CRESCYNT Toolbox – Open Science Framework supports reproducible science

osf

The Open Science Framework, or OSF (osf.io) is a free and open source platform for supporting reproducible science. It’s designed more for documenting work than for streamlining work. It’s potentially a useful place to host a messy spread-out collaborative research project partly because of the add-ons it can connect with, (1) for storage: Amazon S3, Box, Dataverse, Dropbox, figshare, Google Drive, and GitHub, and (2) for references: Mendeley and Zotero. OSF also comes with a dashboard, a wiki, email notifications for your group, OSF file storage with built-in version control, data licensing background and assignment capability, ability to apply permission controls, and ability to make projects and components either private or public. Projects that one chooses to make public can be assigned DOIs (which can be transferred if you move your project elsewhere).

Aside from its primary role as a place to host research documentation and collaboration, OSF has also been used to teach classes in open science and reproducibility, and as a location to host conference products such as presentations and posters.

OSF is not a perfect platform for science – that elusive creature does not yet exist – but it’s a robust start with its ability to integrate other resources you may already be using, gets extra points for being free and open source, and could definitely be worth the learning curve of using with a next project. It continues to be improved over time, and how will we know what to ask of a platform if we don’t wrestle a bit with what’s already been built?

Learn more at the Open Science Framework FAQs and OSF Guides
or on YouTube (where everyone seems to learn new software these days):
+ Getting Started with the OSF (2 mins) (start here!) –
+ Most recent “OSF 101” intro webinar (1 hour) –
+ Deep dive into the OSF (1 hour) (thumbs up!) –
+ and more at OSF’s YouTube channel.

If you try it out, please let us know what you think!

Update: OSF now also connects with Bitbucket and ownCloud. See current Add-ons.

CRESCYNT Toolbox – Open Science Framework supports reproducible science

CRESCYNT Toolbox – Stitched Images – 3D Reef Mapping and 360-Degree Imagery

Imagery REALLY feeds our monkey brains. Today: tools for 3D reef mapping. Bonus: some 360-degree images and video to use with virtual reality headsets.

Several exciting talks at the International Coral Reef Symposium featured 3D mapping of coral reefs using SfM, Structure from Motion techniques, to stitch together large numbers of overlapping images. The resulting 3D mapped images were used to help address a surprising range of research questions. The primary tools used to create these were Agisoft’s PhotoScan or the free and open source Bundler (github) by Noah Snavely.  Part of the challenge of this difficult work is organizing the workflows and data processing pipelines: it’s an example of a type of cyberinfrastructure need that eventually EarthCube architecture should be able to help stage. Look for a guest blog soon by John Burns to learn more!

valensreef2
360 Film by Conservation International

BONUS: The process of creating spherical or 360-degree images or video is at root a similar challenge of stitching together images, though more of the work is done inside a camera or on someone else’s platform. There are some recent beautifully-made examples of spherical coral reef images and 360 videos, viewable through virtual reality (VR) headsets; these have great potential for education and outreach. Consider the XL Catlin Seaview Survey gallery of coral reef photo spheres and videos from around the world, (including bleaching and before-and-after images) and Conservation International’s 8-minute video, Valen’s Reef, both exhibited at the current IUCN World Conservation Congress in Honolulu.

catlinseaviewsurvey
Catlin Seaview Survey – equipment

A new project, Google Expeditions, was launched this past week to facilitate synchronized use by multiple people of 360 videos and photo spheres as a design for class use. Google Streetview is being made more accessible as a venue for education and outreach, including creating and publishing one’s own photo spheres. Also find 360-videos of coral reefs on YouTube.

UPDATE: Visually powerful 360 bleaching images that Catlin Seaview debuted at ICRS, viewed by tablet or smartphone, are now accessible in this article on coral bleaching.

CRESCYNT Toolbox – Stitched Images – 3D Reef Mapping and 360-Degree Imagery

CRESCYNT at ICRS 2016

CRESCYNT IS AT #ICRS2016 – International Coral Reef Symposium in Honolulu, Hawaii!

EVENTS:

WORKSHOP – Cyber Tools and Resources for Coral Reef Research and Analysis
Sun. June 19 8:30am-4:00pm, Hawaii Convention Center rm 314
(breakfast, lunch provided – register here)
ask about materials / future webinars if you miss
sponsored by EarthCube CRESCYNT – some seats still open!

CRESCYNT Node Coordinators Meeting
Mon June 20 6:00-8:30pm, Hawaii Convention Center 307 A/B

OPEN MEETING – CRESCYNT Participants with Node Coordinators
Wed June 22, 11:30am-12:45pm, Hawaii Convention Center 307A/B
(bring your ICRS lunch – we’ll have ice cream)
OPEN TO ALL – come if you’re interested!

DISCUSSION & SYNTHESIS SESSION: Emerging Technologies for Reef Science and Conservation
Fri June 24, 9:30am-3:45pm, Hawaii Convention Center 312icrs2016-footer
(Discussion 11-11:30am. CRESCYNT at 2pm)

UPDATE: Find all the meeting abstracts in this 414-page pdf book

CRESCYNT at ICRS 2016

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. Scope of Sciences within EarthCube

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.

Workflows within CReSCyNT: participants to nodes to collective project outputsThe 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.

WELCOME to CRESCYNT – the Coral Reef Science and Cyberinfrastructure Network