Digital Data in Paleontological Research

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Logistics


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

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

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