Digital Data in Paleontological Research

Logistics

• Event hashtag: #paldigi
• Logistics document (PDF)
• Map: hotel to UCMP
• Hotel information
• Train information
• Map of restaurants near UC Berkeley
• List of sit down restaurant recommendations near UC Berkeley
• Initial Workshop Announcement
• Adobe Connect Room to join us remotely
• If you did not receive a email with a survey link, please complete it here.

Monday, 27 March, 2017

Day One
Time	Topic	Presenter(s)/Leader(s)
7:00-7:30	Breakfast on your own. For participants staying at the Hotel Durant: Complimentary continental breakfast will be provided at the Hotel Durant, starting at 7:00am. Please meet Gil and Talia in the lobby at 7:30am to walk to the Valley Life Science Building.
7:45-8:10	Welcome, Workshop Introduction, Logistics	Pat Holroyd, University of California Museum of Paleontology Gil Nelson, iDigBio/Florida State University
Round up of Existing Paleo Data Projects Lightning Rounds VLSB 2040
8:10-8:20	Brief Introduction to iDigBio, ADBC, Paleo-related TCNs, and Acronyms	Gil Nelson
8:20-8:30	PaleoNiches (2012)	Una Farrell, Stanford
8:30-8:40	Fossil Insect Collaborative (2013)	Diane Erwin, UCMP
8:40-8:50	EPICC (2015)	Erica Clites, UCMP
8:50-9:00	Cretaceous World (2016)	Talia Karim, University of Colorado Museum of Natural History
9:00-9:10	iDigPaleo	Talia Karim
9:10-9:20	PaleoBiology Database	Mark Uhen, George Mason University
9:20-9:30	ePANDDA	Gil Nelson
9:30-9:40	MorphoSource	Doug Boyer, Duke University
9:40-9:50	Digitizing Field Notes at MVZ	Christina Fidler, Museum of Vertebrate Zoology, University of California, Berkeley
Break VLSB 2063
Challenges of Using Paleo Data in New and Expanded Ways VLSB 2040
10:10-10:25	GB3D Fossil Types Online Database	Mike Howe, British Geological Survey
10:25-10:40	Aggregation and the Mechanics of Data Sharing	Pat Holroyd, UCMP
10:40-10:55	Computer Vision	Surangi Punyasena, University of Illinois
10:55-11:10	Assessing Data Management Practices and How they Affect the Interoperability of Collections and Research Data	Amanda Millhouse, Smithsonian Institution National Museum of Natural History
11:10-11:25	Geochemistry Database	Una Farrell, Stanford University
11:25-12:00	Q&A, Discussion, Morning Wrap-up: Identifying Questions for further Discussion
12:00-1:00	Lunch (provided)
Afternoon Sessions
Digital Data Workflows VLSB 2040
1:00-1:20	An Introduction to Workflows	Gil Nelson
1:20-1:50	From field collections to digital data: a workflow and digitization pipeline for reconstruction of a Cretaceous macroflora	Dori Contreras, University of California, Berkeley
1:50-2:10	Workflows: Processing Specimens From Micro-CT scanning to 3-D surface processing to upload to Morphosource	Arianna Harrington, Duke University
2:10-2:30	New Mathematical Approaches to the Automated Segmentation of Teeth	Ethan Fullwood, Duke University
2:30-2:50	Managing and Sharing Data	Mauro Lepore, Smithsonian Tropical Research Institute
2:50-3:10	Steps towards Digitizing and Organizing 175 years Worth of Natural History Data	Dana Ehret, Alabama Museum of Natural History
3:10-3:30	The "Swat Team" project: Addressing a backlog of Quaternary small mammals from the Nullarbor Plain of south Australia	Bill Simpson, Field Museum of Natural History
Break VLSB 2063

Break out Discussion Groups
Time	UCMP Fishbowl	VLSB 2040	VLSB 2063
3:50-4:20	What are our data gaps and how do we assess what data are still needed? Facilitator: Pat Holroyd Google doc link	How do we improve our workflows for efficiency and data quality? Facilitator: Gil Nelson Google doc link	What data are we gathering that do not have consistent standards (morphometric, geochemical, CT, 3D, deep time georeferences, other)? Facilitator: Erica Clites Google doc link
4:20-5:00	Break out Reports (VLSB 2040)
Reception (5:00-7:00 p.m.) The following demonstrations will be offered during the reception: From field collections to digital data: a workflow and digitization pipeline (Dori Contreras) Imaging using a light microscope (Camilla Souto) Imaging using a StackShot (Lillian Pearson) Measuring photographed specimens: an open-source measurement applet developed by Lucy Chang 3-D scanning using a laser scanner (Mackenzie Kirchner-Smith) Viewing histological slides using a petrographic microscope (Ashley Poust)
7:00	Dinner on Your Own

Session Recordings

• Round up of Existing Paleo Data Projects Lightning Rounds
• Challenges of Using Paleo Data in New and Expanded Ways
• Digital Data Workflows
• Breakout Summary

Tuesday, 28 March, 2017

Day Two - Morning Sessions
Time	Topic	Presenter(s)/Leader(s)
7:00-7:30	Breakfast on your own. For participants staying at the Hotel Durant: Complimentary continental breakfast will be provided at the Hotel Durant, starting at 7:00am. Please meet Gil and Talia in the lobby at 7:30am to walk to the Valley Life Science Building.
7:45-8:10	Orientation to the Day	Pat Holroyd
Challenges of Using Paleo Data in New and Expanded Ways - Part 2 VLSB 2040
8:10-8:30	Horses in the cloud: Use case of Digital Equus Data	Bruce MacFadden, Florida Museum of Natural History, University of Florida
8:30-8:50	Managing Big Datasets	Doug Boyer, Duke University
8:50-9:10	Image Analysis of Modern and Fossil Plant Silica Bodies (Phytoliths)	Caroline Stromberg, Burke Museum of Natural History and Culture, University of Washington, Seattle
9:10-9:25	Using GIS for Geologic Field Mapping	Ashley Adams, Drexel University
9:25-9:40	Catalyzing Collections Digitization and Research Using Comprehensive Specimen Inventories	Lindsay Walker, Natural History Museum of Los Angeles County & Natural History Museum of Utah
9:40-9:55	How Digitization Helped Tame the Tully Monster	Paul Mayer, The Field Museum
9:55-10:25	Break
10:25-10:40	Using CT Data to Score Taxa for Phylogenetic Analyses	William Gearty, Stanford University
10:40-10:55	Challenges of Integrating the Tephrochronologic and Stratigraphic Information Using Paleo Specimens and GIS	Kari Prassack, Hagerman Fossil Beds National Monument/National Park Service
10:55-11:10	The Problem of Faunal Lists	Lynn Murray, Anza-Borrego Desert State Park
11:10-11:25	Species delimitation in the Recent and Fossil Record by Analyzing Ranges of Morphological Variability	Natalia Lopez Carranza, University of California, Davis
11:25-11:40	Using Fossil Occurrences in the Neotoma and Paleobiology databases for Landcover reconstructions Through Time	Scott Farley, University of Wisconsin, Madison
11:40-12:15	Q&A, Discussion, Morning Wrap-up
12:15-1:15	Lunch (provided)

Day 2 - Afternoon Breakout/Discussion Sessions
Time	VLSB 2040	VLSB 2063	UCMP Fishbowl
1:15-2:15	How do we deal with irregularities and unevenness of data for addressing paleontological research questions? Facilitator: Pat Holroyd Google doc link	What analytical and computational issues limit the use of digital paleontological data? Facilitator: Bruce MacFadden Google doc link	What are the sources of environmental data (climate, soil, hydrology, land use) for the past, present, and future of digital paleontological data, and what are the limitations of these sources? Facilitator: Talia Karim Google doc link
2:15-3:00	Discussion Group Reports
3:00-3:30	Break
3:30-4:30	Where do we go from here, especially in the development of research tools and training? Facilitator: Erica Clites Google doc link	What potential is there for collaboration between museums, researchers, and citizen scientists? Facilitator: Talia Karim Google doc link	What research is on the horizon that is particularly apropos for digital data? Facilitators: Bruce MacFadden, Gil Nelson Google doc link
4:30-5:00	Discussion Group Reports
5:00	Wrap up

Session Recordings

• Challenges of Using Paleo Data in New and Expanded Ways - Part 1
• Challenges of Using Paleo Data in New and Expanded Ways - Part 2
• Discussion Group Reports - Part 1
• Discussion Group Reports - Part 2

Acronyms

A few important acronyms to be familiar with.

Acronym	Meaning
iDigBio	Integrated Digitized Biocollections
NSF	National Science Foundation
ADBC	Advancing Digitization of Biodiversity Collections
TCN	Thematic Collection Network
PEN	Partner to Existing Network
CSBR	Collections in Support of Biological Research
IMLS	Institute for Museum and Library Services
GBIF	Global Biodiversity Information Facility
BCoN	Biodiversity Collections Network
GRBio	Global Registry of Biodiversity Repositories
DwC	Darwin Core
IPT	Integrated Publishing Toolkit
API	Application Programming Interface
VertNet	Vertebrate data portal, Data mobilization and cleaning services
EOL	Encyclopedia of Life

Workshop Planning Team

• Pat Holroyd, University of California Museum of Paleontology
• Erica Clites, University of California Museum of Paleontology
• Talia Karim, University of Colorado Museum of Natural History
• Gil Nelson, iDigBio/Florida State University