TOM – 02.03.2016

Venue: Biomedicum 1, Meeting room B236a, 2nd floor

Arvydas Dapkunas

Hello Folks! 

The coming Wednesday I will present you a show case of image analysis toolkit ANIMA running on Anduril.

ANIMA is an image analysis workflow environment on top of Anduril an open source component-based workflow framework for scientific data analysis (developed in S.Hautaniemi lab). The Anima was used in visualizing and quantifying properties of 3D cell culture of kidney stem cells. In the presentation I’ll introduce key principles and questions of kidney development. Then I’ll pop the hood of ANIMA with the examples of how scripted image analysis answers question of the project.

WARNING: Lots of images, so you may want to bring popcorn!

Ville Rantanen

NiceCSV is an interactive tabular data browser, as well as a text based tabular data formatter. The browser is capable of giving a quick overview of the data using a simple keyboard interface. The user may view basic statistics, sort by column, format the values, change alignment, or search with a keyword.

NiceCSV works in unison with other Unix tools, such as grep, cut and sed, reusing their capabilities for tabular data processing. 

NiceCSV is freely downloadable and the source code is available at

It has no dependencies other than the standard Python libraries. The program is fully portable to all operating systems that run Python. (Cygwin required for Windows for the interactive browser)



TOM – 17.02.2016

Analysis and visualization software for massive next-generation sequencing data sets

Presented by: Riku Katainen, PhD student, Aaltonen lab, Genome-Scale Biology Program

Due to the massive availability of next- and third generation sequencing (NGS) data, the processing and analysis now constitute a serious challenge for research in life sciences. I will introduce a highly efficient and user friendly analysis and visualization software tool (BasePlayer), which is designed for huge NGS data sets. BasePlayer offers comparative variant analyses not only in genes but also in intergenic regions by integrating regulatory annotation, transcription factor (TF) binding sites and motifs.

I am going to show basic functions of the program in real time with an actual cancer data. BasePlayer is still under development and will be published soon, so I’ll be happy to hear your suggestions and comments.

Screenshot of somatic mutations in APC gene and annotation in Base Player


Screenshot of split screen view at TTC28 LINE1-Element in Base Player