modify the README

openNucleome/parameters/HFF_100KB/README.md

@@ -1,16 +1,14 @@
-alpha.txt: all the parameters for the Chromosomes-Chromosomes
+This folder includes all the parameter files needed for simulating a human nucleus. The parameters were optimized to reproduce experimental data, including Hi-C, DamID, and TSA-Seq.
 
-## Files about the Chromosomes-Nuclear landmarks
-chr_lam_spec.txt: Chr-lamina potential parameters
+- chr_lam_spec.txt: Chromosome-lamina interaction parameters
 
-chr_spec_param.txt: Chr-speckle potential parameters
+- chr_spec_param.txt: Chromosome-speckle interaction parameters
 
-chr_nuc_param.txt: the probability for a chromatin bead to be in the nucleolus state as assigned by the SPIN algorithm
+- chr_nuc_param.txt: Chromosome-nucleoli interaction parameters 
 
-## Files about the Chromosomes-Chromosomes
+- ideal_param.txt: intra-chromosomal interaction parameters
 
-ideal_param.txt: intra-chromosomal potential parameters
+- inter_param.txt: inter-chromosomal interaction parameters
 
-types_param.txt: compt-compt potential parameters
+- types_param.txt: interaction parameters among various compartmental types
 
-inter_param.txt: inter-chromosomal potential parameters

tutorials/HFF_100KB/README.md

@@ -1,36 +1,10 @@
 ## HFF model with nuclear landmarks at 100KB resolution
 
-This example is the HFF nucleus with nuclear landmarks (lamina, speckle, nucleolus) at 100KB resolution.
+This folder provides tutorials for setting up and performing simulations of the HFF nucleusi at the 100KB resolution with the presence of various nuclear landmarks, including nuclear lamina, speckles, and nucleoli.
 
-The model has 60642 chromosome beads, 300 nucleolus beads, 1600 speckle beads, and 8000 lamina beads.
+- SphericalNucleus
+    1. This tutorial explains how to setup simulations of a spherical nucleus.
 
-We implemented the adaptive learning rate optimization (adam) to coarsely optimize the ideal (intra-chromosomal) potential, the compt-compt potential, and the inter-chromosomal potential with Hi-C data; chr-lamina and chr-speckle potential with sequencing data (DamID and TSA-Seq). All the optimization scripts are under the folder "/OpenNucleome/tutorials/optimization".
+- NuclearDeformation
+    1. This tutorial explains how to setup simulations to introduce external forces that deform the nucleus.
 
-To run the simulation:
-```
-python simulation.py
-```
-alpha.txt: all the parameters for the Chromosomes-Chromosomes
-
-human.pdb: the initial structure
-
-simulation.py: run the molecular dynamics simulation
-
-coordinate_transformation.py: convert the position used in OpenMM to reduced unit
-
-final_frame.py: extract the last frame of the simulation to restart the next iteration
-
-## Files about the Chromosomes-Nuclear landmarks
-chr_lam_spec.txt: Chr-lamina potential parameters
-
-chr_spec_param.txt: Chr-speckle potential parameters
-
-chr_nuc_param.txt: the probability for a chromatin bead to be in the nucleolus state as assigned by the SPIN algorithm
-
-## Files about the Chromosomes-Chromosomes
-
-ideal_param.txt: intra-chromosomal potential parameters
-
-types_param.txt: compt-compt potential parameters
-
-inter_param.txt: inter-chromosomal potential parameters

tutorials/README.md

@@ -1,7 +1,4 @@
-## Analysis code
+# Tutorials
 
-This folder contains a HFF model at 100KB resolution and the optimization tutorials.
+This folder provides tutorials for setting up and performing simulations of a human nucleus using existing parameters (HFF_100KB) and for developing a new nucleus model with parameter optimization (optimization).
 
-HFF_100KB: a HFF model at 100KB resolution
-
-optimization: optimization tutorials, including chromosome-chromosome potential and chromosome-nuclear landmarks potential