Short courses > SC2-Data Stewardship

PalaeOpen course (1 day)

Organisers

1. Stefan Engels (Senior Lecturer in Physical and Environmental Geography, University of London, UK)

2. Xavier Benito-Granell (Ramón y Cajal Researcher, Marine and Continental Waters Programme, IRTA, Tarragona, Spain)

The aim of this full-day course is to build capacity and provide support for palaeoecological data sharing. The PalaeOpen COST Action (https://palaeopen.github.io/) aims to achieve FAIR and OPEN sharing of multiproxy (biotic and geochemical) palaeoecological data to understand ecological changes in European ecosystems at large spatial and temporal scales. Practical training using the Tilia and Neotoma softwares for data exploration and uploading will be provided during this 1-day course. For those that are already familiar with Neotoma and Tilia, support is available to stimulate further data sharing (“upload-thon”).

Introduction to PalaeOpen (1h)

We will start the day with an introduction to the PalaeOpen initiative, setting out its organization and its main goals. We will highlight ongoing activities and showcase the potential to achieve a new research agenda using regional compilations of multiproxy paleoecological records.

Training and support in uploading data to Neotoma (5h)

For those participants who are new to Neotoma, we will provide an interactive introduction to uploading data to Neotoma. Using your own laptop, you will learn how to prepare a dataset and how to upload meta-data and count data successfully to Neotoma. 

For those participants who are already more experienced and/or those that participated in previous PalaeOpen meetings, you can use this time to ask any questions you have regarding more complex data uploads, and to interact with other members of the PalaeOpen community.

What to prepare and/or bring with you:

1. Install Tilia: You need to have the latest version of Tilia on your computer. Note that Tilia can only be installed on a Windows PC or Windows simulator.  If you don’t have a license and never used it before, please go to https://www.neotomadb.org/apps/tilia. Under “Installing Tilia” you find a link that takes you to a questionnaire. Once you have completed that an email with the installation instructions will be sent to you. Please carefully read it and follow it including the update on Github. If you are running Tilia 3.0.0 or higher you should be able to directly go to the bug fix: https://github.com/sorghumking/tilia/releases/tag/3.0.2
2. Bring data for upload: If possible, we like to enable you to upload your own datasets. Therefore, if you have data that may go public on Neotoma please bring them. If you like, you can already check how meta-data is organized by looking into Tilia or better, download a dataset from Neotoma into Tilia. 
3. Install neotoma2: If time allows, we will also introduce you to the neotoma2 R package.

Useful links and references

• Neotoma (https://www.neotomadb.org/)
• Williams et al. 2018. The Neotoma Paleoecology Database, a multiproxy, international, community-curated data resource (doi:10.1017/qua.2017.105) 
• Examples of what can be done with open data:

• Mottl et al. 2021. Rate-of-change analysis in paleoecology revisited: A new approach. https://doi.org/10.1016/j.revpalbo.2021.104483

• Flantua et al. 2023. A guide to the processing and standardization of global palaeoecological data for large-scale syntheses using fossil pollen. https://doi.org/10.1111/geb.13693