Data Discovery Science Competition

 

Come Find the Data You Need!

Grow your skills and your data resources in the Data Discovery Science Competition at DataDiscoveryStudio.org

Data Discovery Studio is built to help scientists find data. It hosts records for over 1.6 million datasets and resources from over 40 repositories, and continues to grow. Individuals, classes, and sci-tech teams can compete in two categories:

(1) Build a shareable Collection of datasets from existing resources, and add links to other datasets and resources in other repositories. We show you how!

(2) Modify existing Jupyter Notebooks or create your own to explore a data type of interest. Guidance provided!

Find details at bit.ly/ddscompete or jump in and start exploring at DataDiscoveryStudio.org – enter by May 1, 2019.

Please share broadly! We built this NSF-funded EarthCube gateway for you, want it to be useful, and eagerly welcome your feedback.

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Note to coral reef scientists: the site already includes over 16,600 records of coral reef datasets and resources – enough to begin a select collection of your own to share with collaborators, and point to more.

More Details:

Both competition categories contribute to science. (1) Collections will gather and tag resources, including datasets, with a focus you choose for research or community use. (2) Jupyter Notebooks will help develop workflows for datasets with a common theme or structure. Both areas will help address real science questions, share results and resources with others, and will help improve the gateway for future users. The competition is suitable for individual, team, or class entry.

DDStudio’s strongest holdings in datasets and resources are in earth, ocean, atmospheric, hydrologic, geologic, planetary, ecological, and other geoscience domains, broadly defined. Try out a favorite search term at datadiscoverystudio.org – if DDStudio doesn’t have what you need, you can contribute a new link, or point us to repositories to add. DDStudio goes beyond search: some datasets can be explored right on site using example Jupyter Notebooks (e.g., sensor data) – or develop and contribute your own Notebooks.

You can’t win if you don’t enter – show up and represent your domain! bit.ly/ddscompete

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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.<<<

 

Cyber Tools and Resources for Research and Analysis – Workshop at ASLO

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 omeier@hawaii.edu 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

Mohan Ramamurthy, UCAR [video]


• ECO-GEO Virtual Machine – an environmental genomics workbench

Elisha Wood-Charlson, UH Manoa [video]


• Multidisciplinary Challenges in Ocean Science Research

Jay Pearlman, J&F Ent, U Colo [video]


• SeaView: Connecting Ocean Data Repositories with Science and Visualization
  

Stephen Diggs, Scripps [video]


• Cyber Visualization Tools

Alberto Gonzalez, UH Manoa [video]


• Geoscience Papers of the Future (digital tools training)

Daniel Garijo, USC [video]


• More Cyber Tools for Research – the Toolbox

Ouida Meier, UH Manoa [video]


• EarthCube Integration and Test Environment

Emily Law, JPL [video]


• Workflow Assembly (hands-on conceptual assembly of data and tools)

Ouida Meier & participants


• Trip – visit the Laboratory for Advanced Visualization and Applications

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.

CRESCYNT Toolbox – What do we need on the workbench?

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.

We really want to include YOUR favorite tools and highest priority needs in this review, so please share those – we’ll report back.

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.

Please complete this survey, or comment below. Thank you so much!

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.<<<

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.<<<

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.<<<