omxware 0.1.20

Python wrapper for OMXWare REST services to access Data and Files.

Web Services

https://omxware.sl.cloud9.ibm.com:9420/swagger

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SDK Documentation:

https://pages.github.ibm.com/GrandChallenge-Almaden/omxware-pypi/

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Getting Started

https://pages.github.ibm.com/GrandChallenge-Almaden/omxware-pypi/build/html/usage.html

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Help / Forums

http://omx-forums.sl.cloud9.ibm.com

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Citation

• Please contact the OMXWare Team via the Forums for updated citation information prior to publishing or presenting OMXWare content.

e.g: "OMXWare: Microbial Life at Scale" IBM Research, manuscript in preparation

Use with Docker

In an effort to make it easier for users and developers to get started with 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