Chipster - a user-friendly bioinformatics software for analyzing high-throughput data

by Kimmo Mattila (CSC), Dr Korpelainen Eija (CSC), Mr Petri Klemelä (CSC)


Are you curious to learn more about the user-friendly bioinformatics software for analyzing high-throughput data known as Chipster?

Objective of the webinar

To give an introduction to the Chipster software and provide tools on how to set up and operate it.

Target audience

Life scientists, service providers interested to set-up and operate a Chipster service for supporting bioscientists.

Webinar programme (1h)

  • Introduction to Chipster (25’):

    • Analysis tool content, visualizations, sharing analysis sessions)

    • Demo: how to do things in practice

    • Chipster resources for online learning

  • How to set-up and operate a new Chipster server (25’)

    • Troubleshooting 

  • Q&A (10 min)

Description of the webinar

Chipster is a user-friendly bioinformatics software for analyzing high-throughput data such as RNA-seq and single cell RNA-seq. Chipster provides an easy to use web interface for over 450 analysis tools and a large collection of reference genomes. Chipster allows users to visualize data interactively, and it keeps track of the analysis steps taken. This provenance tracking combined with an easy way to share analysis sessions with other users allows researchers to collaborate efficiently. 

Chipster was developed by CSC – IT Center for Science which also runs a national Chipster server in Finland. The Chipster code base is freely available and many institutes around the world have set up their own Chipster servers. EGI operates a Chipster server which is available for the whole scientific community.

The first half of this webinar gives an overview of Chipster, and how you can use the EGI Chipster service to analyze your NGS data. We will also introduce Chipster training resources ranging from YouTube tutorials to example analysis sessions to get you started. The second half of the webinar is targeted for service providers interested in setting up and operating a Chipster server for their user communities.

About the speakers


Kimmo Mattila works as an application specialist and CSC - IT Center for Science. He has long experience on HPC and storage related customer support for bioscientists using the services CSC.

Eija Korpelainen works currently as a Product manager at CSC – IT Center for Science. Being the national supercomputing centre, CSC provides bioinformatics services for all the universities and research institutes in Finland. Eija has long experience in enabling life scientists to analyze high-throughput data. She has run over 100 training courses in Finland and abroad, and her team has established a popular YouTube channel with tutorial videos. The book “RNA-seq data analysis – practical approach” by Korpelainen et al has been one of the most popular bioinformatics books in recent years. In order to enable biologists to analyze data more efficiently, her team has developed the open source analysis software Chipster which is used worldwide. Eija has participated in several international consortia including the EU funded EMBRACE, AllBio and SeqAhead, and she is currently involved in ELIXIR as the national Training Coordinator and in GOBLET (Global Organization for Bioinformatics Learning, Education and Training) as member of the executive board. Eija holds a PhD from the Medical faculty of University of Adelaide, Australia, and she completed her post doctoral research as an EMBO long term fellow in the University of Helsinki, Finland. Eija has over 40 peer-reviewed publications and an H-index of 22.

Petri Klemelä works as a software developer at CSC - IT Center for Science. He enjoys applying technology to solve new practical problems. He wants to enable people to focus on more meaningful and creative tasks, regardless of whether an improvement is needed in the user interface or deep down in the server performance.