sbl-sdsc/mmtf-workshop-2018

Structural Bioinformatics Training Workshop & Hackathon 2018

Structural Bioinformatics Training Workshop & Hackathon 2018

Application of Big Data Technology and 3D Visualization, San Diego Supercomputer Center, UC San Diego, May 7-9, 2018

Outcomes

Participant survey

Hackathon results

Workshop Tutorials

To try out our Jupyter notebook demos without any installation.

NOTE: Authentication is now required to launch binder! Sign into GitHub from your browser, then click on the launch binder badge below to launch Jupyter Lab.

It can take a few minutes for Binder to setup the environment.

Installation

Please follow the installation guide on mmtfPyspark's GitHub to install the python package.

Clone Repository

Clone this repository by running the following command on your terminal:

git clone https://github.com/sbl-sdsc/mmtf-workshop-2018.git

How to Cite this Work

Bradley AR, Rose AS, Pavelka A, Valasatava Y, Duarte JM, Prlić A, Rose PW (2017) MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures. PLOS Computational Biology 13(6): e1005575. doi: 10.1371/journal.pcbi.1005575

Valasatava Y, Bradley AR, Rose AS, Duarte JM, Prlić A, Rose PW (2017) Towards an efficient compression of 3D coordinates of macromolecular structures. PLOS ONE 12(3): e0174846. doi: 10.1371/journal.pone.01748464

Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prlić A, Rose PW (2018) NGL viewer: web-based molecular graphics for large complexes, Bioinformatics, bty419. doi: 10.1093/bioinformatics/bty419

Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prlić A, Rose PW (2016) Web-based molecular graphics for large complexes. In Proceedings of the 21st International Conference on Web3D Technology (Web3D '16). ACM, New York, NY, USA, 185-186. doi: 10.1145/2945292.2945324

Funding

This project is supported by the National Cancer Institute of the National Institutes of Health under Award Number U01CA198942. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

mmtf-workshop-2018's Issues

Problem with Pisces filter

IndexError: list index out of range when running:

https://hub.aws-uswest2-binder.pangeo.io/user/pwrose/lab/tree/3-mmtf-pyspark/6-Output.ipynb

Launch Binder - service unavailable

The binder.pangeo.io service has been shut down due to [crypto mining]
(pangeo-data/pangeo-binder#195)

Create vis. example with IpyWidgets

/tmp get's wiped out during Mac reboot

Anything saved on /tmp gets wiped out during reboot. So we need to find a better location for the installation instructions and install script.

1-Features has misspelled file name

data.write.mode('overwrite').format('parquet').save('./intput_features')

[!] resources folder is misspelled

resouces -> resources

Additional vis. features

• creating.png files
• color coding by b-factor {'colorscheme': {'prop': 'b'}}