CRESCYNT Toolbox – Discovery of Online Datasets

cinergi-coralscreendump
Data discovery at cinergi.sdsc.edu

Announcing recent progress for data discovery in support of coral reef research!

Take advantage of this valuable community resource: a data discovery search engine with a special nose for locating coral reef research data sources: cinergi.sdsc.edu.

A major way CRESCYNT has made progress is by serving as a collective coral reef use case for EarthCube groups that are building great new software tools. One of those is a project called CINERGI. It registers resources – especially online repositories and individual online datasets, plus documents and software tools – and then enriches the descriptors to make the resources more searchable. The datasets themselves stay in place: a record of the dataset’s location and description are registered and augmented for better find and filter. Registered datasets and other resources, of course, keep whatever access and use license their authors have given them.

CINERGI already has over a million data sources registered, and over 11,000 of these are specifically coral reef datasets and data repositories. The interface now also features a geoportal to support spatial search options.

The CINERGI search tool is now able to incorporate ANY online resources you wish, so if you don’t find your favorite resources or want to connect your own publications, data, data products, software, code, and other resources, please contribute. If it’s a coral-related resource, be sure to include the word “coral” somewhere in your title or description so it can be retrieved that way later as well. (Great retrieval starts with great metadata!)

To add new resources: Go to cinergi.sdsc.edu, and click on CONTRIBUTE. Fill in ESPECIALLY the first fields – title, description, and URL – then as much of the rest as you can.

Try it out!

Thanks to EarthCube, the CINERGI Data Discovery Hub, and the great crew at the San Diego Supercomputer Center and partners for making this valuable tool possible for coral reef research and other geoscience communities. Here are slides and a video to learn more.

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CRESCYNT Toolbox – Discovery of Online Datasets

CRESCYNT at EarthCube All Hands Meeting 2017

EarthCube domain scientists, computer scientists, data scientists, and new members gathered in Seattle June 7-9, 2017 to communicate progress, connect over projects and science challenges, plan for future collaborative work, and welcome new participants.

Most of the presentations and posters from the meeting are available here. CRESCYNT program manager Ouida Meier delivered an invited talk on sci-tech matchmaking (video|slides, helped facilitate breakout sessions focused on clarifying requirements and resources for virtual workbenches (summary), and presented CRESCYNT coral reef use cases and workflow collaboration during a poster session. Discussion and collective brainstorming throughout the meeting was very dynamic and fruitful.

CRESCYNTposter_EC-AHM_Seattle_2017June

Download a larger pdf of the CRESCYNT poster – Earth Cube AHM 2017.

Read more EarthCube in the News.

CRESCYNT at EarthCube All Hands Meeting 2017

Resources for Coral Reef Education – by Judy Lemus

divers_lpittman_pixabay.jpgWe all recognize that communication and education about science concepts and the process of science is more important than ever.  Fortunately, coral reefs are charismatic ecosystems that inspire much curiosity, concern, and interest from many sectors of society.  While there is no shortage of stunning images and videos online, resources that combine these visuals with robust educational content can be more challenging to identify; they do exist and I’ve put together some of my favorites here. The list is not exhaustive, and we welcome your suggestions for great additions.

EDUCATIONAL WEBSITES. These resources provide educational information about coral reefs across multiple levels and concepts, often using multimedia.

Khaled bin Sultan Living Oceans Foundation Coral Reef Ecology Curriculum. The KSLOF has perhaps the most comprehensive website on coral reef ecology. The site is set up as a course with several units and resources with very nice graphics and high quality videos geared specifically for students and teachers. Lessons are aligned with the Next Generation Science Standards, Ocean Literacy Principles, and Common Core State Standards for K-12, but some of the material could easily be used in a college level course. A major downside to this site is that one must register to use it.

Smithsonian Ocean Portal. The Smithsonian’s website for coral and coral reefs is not as media-rich as the KSLOF, but does have a great deal of scientific information about corals.  Only a couple of lesson plans are offered, but the richness of the content lies in the embedded links to additional images and other stories. The science is backed up with oversight by Smithsonian coral reef biologist Nancy Knowlton.

MarineBio Coral Reefs. The MarineBio website is somewhat of a clearinghouse for other marine bio resources, but the educational content on coral reefs is good quality and quite extensive if you follow the links.  Like the Smithsonian site, there are links to both internal and external resources. The short videos featured throughout the site, generally from outside sources, are particularly engaging.

OTHER WEBSITES WITH EXTENSIVE INFORMATION ABOUT CORAL REEFS

National Ocean Service

NOAA Coral Reef Conservation Program

USGS Coral Reef Project

Coral Reef Alliance

Teach Ocean Science

ReefBase

Great Barrier Reef Foundation

Coral Triangle Initiative

Endangered Reefs, Threatened People

Coral Health Atlas

VIDEOS ABOUT CORALS AND CORAL REEFS. There are loads of videos of corals and coral reefs on the web; these excellent examples incorporate educational content.

Catlin Seaview

Chasing Coral (available through Netflix)

Climate Change: Coral Reefs on the Edge

Exploring the Coral Reef: Learn about Oceans for Kids

Corals Under Confocal

Coral bleaching caused by heating water (time-lapse)

Life Noggin – What Happens if All the Coral Dies? (animation)

Coral Bleaching Animation – HHMI BioInteractive Video (animation)

Coral Bleaching on the Great Barrier Reef (animation)

SCIENCE NEWS SITES. These science news websites regularly post stories on coral reefs.

ScienceDaily

LiveScience


Thanks to Dr. Judy Lemus for this cream-of-the-crop list. Judy is a Faculty Specialist in Science Education at the Hawaii Institute of Marine Biology; fortunately for us, she is also the Education Node Leader for CRESCYNT. You can download Judy’s list in pdf format.

Resources for Coral Reef Education – by Judy Lemus

CRESCYNT Toolbox – EarthCube Sci-Tech Matchup – Lightning Talks

Get a fast intro to new Ready-for-Science EarthCube Tools!

We’ve helped arrange a series of lightning talks that will feature tools developed by EarthCube “building block” projects for direct use by scientists. Many EarthCube-built tools are designed to serve as internal components of an EarthCube platform. Other tools were built for scientists as direct end users, and a collection of these are now ripe for adoption. Will some of these help you with your research work?
The current collection will be shown over a span of two online sessions. Find log-in details for Wed., Feb. 15 and Fri., Feb. 17 (no RSVP required – just show up).
Join us!

Wednesday, Feb. 15, 2017
4-5pm EST / 1-2pm PST / 11am-12pm HST – login link HERE
GeoDataspace/GeoTrust, Tanu Malik
ECOGEO Virtual Machine, Elisha Wood-Charlson
LinkedEarth, Julien Emile-Geay
OntoSoft, Yolanda Gil
Flyover Country, Amy Myrbo

Friday, Feb. 17, 2017
4-5:30pm EST / 1-2:30pm PST / 11am-12:30pm HST – login link HERE
CHORDS, Mike Daniels
SuAVE, Ilya Zaslavsky
CINERGI, Ilya Zaslavsky
X-DOMES Ontology Registry, Janet Fredericks
X-DOMES SensorML Registry, Janet Fredericks
iSamplesIGSN, Kerstin Lehnert
GeoDeepDive, Shanan Peters
Digital Crust, Shanan Peters
ECITE, Sara Graves
Earth System Bridge, Scott Peckham

UPDATE: All of the videos from the first rounds of talks are now on the EarthCube YouTube channel – here’s the playlist. Slides are now accessible at the EarthCube Tools Inventory, including additional presentations.

CRESCYNT Toolbox – EarthCube Sci-Tech Matchup – Lightning Talks

CRESCYNT Toolbox – R Resources for Graphing and Visualization

In a previous post we offered some solid supportive resources for learning R – a healthy  dinner with lots of great vegetables. Here we offer a dessert cart of rich resources for data visualization and graphing. It’s a powerful motivation for using R.
rgraphgallery

First up is The New R Graph Gallery – extensive, useful, and actually new. “It contains more than 200 data visualizations categorized by type, along with the R code that created them. You can browse the gallery by types of chart (boxplots, maps, histograms, interactive charts, 3-D charts, etc), or search the chart descriptions. Once you’ve found a chart you like, you can admire it in the gallery (and interact with it, if possible), and also find the R code which you can adapt for your own use. Some entries even include mini-tutorials describing how the chart was made.” (Description by Revolutions.)

Sometimes we want (or need) plain vanilla – something clean and elegant rather than extravagant. Check out A Compendium of Clean Graphs in R, including code. Many examples are especially well-suited for the spartan challenge of conveying information in grayscale. The R Graph Catalog is a similar resource.

If you’re just getting started with R, take a look at the Painless Data Visualization section (p. 17 onward) in this downloadable Beginner’s Guide.

In R, ggplot2,  based on the Grammar of Graphics, is perhaps the single most popular R package for data visualization. The R Cookbook‘s section on Graphs using ggplot2 is a helpful precursor to the R Graphics Cookbook. DataCamp’s DataVis with ggplot2 has a free segment of intro lessons.

For more on visualization and other capabilities, check out this recommended list of useful R packages in the R Studio support blog – succinct and terrific.

If you’re already skilled in R and want a new challenge, an indirect method of harnessing some of the power of D3.js for interactive web visualizations is available through plotly for R. Here’s getting started with plotly and ggplot2, plotly and Shiny, and a gallery. The resources offer code and in some cases the chance to open a visualization and modify its data.

Have a favorite resource? Please share as a comment, or email us!

CRESCYNT Toolbox – R Resources for Graphing and Visualization