CRESCYNT Data Science for Coral Reefs – Workshop Materials

Thanks to Jan Vincente and Ingrid Knapp for this pair of Data Rescue images.

Written while embedded in our CRESCYNT Data Science for Coral Reefs workshops. Amazingly, everyone who participated in workshop 1 – Data Science for Coral Reefs: Data Rescue – learned even more than they thought they would. We’ve had wonderful NCEAS trainers, spectacular participants with amazing datasets, and a lot of hard work over 4 days (March 7-10, 2018).

UPDATE: Here is the Data Rescue workshop agenda we used, with links to all of the training slides.

In the second intensive workshop – Data Science for Coral Reefs: Data Integration and Team Science – people will be introduced to R Studio and GitHub if they have not used them before, and then we will work on exploring techniques for integrating disparate datasets. We’ll start with a pair of datasets at a time, and efforts may involve extracting data from one dataset based on observations from another; upscaling, downscaling, resampling, or summarizing to make intervals and scales mesh – exactly the kind of process that coral reef researchers have said is a recurring challenge in asking bigger science questions.

UPDATE: Here is the Data Integration and Team Science workshop agenda we used, with links to all of those training slides and exercises.

Each workshop group is writing a paper to summarize and share lessons learned, so please stay tuned for those!

We experimented with an unusual process for these workshops: two days of training followed by two days of workathon. We’re liking it! Tell us what you think about these topics and training materials. What other workshop outputs would you like to see?

>>>Go to the blog Masterpost or the CRESCYNT website or NSF EarthCube.<<<

 

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CRESCYNT Toolbox – Data Repositories – Estate Planning for your Data

“Hypotheses come and go but data remain.”    – Ramon y Cajal

Taking care of our data for the long term is not just good practice, allowing us to share our data, defend our work, reassess conclusions, collaborate with colleagues, and examine broader scales of space and time – it’s also estate planning for our data, and a primary way of communicating with future scientists and managers.

Here are some great options for long-term data storage, highlighting repositories friendly to coral reef science.

First, there are some important repository networks useful for coral reef data – these can unify standards and offer collective search portals: we like DataONE (members here) and bioCaddie (members here).

KNB – the Knowledge Network for Biocomplexity offers open and private data uploads; ecological orientation. DataONE network.

NOAA CoRIS: Coral Reef Information System – often free to use and can accept coral reef related data beyond NOAA’s own data; contact them first.

BCO-DMO – Biological and Chemical Oceanography Data Management Office – if you have an NSF grant that requires data storage here, you’re fortunate. Good data management guidelines and metadata templates, excellent support staff. Now a DataONE member.

Dataverse – supported by Harvard endowments. There are multiple organizational dataverses – the Harvard Dataverse is free to use. bioCaddie member.

Zenodo – free to use, supported by the European Commission (this is a small slice of CERN’s enormous repository for the Large Hadron Collider). Assigns dois. We invite you to include the “Coral Reef” community when you upload. bioCaddie member.

NCBI – the National Center for Biotechnology Information is very broadly accepted for ‘omics data of all types. A bioCaddie member.

DataCite – not a repository, but if you upload a dataset at a repository that does not assign its own doi’s, you can get one at DataCite and include it when publishing your datasets.

We’ve not listed more costly repositories such as Dryad (focused on journal requirements) or repositories restricted to institutions. What about other storage options such as GitHub, Amazon Web Services, websites? Those have important uses, but are not curated repositories with long-term funding streams, so are not the best data legacy options.

Most of these repositories allow either private (closed) or public (open) access, or later conversion to open access. Some have API’s for automated access within workflows. These are repositories we really like for storing and accessing coral reef work. Share your favorite long-term data repository – or experiences with any of the repositories listed here – in the comments.