New book chapter on “Data Management in Computational Systems Biology” published

A new book chapter titled “Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices” with co-author Jürgen Pahle was published as part of the book “Yeast Systems Biology“, edited by Stephen G. Oliver and Juan I. Castrillo (pages 285-314).

More details can be found here: doi:10.1007/978-1-4939-9736-7_17.

[Yeast Systems Biology book cover]

Visit from a LG Global Challenger Team

[photo LG Global Challenger Team]

On 16. August 2019, a LG Global Challenger team from South Korea visited our group. The team, consisting of the students Alvin Choi, Wooyoung Jo, Heeryung Heo, and Yoojin Bang from the Korea Advanced Institute of Science and Technology, (KAIST), was on their two-week tour through a handful of research labs all around Europe.

The team was most interested in the various modelling methods currently used for biological processes in the human body, and our modelling software COPASI. We talked about some of the challenges the field is facing now, and discussed about what technologies and services might be available in the future. They wanted to find out how far we are from reliably modelling whole organs, to assist the development of artificial organs in the future.

The LG Global Challenger program competitively selects teams of students, who are then funded to travel the world and visit academic groups in order to talk with them about research questions that the teams chose for themselves to work on.

International Conference on Systems Biology 2018 (ICSB), Lyon, France

Our team is present at the ICSB 2018 in Lyon, from 28. October to 1. November 2018.

Martin Zauser gives a talk titled “Automated image analysis and modeling of calcium waves in plant roots” (Co-authors: Rik Brugman, Janos Löffler, Guido Grossmann & Jürgen Pahle) and we present the following posters:

  • Arne Schoch & Jürgen Pahle “Structural Models for Frequency-Decoding in Calcium Signalling – How Topological Features Allow for Band-Pass Activation”
  • Irina Surovtsova & Jürgen Pahle “Investigating functional connections in biological networks using transfer entropy: Pitfalls and how to avoid them”
  • Jonas Förster & Jürgen Pahle “CoRC – the Copasi R Connector”

In addition Jürgen Pahle is an instructor at both the COMBINE tutorial and the Advanced modelling with COPASI-tutorial on 27. October, just before the main conference.

Release of our new R-package for the generation of customizable, discretized time series of oscillations

Our new R-package, OscillatorGenerator, is available for download on CRAN (The Comprehensive R Archive Network). The package offers several new functions for the generation of time series of oscillations in R. Each function represents a basic oscillation shape such as sinusoids, square-waves, spikes and bursts. By means of a multitude of function arguments, an oscillation’s appearance is widely customizable. Among others, arguments control an oscillation’s frequency, baseline and peak levels as well as duty cycle.

The package is available at: