The Jupyter notebook Lysozyme.ipynb shows a Lysozyme + Mutations tutorial using the BioExcel building blocks biobb.
You may execute the notebook on a free cloud instance using myBinder, or for better performance/extensibility in your on instance of Jupyter Notebook.
The Docker image bioexcel/biobb_workflows is provided, based on myBinder.
Launch it as:
docker run -p 8888:8888 -it bioexcel/biobb_workflows
Then access the Notebook at http://127.0.0.1:8888/ using the provided token.
Tip: If you have an NVIDIA GPU and NVIDIA Docker installed, launch with nvidia-docker instead of docker for hardware-accelerated GROMACS.
For your own installation it is recommended to use BioConda on Linux or OS X. See the BioConda installation instructions for details. In brief:
First, install MiniConda (Python 3.x recommended). Then activate BioConda channels:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
Make a new Conda environment to keep our dependencies:
conda create -n biobb biobb_md biobb_io biobb_model nglview=1.2.0 simpletraj gromacs
Tip: Remove gromacs above if you have already installed GROMACS that you compiled with hardware accelerations like NVidia CUDA.
Activate the Conda environment:
conda activate biobb
After activating the Conda environment for the first time you may see a warning equivalent to:
WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind) or
- Make your system-wide implementation visible by doing 'ln -s /etc/OpenCL/vendors /home/USER/miniconda3/envs/biobb/etc/OpenCL/vendors'
The PyOpenCl documentation suggests how to proceed. OS X users should use conda install khronos-opencl-icd-loader which can use GPU hardware installed, while in Linux you can either provide a software-based OpenCL implementation with conda install pocl or (recommended) use GPU-specific hardware implementation found in /etc/OpenCL/vendors (e.g. apt install nvidia-driver-390) by creating the symlink as suggested.
Activate the nglview extension and start Jupyter Notebook:
jupyter-nbextension enable nglview --py --sys-prefix
jupyter notebook biobb_workflows/lysozyme_tutorial/notebooks/Lysozyme.ipynb
A browser window should appear, or click the link provided.
This software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the BSC (http://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) and eScience Lab group at The University of Manchester for the European BioExcel (http://bioexcel.eu/) CoE, funded by the European Commission (EU H2020 675728, 823830).
- (c) 2018-2019 Barcelona Supercomputing Center
- (c) 2018-2019 Institute for Research in Biomedicine
- (c) 2018-2019 The University of Manchester
The Jupyter Notebook is based on the Lysozyme in Water GROMACS tutorial by Justin A. Lemkul at Virginia Tech Department of Biochemistry.
Licensed under the Apache License 2.0, see the file LICENSE for details.
