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.
Citation
Please cite the following paper if you use opennucleome package:
"OpenNucleome for high resolution nuclear structural and dynamical modeling", eLife, doi: 10.1101/2023.10.16.562451
Environment
We recommend using openmm 7.5.1 together with openNucleome, which can be installed with the following command:
conda install -c conda-forge openmm=7.5.1
Other required packages: numpy, pandas, scikit-learn, MDAnalysis, mdtraj.
Tutorials
Detailed instructions for performing simulations of a human nucleus can be found at: tutorials/HFF_100KB. We also provide a tutorial for parameter optimization to develop new nucleus models at: tutorials/optimization.
Manual
Detailed documentation of the source code can be found at: https://zhanggroup-mitchemistry.github.io/OpenNucleome/
1 maintainer
Release files for openNucleome 1.3.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| openNucleome-1.3.0.tar.gz | 371.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| openNucleome-1.3.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 749.4 kB
Release files / openNucleome-1.3.0.tar.gz
| Download URL | openNucleome-1.3.0.tar.gz |
|---|---|
| Size | 371.7 kB |
| Tags | Source |
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Release files / openNucleome-1.3.0-py3-none-any.whl
| Download URL | openNucleome-1.3.0-py3-none-any.whl |
|---|---|
| Size | 377.7 kB |
| Tags | Python 3 |
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