eLTER Software workshop - Introducing new tools

This workshop will focus on several data collection, analysis and visualization tools that have been developed in the context of eLTER. The workshop is aimed at researchers, administrators and technicians who are involved in a eLTER projects, or long-term ecological research.

The programme includes technical activities, and potential participants should have a background in spatial and/or statistical software. Thus, a basic knowledge of R and python will help to get the most out of the workshop. The format for this workshop will be “hands-on”, such that each participant will learn to use all of the tools using his/her laptop. Sufficient time will be dedicated to each tool to allow participants to install software and work with the tools, and also incorporate data from their own eLTER sites. We will also visit Yzeron catchment as an example of eLTER Site.

Event agenda.

Practical information on travel and accommodation.

This workshop might be interesting for you, if you (expand):

Registration is closed and the workshop is full. You can check if there are free places from Terhi Rasilo (terhi.rasilo@helsinki.fi)

The event will take place at INRAE, Centre Lyon-Grenoble Auvergne-Rhône-Alpes, 5 rue de la Doua, Villeurbanne (Lyon, France).

The tools to be included:

1.       DataLabs: A collaborative platform for scientists to share data, work, code and more.

• Preparation  (expand) 

  • Watch the intro video
  • Create Datalabs account:
    • Go to the DataLab site
    • Create an account with the “Sign up” button
    • Email wilbol@ceh.ac.uk with your username (email) to gain eLTER access
  • Need to create accounts and projects prior to training
  • Install the relevant libraries in the notebooks (R and python) for any of the applications 

• Content (expand)

  • DataLabs project space

    • Using and administering your project space

    • Creating project storage (NFS and object store), uploading files

  • Creating a Jupyter lab (the interface, terminal interface, kernels) and working collaboratively with it

  • Creating new Conda environments and managing packages within Conda

    • Example analysis

  • Create Rstudio project

    • installing packages

    • example analysis

    • manages packages within R (Packrat)

  • DASK

    • Creating DASK cluster

    • Start DASK cluster, access the DASK dashboard, Perform DASK calculation, Delete DASK cluster

  • SPARK

    • Creating a SPARK cluster

    • Start SPARK session, perform SPARK calculation

    • Delete SPARK Cluster

  • Using object storage in DataLabs

    • python

    • terminal

  • Jupyter Dashboards, using Panel and Voila (Creating and using Panel and Voila sites)

  • Using RShiny (Setting up Rshiny sites)

  • Using the DataLabs catalogue

  • User administration tools

2.       DEIMS – SDR: Dynamic Ecological Information Management System - Site and dataset registry, to discover long-term ecosystem research sites and what is measured on them.

• Preparation  (expand)

  While it is recommended to know Python, this session can be completed without knowing Python
  

  • Watch the intro video 
  • If you are a site manager, check if your site record is complete using DEIMS 
  • Install deimsPy on your local Python environment
  • Have a desktop GIS application (e.g. QGIS or ArcGIS) ready if you plan on doing a GIS exercise (there will be exercises to choose from, if you do not know GIS, you can for example work on querying DEIMS using either deimsPy or the REST-API)

• Content  (expand)

  • General overview (scope, usage, quality assurance, basic search functionality)
  • GeoData Services (GIS knowledge recommended)
  • REST-API (basic web programming knowledge recommended)
  • deimsPy (basic Python knowledge is recommended)
    • Showing examples using datalabs
  • Exercise: Working with deims data (probably 2-3 different options depending on skills and interests)
    • Desktop GIS exercise (e.g. making maps of sites and networks using deims data) OR
    • Query deims using either

      1. deimsPy OR

      2. REST-API

3.       ReLTER:  an R package that provides access to DEIMS-SDR, allowing it to interact with software implemented by eLTER Research Infrastructure (RI) and improving the data/information shared among the LTER network.

• Preparation  (expand) 

  • Install recent versions of R (version >= ) and RStudio (version >= 2022.07.2)

  • If you are a Windows users, install also Rtools

  • Install ReLTER, dependencies and other packages from GitHub. For specific instructions see here

  • Furthermore, an introductory video showing how to get started can be viewed here
    
    

• Content (expand)

  • Description about the package’s approach

  • Examples of different functions, including a description of the outputs of the functions

  • Advanced functions: interaction with remote sensing products, biodiversity repositories, data shared with DEIMS-SDR, Zenodo upload and download dataset, interaction with SOS service for download data

  • A mentimeter session will be proposed to collect suggestions for new functions or improvements to the package.

4.       PhenoApp: a tool integrated into a set of tools (GeeLTERMap) that allows to provide an easy mapping interface from which we can visualize, analyze, download and validate Phenology metrics for any eLTER site.

• Preparation (expand)

  • Make sure you have a Google account in case Google Colabs are needed
  • If it’s possible, a PC with QGIS and also QField installed in a phone or tablet
  • Python knowledge would be good, but not required. 

• Content (expand)

  • Access to GeeLTERMap (through either Datalab or Google colab)
  • demonstration of the different available products (MODIS, S2 Phenopy NDVI, Copernicus VPP PPI)
  • Available metrics (SOS, EOS, LOS)
  • Data download for specific eLTER site
  • In situ data upload for eLTER sites with available historical datasets

5.       Cookie cutting: A tool to harmonise official statistics and other data to eLTER site boundaries.

• Preparation (expand)

  • Make sure that there are boundaries uploaded to deims.org for the site of your interest. If they are missing contact the site (and Christoph Wohner)
  • Watch the following videos on User datasets covering site to understand what the tool is for and what kind of dataset for your own site you can bring along (optional): video one and video two
  • Prepare your dataset (optional). There will be a few EU-wide datasets available for everyone.

• Content (expand)

  • Setup (datalabs/local)
  • Introduction to tool
  • Worked raster data example
  • Worked tabular data example