing

Getting useful information out of our image data often requires analysis with computer programs like Fiji/ImageJ. However, when we have very large amounts of data, or particularly complex analyses we need to be able to use those programs in more sophisticated ways. This course looks at ways to automate analyses and develop more complex processing tools.
Half day
Next session June 2021