biodiversity indicator development
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Project Description:
Open source biodiversity indicator development from open data.
Expected Outcomes:
This project aims to advance the state of biodiversity indicators generated from open data.
I intend to document efforts using jupyter notebooks.
Accessibility of Jupyter notebooks will be enhanced using mybinder.org.
My preferred language for this analysis is python but R+julia will also be available.
Visualization & statistics from data will be pursued.
Analyses will specifically focus on one of the three: 1) spatial mapping of biodiversity, 2) biodiversity time-series, 3) species-specific comparisons.
Skills required:
Anybody familiar with python/R/julia, OBIS/GBIF/DwC, or biodiversity indices are welcome.
Difficulty:
Moderate
Topic Lead(s):
Tylar Murray @7yl4r
Relevant links:
One apprehension I have that the mybinder.org service at the core of my plan can be slow at times. We may want to spin up a more performant jupyterhub server to use for this. Something else worth considering is trying to leverage Axiom's "Research Workspace" - for that we need to discuss with someone at Axiom.
What about google colab? Put a bunch of try: except statements in for installing packages w/ pip.
There's also a way to use R in google colab, which could be interesting to explore.
Or, for the sprint you build something that is ran locally. Then, after the sprint, look at ways to integrate with these other services?
@7yl4r are you okay giving this sprint pitch on Monday? We are looking for a brief overview of what the topic will be, what slack channel, and what breakout room to join the effort (along with anything else that might be relevant).
Yes. I plan to just show the topic page. Should we add the slack channel and breakout room info to that page?
I'll present the page if you're up to speaking about it. I've added the slack channel and breakout room to the webpage, but feel free to update as appropriate.
amazing topic! Sorry to discover it now the code sprint is finished.... FYI we are working on such topic (giving access to open source codes / workflows to compute biodiversity indicators) through the Galaxy-E initiative. Briefly, we are focusing on producing biodiveristy indicators through open source workflows (using R / Python / others languages scripts) working notably on 1/ generalization so a workflow can be used widely (spatially and/or taxonomicaly (if frenglish ;) ) notably) 2/ atomization (so each step of a workflow can be reused in another workflow / indepentantly 3/ accessibility-transparency-reproductibility using the Galaxy platform allowing people without knowledge in programming skills to execute these tools/workflows + facilitating sharing the workflow and resulting execution + provenance tracking. If you are interested, don't hesitate to come back to me!
Bonus => you can deploy RStudio or Jupyter notebooks directly from Galaxy if you want to interact with codes on Galaxy datasets!
closing since we sprint is finished.