3rd Annual Digital Data Conference, Yale

Conference Agenda Navigation Quick Links

• Monday: Day 1 agenda
• Monday: Poster session
• Tuesday: Day 2 agenda
• Wednesday: Day 3 agenda

Lodging and Logistics

• Lodging: Dorm lodging is available this year on Yale's campus. For more on this and other lodging, see Lodging information
• Conference announcement
• Conference location: Click here for a map with conference locations
• Dining options: Click for a list of restaurants in the area

Social Media

Twitter: #digidata, @idigbio

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.

Agenda

Monday, 10 June 2019

Day One
7:30 - 8:30 a.m. - Breakfast (On your own)
7:30 - 8:30 a.m. - Registration: Sterling Law School
Keynote Session Location: Sterling Law School Auditorium 8:00 - 10:30 a.m. Moderator: Gil Nelson Timekeeper: Gil Nelson
Time	Title		Presenter(s)
8:30	Welcome Workshop Framing		Gil Nelson, iDigBio, University of Florida
9:00			Rosemary Gillespie, Professor & Schlinger Chair in Systematic Entomology, Berkeley EvoLab, University of California, Berkeley, Essig Museum of Entomology, Department of Environmental Science.
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.
10:00			Caroline Strömberg, Professor, Department of Biology, University of Washington, 2017 recipient of the prestigious Charles Schuchert Award from the Paleontological Society.
10:30-11:00	Break –William L. Harkness Hall
Concurrent Session I-A – William L. Harkness Hall - 11:00 a.m. - 12:30 p.m. Moderator: Timekeeper: Theme: Methods and protocols for enhancing discovery with digitized specimen data
11:00	Mario Moura Yale University		Determinants of the time lag between collection and description dates of global reptiles
11:20	James Hanken Museum of Comparative Zoology Harvard University		Unlocking the vault: mass digitization and imaging of historical slide collections for use in comparative biology
11:40	Rose Aubery 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 – William L. Harkness Hall - 11:00 a.m. - 12:20 p.m. Moderator: Timekeeper: 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		Insights into the Origins of Echinoderm Motion through 3D Digital Modeling
11:40	Alexander White Data Science Lab Smithsonian		Evaluating geographic patterns of morphological disparity in ferns and lycophytes using deep neural networks
12:00	Brandon O'Brien Univesity of New Hampshire		Global domination: Understanding the spread of two invasive seaweeds using habitat suitability models
Concurrent Session I-C – William L. Harkness Hall - 11:00 a.m. - 12:20 p.m. Moderator: Timekeeper: Theme: Gaps and deficiencies in currently available digital data that hinder effective use
11:00-12:20	Nathan Upham, 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 – William L. Harkness Hall - 1:45 p.m. - 3:15 p.m. Moderators/Timekeepers: 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 – William L. Harkness Hall - 1:45 p.m. - 3:15 p.m. Moderator/Timekeeper: 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: Developing a Framework of Core Biodiversity Data Literacy Skills"|
			Discussion Session: Developing a Framework of Core Biodiversity Data Literacy Skills"|
			Discussion Session: Developing a Framework of Core Biodiversity Data Literacy Skills"
Concurrent II-C – William L. Harkness Hall - 1:45 p.m. - 3:15 p.m. Moderator: Timekeeper: 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<br?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 – William L. Harkness Hall - 3:45 p.m. - 4:45 p.m. Moderator: Timekeeper: Theme: Published or publishable biodiversity research using digitized specimen data
3:45	Meredith Zettlemoyer Kellogg Biological Station		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, Warren Wagner, Eric Schuettpelz Department of Botany, National Museum of Natural History, Smithsonian Institution		Biogeography of Polynesian Pteridophytes in a Global Context
Concurrent III-B – William L. Harkness Hall - 3:45 p.m. - 4:45 p.m. Moderator: Timekeeper: 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 Amber Budden, DataONE University of New Mexico Matt Jones, DataONE National Center for Ecological Analysis and Synthesis		Designing a synergistic relationship between undergraduate Data Science education and usability of Biodiversity databases
4:25
Concurrent III-C – William L. Harkness Hall - 3:45 p.m. - 4:45 p.m. Moderator: Timekeeper: Theme:
3:45	Anna Monfils Central Michigan University		No collection left behind: Research contributions of small collections
4:05	Colin Morét Yale Peabody Museum of Natural History Chelsea Graham Institute for the Preservation of Cultural Heritage		At the intersection of technology and artistry
4:25

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: Sterling Law School Auditorium 8:30 - 10:00 a.m. Moderator: Timekeeper:
Time	Title		Presenter(s)
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.
9:00			Pincelli Hull, Assistant Professor, Geology and Geophysics, Department of Geology & Geophysics, Yale University.
9:30			Charles C. Davis, Professor, Organismic and Evolutionary Biology, Curator of Vascular Plants and Director, Harvard University Herbaria.
10:00-10:30	Break - Location TBD
Concurrent IV-A - William L. Harkness Hall - 10:30 a.m. - 12:15 p.m. Moderator: Timekeeper: Theme: Analyzing and visualizing specimen-based and related digital data
10:30	Robert McGuinn Northern Gulf Institute (a NOAA Cooperative Institute)		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		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 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
Concurrent Session IV-B - William L. Harkness Hall - 10:30 a.m. - 12:15 p.m. Moderator: Timekeeper: Theme: Critiques of digital data, aggregators, and data providers
10:30	Rebekah Wallace 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		Discussion Session: Tools for biodiversity data storage, taxonomic harmonization, publishing, analysis, and collaboration
			Discussion Session: Tools for biodiversity data storage, taxonomic harmonization, publishing, analysis, and collaboration
			Discussion Session: Tools for biodiversity data storage, taxonomic harmonization, publishing, analysis, and collaboration
Concurrent IV-C - William L. Harkness Hall - 10:30 a.m. - 12:15 p.m. Moderator/timekeeper: 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: How would you like to be able to search?
12:15-1:30	Lunch (On your own) Restaurant suggestions
Concurrent V-A – William L. Harkness Hall - 1:30 p.m. - 2:15 p.m. Moderators/Timekeepers: 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 - William L. Harkness Hall - 1:30 p.m. - 2:15 p.m. Moderator: Timekeeper: 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: Utilization and potential of social media as a digital data source for wildlife ecology studies
Concurrent V-C - William L. Harkness Hall - 1:30 p.m. - 2:15 p.m. Moderator/timekeeper: 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: What is the future of crowd sourcing in collections?
Capstone Session Location:Sterling Law School Auditorium Moderator: Gil Nelson
2:30-3:00				Joe Miller, Executive Secretary, Global Biodiversity Information Facility (GBIF), Copenhagen, DK
3:00-3:30				Andrea Weeks, National Science Foundation
4:00 - 5:00 p.m. - Poster Session: Environmental Science Center (across from Peabody Museum), 1st floor
5:00 - 7:00 p.m. - Tours - Reception: Peabody Museum, Great Hall

Wednesday, 12 June 2019

Day Three - Workshops & Field Trips
Breakfast (On your own) 7:00 - 8:00 a.m.
Registration 7:00 - 8:15 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 Location & Time: (Morning, exact time TBA) 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: (Morning, exact time TBA) 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: (All day, exact times TBA) 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. Limit 12 people: Must register to attend
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 8:30 am - 12:30 pm 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 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. Please contact David Jennings, GBIF Nodes Regional Representative North America, if you plan to attend. This meeting is intended for Node Managers within the GBIF North America region.