Several of the coral reef scientists featured in the film Chasing Coral are CRESCYNT participants, including our PI, Dr Ruth D Gates, and we congratulate and thank them all for their eloquence, passion, deep experience, scientific integrity, and significant intellectual contributions to this powerful film. Chasing Coral‘s producers are making it available free for public screenings, and its focus now is educating audiences and moving people to action.
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.
Download a larger pdf of the CRESCYNT poster – Earth Cube AHM 2017.
Read more EarthCube in the News.
We 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
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.
Chasing Coral (available through Netflix)
Coral bleaching caused by heating water (time-lapse)
Coral Bleaching on the Great Barrier Reef (animation)
SCIENCE NEWS SITES. These science news websites regularly post stories on coral reefs.
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.
Scientists need better ways to analyze and integrate their data and collaborate with other scientists; new computing technologies and tools can help with this. However, it’s difficult to overcome the challenge of disparate perspectives and the absence of a common vocabulary: this is true of multidisciplinary science teams, and true when scientists try to talk with computer scientists. Workflows, as a way to help design and implement a workbench, are needed both as a collaboration space and a blueprint for implementation.
Take a look at a recent presentation to the EarthCube science committee (video) or an earlier presentation offered at ASLO 2017 (slides and voice) to see a flexible and low-tech way to simultaneously (1) facilitate necessary sci-tech interactions for your own lab and (2) begin to sketch out a blueprint for work that needs to be done. Subsequent technical implementation is possible with new tools including Common Workflow Language (CWL) as a set of specifications, Dockers as modular and sharable containers for either fully developed tools or small pieces of code, and Nextflow as an efficient and highly scalable definitive software language to make the computational work happen. Look for a post in the near future by Mahdi Belcaid to describe the technical implementation of these workflows.
OPPORTUNITY! We will be hosting one or two in-person skills training workshops in the coming months, with your expenses covered by our NSF EarthCube CRESCYNT grant, focused particularly on training early career professionals, and will work through some challenging coral reef use cases and their cyberinfrastructure needs. We collected some great use cases at ICRS, but would like additional cases to consider, so we invite you to describe your own research challenges through this google form. Please contact us for more on this, or other issues. Thanks!
AGENDA with LINKS and REMOTE LOGIN information at bit.ly/cybertools-aslo
Join us for a great workshop!
- When: Sunday, Feb. 26, 2017, 9:00 am – 3:30 pm HST – PLUS optional visit to the LAVA visualization lab – back to convention center by 5:00 pm)
- Where: Hawaii Convention Center, Honolulu, HI, room 323 B
- How: email email@example.com to reserve your space (and your LUNCH).
- Cost to you: None, thanks to generous workshop guides & NSF EarthCube CRESCYNT funding
- Not registered yet? We still want you (but can’t promise lunch or transportation)
Can’t attend in person? Join the workshop online! (starts 11:00am PST, 2:00pm EST)
WORKSHOP TOPICS AND PRESENTERS:
- EarthCube: A Community-Driven Cyberinfrastructure for the Geosciences
- ECO-GEO Virtual Machine – an environmental genomics workbench
- Multidisciplinary Challenges in Ocean Science Research
- SeaView: Connecting Ocean Data Repositories with Science and Visualization
- Cyber Visualization Tools
- Geoscience Papers of the Future (digital tools training)
- More Cyber Tools for Research – the Toolbox
- EarthCube Integration and Test Environment
- Workflow Assembly (hands-on conceptual assembly of data and tools)
- Trip – visit the Laboratory for Advanced Visualization and Applications
Mohan Ramamurthy, UCAR [video]
Elisha Wood-Charlson, UH Manoa [video]
Jay Pearlman, J&F Ent, U Colo [video]
Stephen Diggs, Scripps [video]
Alberto Gonzalez, UH Manoa [video]
Daniel Garijo, USC [video]
Ouida Meier, UH Manoa [video]
Emily Law, JPL [video]
Ouida Meier & participants
Jason Leigh, UH Manoa
If you’re attending ASLO (Association for Sciences in Limnology and Oceanography) in Hawaii or will be in Honolulu on Feb. 26th and care about better ways to collaborate, solve data and workflow challenges, or take the next steps in the relentless digital revolution, join us in person!
We’re excited to be able to offer this workshop as a real-time webinar – please participate remotely if you can! We have an amazing lineup of presenters and workshop guides. Don’t miss out!
Funding gratefully acknowledged from NSF EarthCube CRESCYNT Coral Reef Science and Cyberinfrastructure Network, Ruth D. Gates, PI (crescynt.org)
Update: original post updated with slide links.
Science is a team sport. Collaborations allow us to ask more ambitious science questions, but also intensify the need to connect disparate datasets across scales of time and space. Solving data interoperability challenges requires technological solutions not yet in place, so we’re taking the initiative to review potential solutions.
A platform from EarthCube is some time and distance away, but we have a chance to start assembling tools already at hand and in use for coral reef research workflows and do some testing. The process also helps us ground the ideal in the practical.
What are some criteria for a great infrastructure platform?
Ideally, solutions are: 1) modular, so when an improved tool is available it can be incorporated without restructuring the system; 2) free or low cost, so solutions are sustainable for most research labs; and 3) open source, allowing continued development from multiple disciplines and directions. However, we also want to start where people are, with the tools we’re already using – many of these are less than ideal but we make them work. That’s our starting place, and we want to hear about all of your tools.
It is tempting to set up a workbench for the challenge of analysis alone, but in a coral reef research lab we immediately crash into the realities of group data collection, field and lab work, physical specimens, and intersecting projects. All of these characteristics create additional layers of challenge. In the long run, infrastructure should help capture data and metadata generation at the source, and ease tracking, analysis, and replicability.
Good infrastructure solves more problems than it creates in compliance, skill demand, and management. An effective system helps graduate students and postdocs develop robust skills in managing data into the future, with guidelines that work for people, labs, and collaborators. Interoperability challenges must be solved for datasets that range from remote sensing to ecological surveys to bioinformatics work. Data cleaning, analysis, visualization, and mapping must be supported in flexible ways to clearly communicate research insights.
We have an opportunity to construct a preliminary array of tools and workflows on a cyberinfrastructure workbench for coral reef research, so if this is going to be a broadly useful start we need to know what you already like using and what more you wish you had. Dream big to start with, and along the way we’ll acknowledge the distinction between perfect and good-enough solutions.