ZigCell3D (2011-2013)
The goal of the ZigCell3D project is to develop an innovative simulation and analysis tool, that enables study of spatial cellular processes, connecting wet biology with systems biology, to accurately model complex signal transduction networks and visualise their dynamics in three dimensional space. The wider aim of this tool is to play an important role in the development of better quality and higher efficiency therapeutic drugs. This software product is the result of a CTI project executed by the ScienceVisuals team together with Prof. Heinz Koeppl and his team from the Biomolecular Signaling and Control Group (BISON) at the Swiss Federal Institute of Technology in Zurich (ETHZ) (now Bioinspired Communication Systems Lab at TU Darmstad).
Technology: The ScienceVisuals in-house ray tracing and simulation engine BioInspire, researched and developped by Dr. Pablo de Heras Ciechomski, was given a user interface brush-up to handle biophysical simulations done at ETHZ, Zurich.
Relevant publications:
- “From Biochemical Reaction Networks to 3D Dynamics in the Cell: the ZigCell3DModeling, Simulation and Visualisation Framework” by P. de Heras Ciechomski, M. Klann, R. Mange and H. Koeppl, IEEE Symposium on Biological Data Visualization 2013 (BioVis), Atlanta, 2013.
- “From Microscopy Data to in silico Environments for in vivo Oriented Simulations” by N. Hiroi, M. Klann, K. Iba, P. de Heras Ciechomski, S. Yamashita, A. Tabira, T. Okuhara, Y. Okada, Y. Oka, C. Flamm, R. Mange, M. Unger, A. Funahashi and H. Koeppl, EURASIP Journal on Bioinformatics and Systems Biology, 2012.
- "ZigCell3D An Interactive Simulation and Visualization Tool for Intracellular Signaling Dynamics", Heinz Koeppl, Pablo de Heras Ciechomski, CTI MedTech Event 2012. A poster presented for the Commision for Technologx and Innovation (CTI) about the ongoing project ZigCell3D and its application to simulate chemical signalling cascades to better understand and optimize chemical reactions in single cell processes.
