This repo is modified from the Jupyter Notebok Stacks base-notebook.
The Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structures for fast 3D visualization and analysis.
This Docker image contains tools needed to run MMTF (Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.)
Originally created as part of the 2018 UCSD Structural Bioinformatics Hackathon - https://github.com/sbl-sdsc/mmtf-workshop-2018
Methods for mapping genomic data onto 3D protein structure.
Methods for mapping proteomics data on 3D protein structure.
Instructions provided by Docker.
git clone https://github.com/sbl-sdsc/mmtf-genomics.git
docker run -it --rm -v `pwd`:/home/jovyan/work -p 8888:8888 stevetsa/mmtf-docker
Alternatively, you can also run this Docker image from commercial cloud service providers.
From a local machine, connect to an AWS instance.
### Replace [email protected] with your AWS Public DNS
ssh -i "/path/to/sshkey.pem" -L 8888:0.0.0.0:8888 [email protected]
From AWS (ubuntu) instance, install docker and run -
### install Docker if needed
sudo apt-get update
sudo apt-get install -y docker.io
### run Docker image from a directory containing your Jupyter Notebook
git clone https://github.com/sbl-sdsc/mmtf-workshop-2018.git
git clone https://github.com/sbl-sdsc/mmtf-genomics.git
docker run -it --rm -v `pwd`:/home/jovyan/work -w `pwd` -p 8888:8888 stevetsa/mmtf-docker
Point browser to http://localhost:8888/?token=abc........ (Last line of output from the previous command)
Please visit the documentation site for help using and contributing to this image and others.
Content type
Image
Digest
Size
1.2 GB
Last updated
about 7 years ago
docker pull stevetsa/mmtf-docker