CRESCYNT Toolbox – One Search through Multiple Data Repositories

“Search One and Done”… don’t you wish there was a KAYAK search tool for datasets?

Currently, the closest thing to a single search interface that pulls from a broad collection of heterogeneous data repositories at diverse scales is DataONE (http://dataone.org). Available DataONE repositories (“member nodes”) that host a substantial number of datasets about and relevant to coral reef work include:

• LTER Long Term Ecological Research network (e.g., Moorea Coral Reef LTER),
• NOAA NCEI Nat’l Centers for Environmental Information (incl. historic sea surface temperature data, some coral reef monitoring data),
• Dryad (wide ranging publication-associated datasets),
• KNB Knowledge Network for Biocomplexity (including coral reef studies),
• and many more (https://www.dataone.org/current-member-nodes)

 

You can get your own data into DataONE through KNB or ONEShare member nodes if other repositories are not a good fit.

DataONE continues to be actively developed and improved, and to add new member nodes. It currently provides access to over 630,000 metadata and datasets. Don’t miss DataONE’s Investigator Toolkit (https://www.dataone.org/investigator-toolkit).

Please check it out and let us know what you think!

 

 

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

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CRESCYNT Toolbox – Developing and Sharing Protocols

Reproducibility is a challenge. Features of Protocols.io (http://protocols.io) make it an attractive way to capture, develop, refine, share, and – when you’re ready – publish protocols and procedures. It’s optimized for both computer and mobile access, and also allows one to start with an existing protocol, fork it, make modifications, reference the original so that credit is preserved for both old and new versions, and when published at protocols.io becomes a way to reference the procedure as a citation.

A short video at http://protocols.io offers more detail. Consider it when you need to document a stepwise process or capture a workflow, then share your effort in a reproducible way, and get credit for your digital research products.

 

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

EarthCube All Hands Meeting 2016

CRESCYNT was delighted to participate with other science, technical, and governance groups at the EarthCube All Hands Meeting 6-8 July 2016 in Denver. This was a terrifically useful gathering – so helpful to be face-to-face once a year or so to accelerate the collective work that happens through conference calls, emails, google docs, sheets, and webinars.

Here’s the poster that CRESCYNT presented to deepen and broaden interactions with other EarthCube groups in our unified goal of meeting the technological needs of geoscience research in answering critical science questions that can only be managed with the assistance of essential cyberinfrastructure. The poster and a slide presentation both emphasized that (1) the challenges for coral reef research span a significant range of scales, and a broad collection of disciplines; and (2) integrating data and analysis vertically and horizontally – in both the figurative and literal senses! – are essential challenges for coral reef work. This area also faces the need to (3) manage multiple forms of critical imagery and other complex data forms, and (4) manageably use and share an explosion of new software, tools, and techniques, and (5) to figure out how to do it without the existence of a community-consensus data repository and community-tailored metadata standards and semantics – or (6) to arrive at the most critical of these standards quickly as a community, borrowing on work already accomplished for narrower, specific coral reef projects or in other fields.

 

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

Coral Reef Research Use Cases

During the International Coral Reef Symposium we were able to gather a collection of coral reef research use case summaries, particularly during our workshops and node meetings; some of these will be further developed into full use cases. In this instance, “use case” refers to a real research example that particularly emphasizes data and analysis workflows and associated pain points – defining the challenges researchers face with technological needs. and a way of gathering user requirements from this community for EarthCube architecture. We’re working in conjunction with a broader effort at EarthCube to collect use cases from multiple geoscience communities for just this purpose.

Below is a selection of these summary use cases for coral reefs – the range of scales and diversity of  disciplines is both remarkable and very characteristic of coral reef research work. We invite you to submit your own coral reef use case summary information!

Interestingly, while the range of scales and diversity of disciplines are both very great, the reported COLLECTIVE DATA NEEDS of coral reef researchers are remarkably consistent. Here’s a quick word cloud reflecting the expressed data needs of researchers – very similar even though the tools required to address the science questions vary by scale and discipline. (Specific statements underlying this representation listed above underneath Coral Reef Use Cases heading for summaries).

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

Who needs CRESCYNT? You do!

CRESCYNT is designed to benefit coral reef scientists at every career stage.

Early – If you’re a graduate student, postdoc, or early career scientist, you need the tools and resources that CRESCYNT is working in partnership with EarthCube to see developed. The coming data standards and technologies will be a basic requirement of all your work to come. Extra perk: Additional technical skills make you a better team member and allow you to offer more to potential employers (plus you know only too well that keeping up with constantly changing technology is a hamster wheel – best to pick up skills you care about).

Mid – Funding agencies and journals are increasingly requiring more open data, more transparent processes, and better data management, from metadata to backup to repositories to access. The ability to share and re-use data means more potential collaborators and a more efficient and productive lab. Extra perk: You’ve worked hard to develop practical workflows and good quality data; by documenting your efforts in a standard, shareable, and potentially public way (when you’re ready), you earn credit for all of your research output, not only publications, and are more likely to gain additional citations, collaborators, and maybe even minions.

Late – This is Estate Planning For Your Data! Your research is a professional legacy – make your data and your work discoverable and reusable for many years into the future! For coral reef work in particular, the data and images you’ve captured represent a unique intersection of space, time, and process that will never occur again in the universe.  Extra perk: Immortality (of a sort), continuing to contribute to coral reef understanding and protection long into the future, and the amplification of your work through the power of indirect effects – dropping your solid research pebble into the water and allowing others to benefit from its ripple effect makes your work matter even more.

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

Join CRESCYNT today and become part of these positive feedback loops!
Learn more at crescynt.org.

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Longer quotation: “…a scholar’s positive contribution is measured by the sum of the original data that he contributes. Hypotheses come and go but data remain. Theories desert us, while data defend us. They are our true resources, our real estate, and our best pedigree. In the eternal shifting of things, only they will save us from the ravages of time and from the forgetfulness or injustice of men. To risk everything on the success of one idea is to forget that every fifteen or twenty years theories are replaced or revised.”
– Santiago Ramon y Cajal, from Advice for a Young Investigator.

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

WELCOME to CRESCYNT – the Coral Reef Science and Cyberinfrastructure Network

The Coral Reef Science & Cyberinfrastructure Network (CRESCYNT) is a multi-tiered and multidisciplinary network of coral reef researchers, ocean scientists, cyberinfrastructure specialists, and computer scientists, and we invite you to join us. 

As an EarthCube Research Coordination Network, our goals are to foster a dynamic, diverse, durable, and creative community; to collectively consider and develop standards and resources for open data, research documentation, and data interoperability while making best use of work already accomplished by others; and to offer input to those groups within EarthCube who will ultimately create the data architecture for all of EarthCube. Along the way CRESCYNT expects to collect and share community resources and tools, and to offer training opportunities in topics prioritized by our members through widely accessible formats such as webinars and their recordings. We will also work to nurture unforeseen collaborative opportunities that emerge from our integrated collective work.

Because the coral reef community has exceptionally diverse data structures and analysis requirements needed to forward integrative science, it is an exemplar for cyberinfrastructure-enabled advances to other geosciences communities. The CRESCYNT network is working to match the data sources, data structures, and analysis needs of the coral reef community with current advances in data science, visualization, and image processing from multiple disciplines to advance coral reef research and meet the increasing challenges of conservation. The network has begun to assemble to coordinate, plan, and prioritize cyberinfrastructure needs within the coral reef community.

The structure of CRESCYNT is a network of networks, currently including 18 disciplinary nodes and 7 technological nodes, where each network node represents an area of coral reef science (disciplinary nodes: e.g., microbial diversity, symbiosis regulation, disease, physiology & fitness, reef ecology, fish & fisheries, conservation & management, biogeochemistry, oceanography, paleontology, geology) or an area of computer science or technical practice (technological nodes: e.g., visualization, geospatial analysis & mapping, image analysis, legacy & dark data, database management). These nodes may expand, coalesce, or divide to meet the needs and interests of the subdisciplinary communities, while maintaining connections to CRESCYNT through node coordinators and ongoing network activities. We invite you to become a member of CRESCYNT, join one or more nodes that would advance your own work, collaborate on shared resources and tools for the coral reef community, and ensure that the data architecture and cyberinfrastructure of EarthCube will meet the needs of the coral reef community, and that broader data interoperability within EarthCube will benefit both coral reefs and our ability to answer complex questions.

PLEASE VISIT OUR WEBSITE at http://crescynt.org to enroll in CRESCYNT, join a node, work on tasks, discuss data and research priorities, and help determine the future shape of cyberinfrastructure for supporting coral reef research and other geoscience work. This collaborative work is supported by the NSF EarthCube initiative.  Dr. Ruth D. Gates, Director of the Hawaii Institute of Marine Biology, University of Hawaii, is the Principal Investigator of the CRESCYNT project. The CRESCYNT blog is written by Dr. Ouida Meier, the project’s program manager (crescyntrcn@gmail.com).

This material is based upon work supported by the National Science Foundation under Grant Number 1440342. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

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