The Schiessel Lab code repository

You're on the GitHub page for the Theoretical Physics of Life Processes group at Leiden University, led by Helmut Schiessel. Below you'll find information about the projects in our GitHub repositories. More information about the group itself and its research can be found on the group website.

Our repositories

The Schiessel Lab's GitHub repositories can be found at github.com/SchiesselLab. Here follow descriptions of our various computational projects.

Nucleosome Mutatation Monte Carlo

Implementation of the Mutation Monte Carlo method of Eslami-Mossallam et al. (2016) [open access] for the nucleosome. Variations of this implementation have been used in various publications:

  • Tompitak et al., BMC Bioinformatics 18 (2017) 157 [open access]
  • Tompitak et al., EPL 116 (2016) 68005 [doi]

Nucleosome Positioning with Markov Chains

Combining the basic idea for a Markov chain model for sequence-dependent nucleosome positioning presented by Segal et al. (2006) [doi] with nucleosomal sequence preference statistics derived from the Mutation Monte Carlo method of Eslami-Mossallam et al. (2016) [open access] leads to a computationally efficient method for predicting nucleosome affinity from based on a theoretical model of the nucleosome.

This methodology is explained and applied in the following publications:

  • Tompitak et al., BMC Bioinformatics 18 (2017) 157 [open access]
  • Tompitak et al., Biophysical Journal 112 (2017) 505-511 [doi]

3D Visualization of the RBP Model

Built on three.js, this project provides in-browser 3D visualization of the Rigid Base Pair model. Live version here. It has been used to provide visuals for various publications:

  • Tompitak and Schiessel, Nederlands Tijdschrift voor Natuurkunde 83 (2017) 164-167
  • Tompitak et al., Phys. Rev. E 95 (2017) 052402 [doi]
  • Tompitak et al., EPL 116 (2016) 68005 [doi]
  • De Bruin et al., J. Phys. Chem. B 120 (2016) 5855-5863 [doi]