Blog

Arne Schoch and Jürgen Pahle’s article on their study of the requirements for band-pass activation of Ca²⁺-sensitive proteins such as NFAT appears in Biophysical Chemistry 245:41, doi:10.1016/j.bpc.2018.10.005.

Jürgen Pahle gave a talk on Information Biology at the 35th Chaos Communication Congress in Leipzig, Germany (27.-30. December 2018).

The video of the talk is embedded below. You can also watch it directly at media.ccc.de. Please find more information at https://fahrplan.events.ccc.de/congress/2018/Fahrplan/events/9734.html.

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.

Jürgen Pahle is teaching Copasi (copasi.org) and CoRC (jpahle.github.io/CoRC) at the BioModelling Spring School in Riga, Latvia (15-17 May 2018).

This course is organized by Egils Stalidzans at the Institute of Microbiology and Biotechnology of the University of Latvia. It is also an EU-funded COST action OpenMultiMed Training School (TS5).

For further information go to www.lu.lv/mbi/biomodriga/.

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: https://CRAN.R-project.org/package=OscillatorGenerator.

We would like to announce the BIOMS symposium 2018, a symposium to celebrate 15 years of modeling and simulation in the biosciences in Heidelberg.

BIOMS (the Center for Modeling and Simulation in the Biosciences) in Heidelberg, Germany, started in the year 2004. This initiative had the aim to establish modeling approaches in the life sciences as a central discipline in Heidelberg with an impact also nationally and internationally. In the end of 2018 this initiative will finally come to an end. BIOMS financed junior groups and PostDocs over the years, many of which are now full professors at different institutions in Germany.

The symposium will focus on what is at the heart of BIOMS – modeling and simulation in the biosciences with a special focus on biomechanics, multi-scale processes, information processing and methods.

The programme is available at: http://www.bioms.de/symposium2018

Registration and abstract submission for contributed talks and posters is now open!

F. Graw, F. Matthäus and J. Pahle (eds.) (2017)
Modeling Cellular Systems,
Springer International Publishing, Cham, Switzerland, ISBN 978-3-319-45831-1, springer.com, amazon.de, doi:10.1007/978-3-319-45833-5