Cyberinfrastructure Working Group

About

The Cyberinfrastructure Working Group (CYWG) was established as an outcome of the iDigBio IT Standards Workshop held in Gainesville, FL on March 28-30, 2012. In line with the iDigBio roadmap, the focus of the initial group will be on the iDigBio data ingestion procedures related to API (Application Programming Interface) or appliance specification, implementation and test.

The working group will produce material with concrete data ingestion use cases from TCNs, provide input about the existing cyberinfrastructure, produce data ingestion requirements, and help evaluate iDigBio services and appliances implementations.

Members

To express an interest in joining the working group, please contact Renato Figueiredo.

Current members:

• Renato Figueiredo (Co-Lead), iDigBio IT
• Joanna McCaffrey (Co-Lead), iDigBio Biodiversity Informatics Manager
• Dan Stoner, iDigBio IT
• Kevin Love, iDigBio IT
• Robert Anglin Great Lakes Invasives TCNs IT
• James Beach, Paleoniches TCN IT/Co-PI, University of Kansas
• Reed Beaman
• Jason Bond, InvertEBase
• Andrew Brown Axiell Software / EMu
• Herrick Brown‎ SERNEC TCN
• Robert Bruhn Biospex, IT expert, FSU
• Nico Franz Great Lakes Invasives TCNs IT
• Larry Gall Yale Peabody
• Edward Gilbert, Lichens & Bryophytes, SCAN and Great Lakes Invasives TCNs IT, Symbiota
• Corinna Gries, Lichens & Bryophytes, PI
• Paul L Heinrich, SCAN TCN
• Chris Hoffman University of California, Berkeley
• Derek Masaki, BISON
• Gary Motz Indiana University
• Ben Norton, North Carolina Museum of Natural Sciences
• Katja Seltmann, Tri-trophic TCN IT, AMNH
• Petra Sierwald InvertEBase
• Melissa Tulig Tri-trophic TCN NYBG
• Kim Watson Tri-trophic TCN NYBG
• Ex Officio: José Fortes, iDigBio Director for Computational Activities

CYWG Meetings

Presentations from iDigBio IT:

• Wed, January 23rd, 2013 - 1:00pm EST (iDigBio DwC-A Pull Ingestion)
• Tue, February 19th, 2013 - 1:00pm EST (iDigBio Image Ingestion Appliance - presentation slides)
• Mon, September 9th, 2013 - 10:00am EDT (CYWG iDigBio v3 Preview - presentation slides) - release of v3 APIs as described in this document has been delayed.
• Friday, October 10, 2014 - 11:00am EDT (List of all links to ppt and other useful resources):
  • iDigBio Search Portal (queries and GUI features), by Greg Traub (watch)
  • iDigBio Data Ingestion (formats, process, etc.), by Dan Stoner (watch)
  • iDigBio Architecture, by Alex Thompson (watch)
  • iDigBio Infrastructure, by Matt Collins (watch)
  • iDigBio Research Tools, Andréa Matsunaga (watch)
  • iDigBio Appliances update, by Renato Figueiredo (watch)

Meetings with individual TCNs:

• Wed, September 04, 2013 3:00 PM-3:30 PM (NEVP)
• Wed, September 04, 2013 2:00 PM-2:30 PM (Paleoniches)
• Tue, August 20, 2013 1:00 PM-1:30 PM (SCAN)
• Mon, May 13, 2013 - 2:00pm EST (InvertNet)
• Tue, June 26th, 2013 - 10:00am EST (TTD-AMNH Data ingestion)
• Tue, July 3rd, 2013 - 10:00am EST (TTD-AMNH Image ingestion)

Meeting with external participation:

• Friday, April 23, 2015 - 4PM EDT (Data quality, usage, and issue tracking using GitHub, by John Wieczorek, et al at VertNet), in conjunction with the Data Management Interest Group.
• Thursday, May 28, 2015 2:00 PM-4:00 PM (Towards user-definable, semi-automated workflows for curating biodiversity data, by Bob Morris, Paul Morris et al. at Filtered PUSH, Kepler Kurator, and *Akka), in conjunction with the Data Management Interest Group. Webinar announcement here.
  • Part 1: Kurator presentation (pdf)
  • Part 2: designed for IT-oriented folks wanting to install and test. Full workflow described at: http://wiki.datakurator.net/web/iDigBioWebinar_May2015

Documentation

Related documentation from iDigBio:

• Data Ingestion Guidance
• GUID Guide (June 26, 2013)
• Data Ingestion Requirements and Guidelines (May 2013)
• Image Format Requirements and Recommendations (September 21, 2012)
• iDigBio Virtual Appliances (November 2013)
• iDigBio APIs (November, 2013)
• iDigBio APIs v2 webinar (April 28, 2015)
  • Presentation slides:
    • Introduction, by Matt Collins
    • Search, Spatial Mapping, and Summary APIs, by Alex Thompson
    • Examples of iDigBio API uses, by Greg Traub
    • General hackathon resources and process, by Dan Stoner
  • AdobeConnect session, includes Q/A session
  • Vimeo video without Q/A
• iDigBio API Hackathon (June 3-5, 2015):
  • Hackathon wiki
  • Hackathon reports
• Intellectual Property Policy (April 17, 2012)
• View the overall count and distribution of datasets ingested into the portal
• iDigBio Nuts and Bolts - Data Integration and Ingestion

Miscellaneous documentation:

• Example of trivial transformations on INHS fish dataset
• Example of transformations on InvertNet image metadata dataset

Join us via AdobeConnect: http://idigbio.adobeconnect.com/it

Cyberinfrastructure Working Group listserv idigbio-cywg-l@lists.ufl.edu

Ex Officio: José Fortes, iDigBio Director for Computational Activities

Please feel welcome to explore other working groups.