diff --git a/tutorials/README.md b/tutorials/README.md index 81ef368..b70632f 100644 --- a/tutorials/README.md +++ b/tutorials/README.md @@ -1,13 +1,13 @@ # Tutorials -This folder provides tutorials for the simulation and analysis with our model. +This folder provides tutorials using Jupyter Notebooks for various functionality supported by the software. -- HFF_100KB: Set up and performing simulations of a human nucleus using existing parameters, with Langevin dynamics or Brownian dynamics, with default setup or customized setup, with nuclear deformation or not. +- init_configs: Detailed instructions for generating, relaxing, and selecting initial configurations for MD simulations. -- compute_contact_prob: Compute the contact probablities within chromosomes and chromosome-Nuclear landmarks (DamID, TSA-Seq). +- HFF_100KB: Instructions for setting up and performing MD simulations of a human nucleus using optimized parameters. Two integrators, Langevin dynamics or Brownian dynamics, can be used to simulations. The model also supports deforming the nucleus from a perfect spherical geometry. -- init_configs: Include the configuration generation, configuration relaxation, and configuration selection for the following parameter optimization and analysis. +- compute_contact_prob: Instructions for computing contact probablities between chromosomes to compare with Hi-C data, and for computing chromosome-nuclear landmarks contact probabilities to compared with Lamin B DamID and SON TSA-Seq. -- optimization: Include the parameter optimization for ideal, compt-compt, inter-chromosomal interactions, and Chromosome-Speckle, Chromosome-Nucleolus interactions. +- optimization: Instructions for optimizing model parameters. -- new_feature: Tutorials for how to include new features and new beads into the system +- new_feature: Tutorial for expanding the software to introduce new features and components to the nucleus model.