IBM Functional Genomics Platform

Web Services

https://ibm.biz/functional-genomics-api

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SDK Documentation:

https://ibm.biz/functional-genomics-sdk-docs

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Getting Started

https://ibm.github.io/omxware-pypi-docs/build/html/usage.html

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Help / Forums

https://ibm.biz/functional-genomics-forum

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Citation

• Please contact the IBM Functional Genomics Platform Team via the Forums for updated citation information prior to publishing or presenting IBM Functional Genomics Platform content.

  “OMXWare, A Cloud-Based Platform for Studying Microbial Life at Scale”

  Edward E. Seabolt, Gowri Nayar, Harsha Krishnareddy, Akshay Agarwal, Kristen L. Beck, Ignacio Terrizzano, Eser Kandogan, Mary Roth, Vandana Mukherjee, James H. Kaufman

  arXiv:1911.02095v2

Use with Docker

In an effort to make it easier for users and developers to get started with IBM Functional Genomics Platform (previously ‘OMXWare’), We have a 2 base docker images with python and OMXWare pre-installed. It also comes with a bunch of python libs like matplotlib, numpy along with some others.

1) Minimal: docker pull c0mpiler/alpine-omxware-base:latest

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docker run -it --rm --name omxware -v "$(pwd):/opt/my_work" c0mpiler/alpine-omxware-base:latest ash

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• This is a relatively small docker image with just the required packages / libraries installed and setup.
• Change the mount point to whatever you want on you host machine.
• You may use this image as a base to build other docker containers / applications. Refer to: https://github.com/c0mpiler/alpine-omxware-base/blob/master/Dockerfile for specifics.

2) JupyterLab: docker pull c0mpiler/jupyter:latest

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docker run -d --name jupyter --restart always -p 8888:8888 -e JUPYTER_ENABLE_LAB=yes \
-v /mnt/storage/jupyter:/home/jovyan/work c0mpiler/jupyter start.sh jupyter lab --LabApp.token=‘omxware’

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• This image has JupyterLab pre-installed and setup with some example OMXWare Jupyter notebooks.
• Change the mount point /mnt/storage/jupyter to whatever you want on you host machine – so you can share files from your host with this docker image.
• This image also has some example Jupyter notebooks for you to look at and get started.
• Once you run the docker image – you can open up http://<host-name>:8888/lab? in your browser and the pwd is omxware.
• The host-name is that of your host machine you run this docker image on. If you are running it on your laptop, the host-name is either localhost or 0.0.0.0