3rd Annual Digital Data Conference, Yale

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Conference Agenda Navigation Quick Links

Lodging and Logistics

Social Media

Twitter: #digidata, @idigbio

Internet Access

YaleGuest provides limited internet access. No password is required.
eduroam is also available if you have an account through your institution.

Traveling to New Haven

Airports: The closest airport is in New Haven. Being a small airport flights are limited.
The Bradley International Airport in Hartford, CT is the second closest option, 45 minutes away.
Transportation options from Hartford to New Haven:
Public Transportation
Ground/Airport Shuttle Service
Campus Parking: Yale Event Services advises commuters register to park using this link. The fee is $8 daily, and parking is located at the Pierson Sage Garage, which is about 0.8 miles from the meeting venues and adjacent to the Peabody. Overnight parking is allowed.
Ride Share from Airport to New Haven: Click here

Conference Registration

Registration opens 28 January 2019 and will be handled by Eventbrite.

PLEASE REGISTER EARLY. WE HAVE LIMITED CAPACITY AND MAY BE REQUIRED TO CLOSE REGISTRATION EARLY IF THE CONFERENCE FILLS UP.

Registration fees Registration fees include the conference, workshops, refreshments and hors d'oeuvres at Tuesday's reception:

  • $100.00 for professionals,
  • $ 50.00 for students.

Registration deadlines.

  • Early registration deadline for workshop proposals: 23 March 2019
  • Registration deadline for those submitting an abstract: 30 April 2019
  • Final Registration deadline: 17 May 2019

To register: Click here

A link to submit abstracts will be provided in the confirmation email sent after registering.

Sustaining Biological Infrastructure: Strategies for Success (SBI) Course

We are pleased to offer the Ecological Society of America’s (ESA) popular and successful Sustaining Biological Infrastructure: Strategies for Success (SBI) course, to be co-located with the conference. This course helps leaders of digital data resources, collections, field stations, and labs enhance their skills in strategic planning, communication, and financial management to make their projects more successful and sustainable. The course will be held June 12-14. Enrollment: $849 (discounted from $975). Colleague discount:(second team member from the same project/lab/etc) $649. Limited space available.
Please contact Jill Parsons, ESA’s Associate Director of Science Programs, at jill@esa.org or Emily Mastrianni, Science Programs Specialist, at emily@esa.org for more information.

Poster Specifications

Poster Specifications: Posters should not exceed 3’ tall and 4’ feet wide and should be displayed in landscape orientation.

Conference Abstracts

This year we offered attendees an opportunity to propose oral and poster presentations as well as to propose and lead an open discussion session about a critical topic in the research use of digital data. Each of these required an abstract submission. Each abstract was tied to one of the five conference themes:
Methods and protocols for enhancing discovery with digitized specimen data,
Ongoing research projects that utilize digital data,
Gaps and deficiencies in currently available digital data that hinder effective use,
Pipelines that integrate digitization, data use, and research,
Use of digitized biodiversity specimen data within ecological research and practice


Submitted abstracts can be found by clicking the following links:

Presentations

Please bring your presentation to the room you will be presenting in during the break prior to that session. Moderators for that session will be there to accept. Adania Flemming will be accepting presentations for A sessions, Allie Blackwell for B sessions and Natasza Fontaine for C sessions.

Agenda

Monday, 10 June 2019

Day One
7:30 - 8:30 a.m. - Breakfast (On your own)
7:30 - 8:30 a.m. - Registration: William L. Harkness Hall

Keynote Session
Location: Sudler Room, William L. Harkness Hall - 8:30 - 10:30 a.m.
Time  Presenter(s) Title
8:30 Dave Skelly, Director, Yale Peabody Museum
Gil Nelson, iDigBio, University of Florida
Patrick Sweeney, Senior Collections Manager, Yale Peabody Museum
Welcome
Conference Framing
Logistics
9:00 Rosemary Gillespie, Professor & Schlinger Chair in Systematic Entomology, Berkeley EvoLab,
University of California, Berkeley, Essig Museum of Entomology,
Department of Environmental Science.
Eco-evolutionary data across time to infer biodiversity dynamics
9:30 Nico Franz, Professor, School of Life Sciences, Arizona State University (ASU)
Curator of the Hasbrouck Insect Collection, Lead Coordinator of the Natural History Collections,
Director of the Biodiversity Knowledge Integration Center (BioKIC),
and Director of the National Ecological Observatory Network (NEON) Biorepository.
De-centralized but global: Redesigning biodiversity data aggregation for improved engagement and impact
10:00 Caroline Strömberg, Estella B. Leopold Professor in Biology and Curator of Paleobotany, Burke Museum of Natural History & Culture, Department of Biology, University of Washington,
2017 recipient of the prestigious Charles Schuchert Award from the Paleontological Society.
Shedding light on the evolution of grasses and grasslands through automated, quantitative imaging analyses of plant silica microfossils
10:30-11:00 Coffee Break – William L. Harkness Hall
Concurrent Session I-A – Sudler Room, William L. Harkness Hall - 11:00 a.m. - 12:30 p.m.
Theme: Methods and protocols for enhancing discovery with digitized specimen data
11:00 Mario Moura, Yale University
Jhonny Guedes, Federal University of Viçosa
Determinants of the time lag between collection and description dates of global reptiles
11:20 James Hanken, Stephen Turney, Linda Ford
Harvard University, Museum of Comparative Zoology
Unlocking the vault: mass digitization and imaging of historical slide collections for use in comparative biology
11:40 Rose Aubery, Surangi W. Punyasena
University of Illinois Urbana-Champaign
A high-throughput automated method for analyzing plant cuticle specimens
12:00 David Blackburn
Florida Museum of Natural History, University of Florida
The openVertebrate (oVert) Project
Concurrent Session I-B – Room 208, William L. Harkness Hall - 11:00 a.m. - 12:20 p.m.
Theme: Ongoing research projects that utilize digital data
11:00 Marion Holmes
University of Pittsburg
Testing the influence of land-use history and forest stand age on distributions of parasitic plants
11:20 Elizabeth Clark, Yale University
John R. Hutchinson, Royal Veterinary College; Peter J. Bishop, Royal Veterinary College;
Bhart-Anjan S. Bhullar, Yale University; Derek E. G. Briggs, Yale University
Insights into the Origins of Echinoderm Motion through 3D Digital Modeling
11:40 Alexander White, Data Science Lab, Smithsonian
Paul Frandsen, Department of Plant and Wildlife Sciences, Brigham Young University;
Laurence Dorr, Department of Botany, Smithsonian Institution;
Eric Schuettpelz, Department of Botany, Smithsonian Institution;
Rebecca Dikow, Data Science Lab, Smithsonian Institution
Evaluating geographic patterns of morphological disparity in ferns and lycophytes using deep neural networks
12:00 Brandon O'Brien, Christopher Neefus, Jennifer Dijkstra
University of New Hampshire
Global domination: Understanding the spread of two invasive seaweeds using habitat suitability models
Concurrent Session I-C – Room 116, William L. Harkness Hall - 11:00 a.m. - 12:20 p.m.
Theme: Gaps and deficiencies in currently available digital data that hinder effective use
11:00-12:20 Nathan Upham Yale University, Ruth Oliver
Yale University
Discussion Session: Synonyms: can we find durable solutions to name-based biodiversity data?
Discussion Session: Synonyms: can we find durable solutions to name-based biodiversity data?
Discussion Session: Synonyms: can we find durable solutions to name-based biodiversity data?
Discussion Session: Synonyms: can we find durable solutions to name-based biodiversity data?
12:30-
1:40
Lunch (On your own) - Restaurant suggestions
Concurrent II-A – Room 208, William L. Harkness Hall - 1:45 p.m. - 3:15 p.m.
Theme: Pipelines that integrate digitization, data use, and research
1:45 Dean Pentcheff, Regina Wetzer
Natural History Museum of Los Angeles County
Fielding the field-to-fields pipeline: From sampling through sequences in practice
2:05 Surangi W. Punyasena
University of Illinois Urbana-Champaign
Kenton McHenry, National Center for Supercomputing Applications, University of Illinois Urbana-Champaign
An automated image analysis platform for palynological specimens
2:25 Rachel Hackett, Michigan Natural Features Inventory
Michael Belitz, University of Florida; Edward Gilbert, Arizona State University;
Anna Monfils, Central Michigan University
A data management workflow of biodiversity data from the field to data users
2:45 Michelle Duong
Yale Ecology and Evolutionary Biology
Ajay Ranipeta, Yale; Walter Jetz, Yale; Robert Guralnick, University of Florida
Map of Life: A platform for synthesizing heterogeneous biodiversity data for research, education, and conservation
Concurrent II-B – Room 116, William L. Harkness Hall - 1:45 p.m. - 3:15 p.m.
Theme: Discussion Session: Developing a Framework of Core Biodiversity Data Literacy Skills
1:45-3:05 Anna K. Monfils, Central Michigan University
Elizabeth R. Ellwood, La Brea Tar Pits & Museum;
Lisa White, University of California Museum of Paleontology;
Debra L. Linton, Central Michigan University;
Natalie Douglas, Central Michigan University;
Molly Phillips, University of Florida
Discussion Session: Developing a Framework of Core Biodiversity Data Literacy Skills
Discussion Session continued
Discussion Session continued
Discussion Session continued
Concurrent II-C – Sudler Room, William L. Harkness Hall - 1:45 p.m. - 3:15 p.m.
Theme: Use of digitized biodiversity specimen data within ecological research and practice
1:45 Kelley D. Erickson, Center for Conservation and Sustainable Development, Missouri Botanical Garden
David Henderson, Washington University in St. Louis;
Stephen J. Murphy, Center for Conservation and Sustainable Development, Missouri Botanical Garden;
Adam B. Smith, Center for Conservation and Sustainable Development, Missouri Botanical Garden
Incorporating collector behavior into large-scale range models for digital biodiversity data
2:05 Robert Guralnick, Bryan McLean
Florida Museum of Natural Histeory
University of Florida
Assembling specimen-based trait knowledgebases to test broad-scale drivers of life-history variation
2:25 Katherine LeVan
National Ecological Observatory Network / Battelle
The National Ecological Observatory Network and the Extended Specimen Paradigm
2:45 Tom Giermakowski
University of New Mexico
Bruce L. Christman
Searching for a polar bear in a snowstorm: distribution of Arizona Black Rattlesnakes in southwestern New Mexico
3:15-3:45 Break – William L. Harkness Hall
Concurrent III-A – Sudler Room, William L. Harkness Hall - 3:45 p.m. - 4:45 p.m.
Theme: Published or publishable biodiversity research using digitized specimen data
3:45 Meredith Zettlemoyer, Kellogg Biological Station
Katarina Renaldi, Michigan State University
Failure to shift phenology may be associated with local extinction
4:05 Barnabas Daru
Texas A&M University, Corpus Christi
Temperature controls phenology in continuously flowering Protea species of subtropical Africa
4:25 Joel Nitta, Department of Botany, Smithsonian Institution
Alexander White, Data Science Lab, Smithsonian Institution
Warren Wagner, Department of Botany, Smithsonian Institution
Eric Schuettpelz, Department of Botany, Smithsonian Institution
Biogeography of Polynesian Pteridophytes in a Global Context
Concurrent III-B – Room 208, William L. Harkness Hall - 3:45 p.m. - 4:45 p.m.
Theme:
3:45 Rebecca Dikow, Michael G. Trizna, Mirian T. N. Tsuchiya, Alexander E. White
Data Science Lab, Smithsonian Institution
Data-intensive approaches to digitized museum collections
4:05 Ciera Martinez
University of California, Berkeley
Designing a synergistic relationship between undergraduate Data Science education and usability of Biodiversity databases
4:25
Concurrent III-C – Room 116, William L. Harkness Hall - 3:45 p.m. - 4:45 p.m.
3:45 Open Discussion - All topics welcome
4:05 Open Discussion - All topics welcome
4:25 Open Discussion - All topics welcome
Invited Afternoon Meetings - Room 116, William L. Harkness Hall
4:45-5:45 Please contact Patrick Sweeney (patrick.sweeney@yale.edu), if you plan to attend.
This meeting is intended for CNH members.
Consortium of Northeastern Herbaria business meeting

Tuesday, 11 June 2019

Day Two
7:30 - 8:30 a.m. - Breakfast (On your own)
7:30 - 8:30 a.m. - Registration: William L. Harkness Hall
Plenary Session
Location: Sudler Room, William L. Harkness Hall
8:30 - 10:00 a.m.
Time  Presenter(s) Title
8:30 Walter Jetz, Professor of Ecology and Evolutionary Biology and of Forestry and Environmental Studies,
Jetz Lab: Global Biodiversity, Ecology & Conservation,
Department of Ecology and Evolutionary Biology, Yale University.
Novel data, technologies, and methods to predict and manage global biodiversity change
9:00 Pincelli Hull, Assistant Professor, Geology and Geophysics,
Department of Geology & Geophysics, Yale University.
Endless Specimens Most Beautiful: leveraging large collections for evolutionary and ecological research
9:30 Charles C. Davis, Professor, Organismic and Evolutionary Biology,
Curator of Vascular Plants and Director, Harvard University Herbaria.
Leveraging a global online herbarium to understand plant phenological response to climate
10:00-10:30 Coffee Break - William L. Harkness Hall
Concurrent IV-A - Room 208, William L. Harkness Hall - 10:30 a.m. - 12:15 p.m.
Theme: Analyzing and visualizing specimen-based and related digital data
10:30 Robert McGuinn
Northern Gulf Institute (a NOAA Cooperative Institute)
Scott L. Cross, National Oceanic and Atmospheric Administration;
David E. Sallis, Northern Gulf Institute; L. Matt Dornback, Northern Gulf Institute;
Thomas F. Hourigan; National Oceanic and Atmospheric Administration
Advancing the Use of NOAA’s National Database for Deep Sea Corals and Sponges: Leveraging R, RMarkdown, ERDDAP,
and Leaflet interactive maps for enhanced data exploration, analysis, and reporting.
10:50 Ingrid Romero, University of Illinois at Urbana- Champaign
Shu Kong, Department of Computer Science, University of California- Irvine;
Charless C. Fowlkes, Department of Computer Science, University of California- Irvine;
Surangi W. Punyasena, Department of Plant Biology, University of Illinois at Urbana-Champaign
Identification of the Cenozoic pollen morphospecies Striatopollis catatumbus (Amherstieae, Fabaceae) using convolutional neural nets
11:10 Katelin Pearson
Cal Poly University, San Luis Obispo
Working smarter, not harder: more precise (phenological) data are not always better
11:30 Stephen J. Murphy, Adam B. Smith
Missouri Botanical Garden
A protocol for linking georeferenced locality information to high resolution spatial polygons data: a method for incorporating
spatial uncertainty into biodiversity models
11:50 Collin Morét, Yale Peabody Museum of Natural History
Chelsea Graham, Institute for the Preservation of Cultural Heritage
At the intersection of technology and artistry
Concurrent Session IV-B - Sudler Room, William L. Harkness Hall - 10:30 a.m. - 12:15 p.m.
Theme: Critiques of digital data, aggregators, and data providers
10:30 Rebekah Wallace, University of Georgia
Charles Bargeron, University of Georgia
Challenges in aggregating invasive species occurrence data
10:50 Carole Sinou
Canadensys/University of Montréal
Anne Bruneau, IRBV, University of Montréal
Global vs. national portals: why is it still important to develop specific portals?
11:10-12:10 Michelle Duong, Yale University
Ajay Ranipeta, Yale; Walter Jetz, Yale; Robert Guralnick, University of Florida
Discussion Session: Tools for biodiversity data storage, taxonomic harmonization, publishing, analysis, and collaboration
Discussion Session continued
Discussion Session continued
Concurrent IV-C - Room 116, William L. Harkness Hall - 10:30 a.m. - 12:15 p.m.
Theme: Gaps and deficiencies in currently available digital data that hinder effective use
10:30 Anna Monfils
Central Michigan University
No Collection Left Behind: Research Contributions of Small Collections
10:50 Bruce Young, NatureServe
Noel Dodge, Vermont Department of Fish & Wildlife;
Pamela D. Hunt, New Hampshire Audubon; Margaret Ormes, NatureServe;
Matthew D. Schlesinger, New York Natural Heritage Program;
Hollie Shaw, New York Natural Heritage Program
Separating Signal from Noise: Using Citizen Science for Regulatory Decision Making
11:10 Catherine Early, University of Florida
John Bates, Field Museum of Natural History;
Stephanie Baumgart, University of Chicago; A. Townsend Peterson, University of Kansas;
Heather L. Prestidge, Texas A&M University; Mark Robbins, University of Kansas;
Gregory Watkins-Colwell, Yale Peabody Museum; David C. Blackburn, University of Florida
Information Gaps in Digital Databases as Identified by a Multi-institution Initiative to Digitize Avian Specimens
11:30-12:15 Jen Hammock
Smithsonian
Discussion Session: How would you like to be able to search?
Discussion Session continued
12:15-
1:30
Lunch (On your own) Restaurant suggestions
Concurrent V-A – Sudler Room, William L. Harkness Hall - 1:30 p.m. - 2:15 p.m.
Theme:
1:30 Dave Vieglais, DataONE/University of Kansas
Amber Budden, DataONE/University of New Mexico
Matt Jones,DataONE
National Center for Ecological Analysis and Synthesis
Making Data Count: Best Practices for Tracking and Exposing Data Usage Metrics
1:50 Wendy Clement,The College of New Jersey
Kathleen L. Prudic, University of Arizona; Jeffrey C. Oliver, University of Arizona Libraries
Enhancing classroom and undergraduate research opportunities with natural history collections
Concurrent V-B - Room 208, William L. Harkness Hall - 1:30 p.m. - 2:15 p.m.
Theme: Social media
1:30-2:15 Anna Willoughby
University of Georgia, Odum School of Ecology
Discussion Session: Utilization and potential of social media as a digital data source for wildlife ecology studies
Discussion Session continued
Concurrent V-C - Room 116, William L. Harkness Hall - 1:30 p.m. - 2:15 p.m.
Theme: Crowd sourcing
1:30-2:15 Quentin Groom
Meise Botanic Garden
Discussion Session: What is the future of crowd sourcing in collections?
Discussion Session continued
Capstone Session
Location: Sudler Room, William L. Harkness Hall
2:30-3:00 Joe Miller, Executive Secretary, Global Biodiversity Information Facility (GBIF), Copenhagen, DK GBIF and the alliance for biodiversity knowledge
3:00-3:30 Andrea Weeks, National Science Foundation The Ecosystem of Biodiversity Research Funding at the National Science Foundation.
3:30 - 4:00 p.m. - Poster Set-up: Peabody Museum, Great Hall
4:00 - 5:00 p.m. - Poster Session: Peabody Museum, Great Hall
5:00 - 7:00 p.m. - Tours - Reception: Peabody Museum, Great Hall
Welcome and remarks
Michael Donoghue
Curator of Botany
Yale Peabody Museum
Professor, Department of Ecology and Evolutionary Biology
Yale University

Poster Session

Poster Session - 4:00 - 5:00 p.m. - Peabody Museum, Great Hall
Title Authors
Natural language processing for the semi-automated extraction of habitat trait information from butterfly field guides Vaughn Shirey, Georgetown University
Leslie Ries, Georgetown University
Increasing understanding of alien species through citizen science Quentin Groom, Meise Botanic Garden
Helen Roy, Centre for Ecology & Hydrology
Life Cycle of EDDMapS Occurrence Data Rebekah Wallace, University of Georgia
Charles, Bargeron, University of Georgia; Joseph LaForest, University of Georgia;
Bilal Bush, University of Georgia
Extending the ESN to History Maura Flannery, St. John's Univerity
Specimen search facets via taxon->attribute inference Jen Hammock, Smithsonian
Katja Schulz, Smithsonian
Native Plants Exhibit a Historic Phenological Response to Changing Temperature Rachel Reeb, University of Pittsburgh
Sara Kuebbing, University of Pittsburgh; Mason Heberling, Carnegie Museum of Natural History;
Isabel Acevedo, University of Pittsburgh
The life after digitization: examples from the lichen and bryophyte collections at Chrysler Herbarium (Rutgers University, New Jersey)

Rob Helsel, Rutgers University
Natalie Howe, Rutgers University; Megan King*, Rutgers University;
Lena Struwe, Rutgers University; Dennis Waters, Rutgers University

The broadest impacts: The inadvertent and unexpected building of life skills from biodiversity collection digitization in Rutgers’ undergraduate Herbarium Army

Megan King, Rutgers University
Janel Borden*, Rutgers University; Alexis Crouch, Rutgers University;
Mia Furci, Rutgers University; Rob Helsel, Rutgers University; Devika Jaikumar, Rutgers University;
Eva Popp, Rutgers University; Kenda Svoboda, Rutgers University; Eva Tillett, Rutgers University;
Lena Struwe, Rutgers University

Fostering engagement and discovery using digital data: examples from iNaturalist and other observation platforms and herbarium specimen data Lena Struwe, Rutgers University
Myla Aronson, Rutgers University; Thierry Besancon, Rutgers University; Mason Heberling, Carnegie Museum of Natural History;
Natalie Howe, Rutgers University; Megan King, Rutgers University.
Capturing flowering time data from herbarium specimens: The California Phenology TCN Katelin Pearson, Cal Poly University, San Luis Obispo
Jenn Yost, Cal Poly University San Luis Obispo
speciesRaster: a platform in R for integrating species ranges, morphology and phylogeny. Pascal Title, Environmental Resilience Institute
Miriam Zelditch, University of Michigan
Using Digital Imagery to Reanalyze Traditional Characters in Fusulinacean (Foraminifera) Systematics Susan Richardson, Wilkes Honors College, Florida Atlantic University
Designing a synergistic relationship between undergraduate Data Science education and usability of Biodiversity databases Ciera Martinez, University of California, Berkeley
The Smithsonian Sequence Hub: a dashboard to illuminate collection impacts via genomic sequencing Mike Trizna, Data Science Lab, Smithsonian Institution
Mirian T. N. Tsuchiya, Data Science Lab, Smithsonian Institution; Niamh Redmond, Smithsonian DNA Barcode Network, Smithsonian Institution;
Rebecca Dikow, Data Science Lab, Smithsonian Institution
Management of taxonomic data in the Encyclopedia of Life Katja Schulz, Smithsonian Institution National Museum of Natural History Institution
Ecological causes of uneven diversification and richness in the mammal tree of life Nathan S. Upham, Yale University
Jacob A. Esselstyn, Louisiana State University; Walter Jetz, Yale University
Assessing individual variation in white stork foraging habitat niches Ben Carlson, Yale University
Shay Rotics, Hebrew University of Jerusalem; Ran Nathan, Hebrew University of Jerusalem; Martin Wikelski, Max Planck Institute for Ornithology; Walter Jetz, Yale University
Advancing mountain species distribution information through model-based data integration Diego Ellis Soto, Yale University
Cory Merow, Yale University; Giuseppe Amatulli, Yale University; Walter Jetz, Yale University
Collector bias in native and non-native herbarium specimens Lauren E. Schricker, University of Pittsburgh
J. Mason Heberling, Carnegie Museum of Natural History; Sara E. Kuebbing, University of Pittsburgh
A targeted genetic database of local fauna for analysis of aquatic community metabarcode data Michelle Jungbluth, San Francisco State University, Estuary & Ocean Science Center
Sean Jungbluth, J1ab Consulting, Petaluma, CA, USA; Wim Kimmerer, San Francisco State University, Estuary & Ocean Science Center
Arctos: A Collaborative Collection Management Solution J. Tom Giermakowski, Museum of Southwestern Biology, University of New Mexico
Emily M. Braker, University of Colorado Museum of Natural History; Mariel Campbell, Museum of Southwestern Biology, University of New Mexico;
Carla Cicero, Museum of Vertebrate Zoology, University of California; John R. Demboski, Denver Museum of Nature& Science;
Andrew Doll, Denver Museum of Nature & Science; Kyndall Hildebrandt, University of Alaska Museum of the North;
Michelle Koo, Museum of Vertebrate Zoology, University of California, Berkeley; Angela Linn, University of Alaska Museum of the North;
Teresa J. Mayfield-Meyer, Museum of Southwestern Biology, University of New Mexico; Carol Spencer, Museum of Vertebrate Zoology, University of California, Berkeley
Teaching Digital Botany: Making Change, Maintaining Standards Hilary Callahan, Department of Biology, Barnard College
Caroline Dolt, Department of Biology, Barnard College; Jared Meek, Department of Ecology, Evolution and Environmental Biology, Columbia University
Introducing the National Ecological Observatory Network - NEON Biorepository Data Portal Nico Franz, Arizona State University
Edward Gilbert, Arizona State University; Azhar Husain, Arizona State University; Andrew Johnston, Arizona State University;
Laura Rocha Prado, Arizona State University; Laura Steger, Arizona State University; Kelsey Yule, Arizona State University
Biodiversity Heritage Library as a Data Repository as well as a Literature Repository: Help us to Identify how to Better Surface Content Constance Rinaldo, Ernst Mayr Library and Archives of the Museum of Comparative Zoology, Harvard University

Martin R. Kalfatovic, Smithsonian Libraries

Using collections data to detect patterns of co-occurrence between adult moths and their larval host plants Karaline E. Black, Marquette University;
Jennifer M. Zaspel, Milwaukee Public Museum;
Jerome J. Weis, Milwaukee Public Museum;
Christopher D. Tyrrell, Milwaukee Public Museum;
Joseph A. LaManna, Marquette University

Wednesday, 12 June 2019

Day Three - Workshops & Field Trips
Breakfast (On your own) 7:00 - 8:00 a.m.
Morning Coffee 8:30 - 9:00 a.m.
To register for any of the following workshops, please visit [this link]. You must register for the conference before registering for a workshop or field trip.
Workshop 1- Mobilizing museum collections and citizen science data to predict species distribution
Facilitators: Erica Stuber and Walter Jetz, Yale University
Location & Time: 9:00 a.m.-Noon, Sudler Room

Species distribution models (SDM) are powerful tools for inferring species ecology, response to environmental change, and biodiversity at multiple spatial and temporal scales. However, understanding species’ ranges at landscape or global scales typically requires moving beyond designed studies, which are relatively small scale, to capitalize on museum collections and citizen science projects which can represent data spanning entire species ranges across current and historic habitats. Understanding species’ range-wide distribution is a requirement for developing evidence-based conservation plans and predicting species’ response to global change, facilitated by digitization efforts and open-source observations databases. In this hands-on workshop, participants will review the state of the science in species distribution modelling, consider best-practices in mobilizing collections-based and citizen-science data sources for distribution modeling, and fit a basic SDM (i.e., access species and environmental data, process, and fit a statistical distribution model). Participants should bring their own laptop; hands-on sessions will use the free R programming environment. Example code and data for modeling will be provided, although some previous practice working with R will be useful.

Workshop 2 - Basic Biodiversity Data Manipulation in R
Facilitator: Katelin Pearson
Location & Time: Room 116, 9:00 a.m.-Noon

Not all of us entered biological research with the intent of learning to code, yet coding skills are increasingly crucial in our work. In this workshop, we will discuss and demonstrate basic workflows in working with biodiversity data in R, including downloading, cleaning, preparing, and analyzing data from iDigBio and GBIF. Basic data structure, useful functions, and tips and tricks will be addressed. Please indicate any specific questions or topics you would like to see covered during this session when you register. This is a hands-on workshop, so bring a laptop with R or R Studio already installed. The workshop leader will be demoing in R Studio.
Workshop 3 - Tools and Best Practices for Biodiversity Data Science: A Data Carpentries Introduction with Python
Facilitators: Holly Little, Deb Paul and Mike Trizna
Location & Time: Room 208, 9:00 a.m.- 2:00 p.m.

Carpentries Workshop Page and Software Download Instructions
The Carpentries (comprised of Data Carpentry, Library Carpentry, and Software Carpentry) is a project whose mission is to teach foundational computational and data science skills to researchers and others who create, manage, and use data. Specifically, Data Carpentry lessons are designed to be picked up by learners who do not have any previous programming experience. Data Carpentry workshops are typically organized in a 2-day format, but we will compress the lessons in this workshop to 1 day to focus on learning Python and Jupyter notebooks to work with data files in a reproducible manner. Before covering Python, we will go through a lesson using Excel to learn about the "tidy data" format, and best practices for working with tabular data files. We will also spend some time discussing community-building around the Carpentries, and how we can partner together to build biodiversity data science literacy at our organizations.
To register for any of the following field trips, please contact Jill Goodwin at jvgoodwin@fsu.edu. You must register for the conference before registering for a field trip.
Field Trip 1 - Horse Island Field Trip
8:15 am - 1:00 pm

On this short excursion to a 17-acre uninhabited island in Long Island Sound, we’ll see a mix of coastal and early successional vegetation, with wide rocky intertidal zones. The island is almost completely wooded with small stands of beech, pine and cedar trees among mixed scrub and hardwoods. Please be aware that some of the walking will be over uneven, sometimes slippery, very rocky terrain so appropriate footwear is required. Horse Island is among Connecticut’s Thimble Islands, 1.5 miles offshore from Stony Creek in Branford, Connecticut. Upon returning from the island, there will be an opportunity to have lunch in one of the local eateries in Stony Creek, a small seaside village which retains its roots as a summer vacation location with old Victorian hotels and a working granite quarry. This field trip will cost $12 for the water taxi. Free transportation from New Haven to Branford will be provided.

THIS FIELD TRIP IS FULL

Field Trip 2 - Bird Walk in East Rock Park
8:30 am - 11:00 am

Late spring migrants may still be lingering in this urban park as we walk along the Mill River in search of birds. East Rock Park, located close to New Haven Harbor, acts as a green haven to migrating birds coming in from the ocean, with upwards of 20 warbler species per day present during peak migration. From our starting point at the Eli Whitney Museum, we will make a 2-mile easy loop through riparian habitat where we may find swimming Wood Ducks with their young and Yellow Warblers on nests. The dirt path meanders along the deciduous woodland slope, where Scarlet Tanagers and Wood Thrush are common.

Limit 12 people: Must register to attend

Field Trip 3 - Walking Tour of the Natural History of New Haven and the Yale Campus
9:30 am - 12:00 pm

A walking tour of New Haven and the Yale campus will explore the city, campus architecture, major monuments, and highlights of the natural history of the Yale. The tour will include a stop at the Grove Street Cemetery to say "hello" to Peabody Museum founder, O. C. Marsh, and other Peabody luminaries.

Limit 12 people: Must register to attend

Field Trip 4 - Geology Walk at East Rock Park
9:00 am - 12:00 pm

Join Jessica Utrup of the Peabody Museum's Invertebrate Paleontology Department as she leads a hike and introduction to the recent geologic events at East Rock Park. Geologic features to be highlighted on this walk include kettles, lunar fractures and striated bedrock.

The hike itself will last two hours and there will be a half hour walk between the museum and the park. The route will include road and trail walking as well as some steep slopes. Participants are advised to wear long pants, sturdy shoes and dress for the weather. Participants may also want to bring water and snacks. There are no bathroom facilities along the intended route.
Limit 12 people: Must register to attend

To register for any of the following invited business meetings, please see instructions below. You must register for the conference before registering for an invited meeting.
Business Meeting 1 - 2019 Regional Meeting of GBIF Participant Nodes in North America
Facilitators: David Jennings and Carole Sinou
9:00 am - 12:30 pm
Room 009

The North America Regional Nodes meeting brings together Node Managers and other designated representatives from the participant nodes in the GBIF North America region. The goal of the meeting is to inspire collaboration and discussion of shared goals, challenges, and opportunities. The meeting will focus on progress updates from the represented nodes, preparations for the upcoming Governing Board meeting, and a discussion of strategies/goals for the coming year. A link to a more detailed agenda will be provided at a later date.

Agenda with remote connection instructions: https://docs.google.com/document/d/1hlK-ieN0IDnmCuhICBXnungLm9_ZdCeyoZye_3ojvO4/edit?usp=sharing

Please contact David Jennings, GBIF Nodes Regional Representative North America, if you plan to attend. This meeting is intended for Node Managers, Node Staff, Heads of Delegation, and Other Delegates within the GBIF North America region.