From 50cfb2e3161adbf79053b2b379f4d7acc7d17da8 Mon Sep 17 00:00:00 2001
From: binzhangMIT <38547734+binzhangMIT@users.noreply.github.com>
Date: Fri, 22 Sep 2023 13:35:05 -0400
Subject: [PATCH] Update README.md

---
 README.md | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/README.md b/README.md
index da7f4bc..9c78da2 100644
--- a/README.md
+++ b/README.md
@@ -1,20 +1,16 @@
-## openNucleome
+## OpenNucleome
 
 OpenNucleome is an open-source software designed for conducting molecular dynamics (MD) simulations of the human nucleus. This software streamlines the process of setting up whole nucleus simulations through just a few lines of Python scripting. OpenNucleome can unveil intricate, high-resolution structural and dynamic chromosome arrangements at a 100 KB resolution. It empowers researchers to track the kinetics of condensate formation and fusion while also exploring the influence of chemical modifications on condensate stability. Furthermore, it facilitates the examination of nuclear envelope deformation's impact on genome organization. The software's modular architecture enhances its adaptability and extensibility. Leveraging the power of OpenMM, a GPU-accelerated MD engine, OpenNucleome ensures efficient simulations.
 
-## Manual
-
-The output html manual file is docs/index.html. 
+<img src="./images/Figure1.png" width="500px"><img>
 
-The manual is also shown in: https://zhanggroup-mitchemistry.github.io/OpenNucleome/
+## Examples
 
-Instructions for class methods and functions are also included as comments in the source code. 
+Details on setting up simulations of a human nucleus can be found at: examples/HFF_100KB. Scripts for analyzing simulation trajectories to compute contact probability maps are provided in: analysis.
 
 ## Environment
 
-We recommend using openmm 7.5.1 for using openNucleome, as openNucleome is built based on openmm 7.5.1. 
-
-Install openmm 7.5.1 with the following command: 
+We recommend openmm 7.5.1 when using openNucleome, which can be installed with the following command: 
 
 ```
 conda install -c conda-forge openmm=7.5.1
@@ -22,11 +18,14 @@ conda install -c conda-forge openmm=7.5.1
 
 Other required packages: numpy, mdanalysis, mdtraj.
 
+## Manual
 
-## Workflow for creating the whole nucleus model and efficiency across different platforms
+Detailed documentations are included in the source code and can be viewed at: https://zhanggroup-mitchemistry.github.io/OpenNucleome
 
-<img src="./images/Figure1.png" width="2000px"><img>
+## Citations
+
+Please cite the following paper if you use openabc package: 
+
+    "OpenNucleome for high resolution nuclear structural and dynamical modeling", doi: XXX
 
-## Examples
 
-We provide an example in examples/HFF_100KB, and we also show how to calculate the contact probabilities and compare with experiments to obtain optimized potential parameters in ./analysis_code.