2017 BiG-CZ / ODM2 Hands-On Workshop
November 15-16, 2017 at UC Riverside, CA.
2017-BiGCZ-WorkshopAgenda Google Doc.
We provide information, links and other helpful content on separate pages for each of the twelve workshop topics:
- Introduction to BiG-CZ & ODM2
- Demo of ODM2 on Jupyter Hub
- More on ODM2 Controlled Vocabularies
- Installing ODM2 from Conda
- ODM2 Datasets, YODA file & Spreadsheet Ingest
- Demo of ODMToolsPython Desktop Application
- Tour of ODM2 Web Applications
- Tour of BiG-CZ Data Portal
- Using ODM2 with Python & R to Integrate Data
- Using the ODM2 Admin Web Application
- ODM2RESTfulWebServices & WOFpy
For this workshop, participants will only need a web-browser and a GitHub account.
Hands-on activities in Python and R will be provided a Jupyter notebooks dynamically running code in a customized, personal environment on JupyterHub. All required notebook files, supporting code, data files, and Conda environment files will be cloned from on a second repository:
- This repository is intended for
gitcloning into your personal JupyterHub user space or your local computer.
- Note for BiG CZ Team: See the issues created on that repo for info on where we're at vis a vis JupyterHub and tutorial contents, problems we're addressing, etc
All other hands-on activities will use web applications.
Additional Workshop Resources
JupyterHub test setup
- More details, for now, at https://github.com/BiG-CZ/wshp2017_tutorial_content/issues/3
- JupyterHub tutorial from Geohackweek 2017
ODM2 Jupyter Notebooks
From May 2017 presentation/demo. Hosted on HydroShare, uploaded here as a temporary convenience
- ODM2 IPython Notebook Examples
- ODM2_Example1.ipynb: Create a blank ODM2 database and load controlled vocabulary terms from http://vocabulary.odm2.org in preparation for data loading.
- ODM2_Example2.ipynb: Parse water quality sample data from an ODM2 Excel Template file using the ODM2 Python API and write data to an ODM2 database instance and a YAML Observations Data Archive (YODA) file.
- ODM2_Example3.ipynb: Read water quality sample data from an ODM2 database instance using the ODM2 Python API for manipulation or visualization of the data.
- ODM2: An Information Model and Software Ecosystem for Spatially-Discrete Earth Observations (Powerpoint)
- Ben Crary's Jupyter Notebook in R, that uses HISCentral & WOFpy, via the WaterML R package: EnviroDIY_Rnotebook.ipynb
- Dylan Beaudette's (et al) "NCSS-Tech" R packages for soil data, including Algorithms for Quantitative Pedology (
- Look into using Feather as common data-frame binary storage format for two-way exchange/interoperability between R and Python-Pandas (see also this 2016 article about feathers).