Biophysical Society Thematic Meeting| Les Houches 2019

Multiscale Modeling of Chromatin: Bridging Experiment with Theory

Poster Abstracts

29-POS Board 29 MODELLING SPATIAL STRUCTURE OF CHROMATIN BASED ON EXPERIMENTAL POSITIONS OF NUCLEOSOMES Tilo Zülske 1 ; Michael Möhrl 1 ; Robert Schöpflin 1 ; Gero Wedemann 1 ; 1 University of Applied Sciences Stralsund, Institute of Applied Computer Sciences, Stralsund, Mecklenburg-Vorpommern, Germany In chromatin DNA is wrapped around histone proteins forming nucleosomes. The nucleosome chain folds into higher order structures as topological domains, chromosomes and the whole nucleus. Despite experimental advancements in electron microscopy, single molecule techniques and mapping of nucleosomes and their modifications, many fundamental features of chromatin remain undiscovered. Due to the poor experimental accessibility of chromatin, computer simulations are valuable tools for research. Computer simulation models of chromatin are usually coarse-grained models describing the main characteristics of the chromatin-fiber. While it is common practice in systems biology to make experimental data publicly available, simulation data of computer models is usually not published since no easy to use standard exchange format has been established. We analyzed the workflow from the experimental determination of the positions of the nucleosomes to the analysis of the output of the computer model describing this system. We defined standardized formats based on XML for artifacts generated by steps in this workflow. We found that XML is practical since it is possible to transform the XML-files applying XSLT into other formats for usage in other groups. We proved this workflow and the file formats with a complete example of computer simulation of chromatin domains based on experimentally determined nucleosome positions.


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