Resources

Biodiversity Informatics Training Workshop 2013

BITW II Students and Instructors. © David Bloom. 2013
BITW II Students and Instructors. © David Bloom. 2013

The Biodiversity Informatics Training Workshop (BITW), June 24-28, 2013, provided participants with the training and experience to work with primary biodiversity data sources and new tools necessary to become proficient in biodiversity informatics and conduct biodiversity research. Led by experienced informaticists and researchers, the BITW emphasized the use and analysis of aggregated biodiversity data from VertNet, and other sources, for a wide of variety of research.

Hour Activity
09:00 Welcome, Introductions, and Housekeeping
(Dave Bloom)
10:00 Opening, Work Groups,
Data Set Selection, and Research Questions
(Dave Bloom)
10:15 Data Basics - Darwin Core Standard
(Rob Guralnick)
10:45 Introduction to Geographic Concepts,
Introduction to Georeferencing,
Point-Radius Method & Sources of Uncertainty,
Georeferencing Calculator - Manual, Example,
Online Resources,
Semi-Automated Tools (GEOLocate)
Georeferencing Template, Online Exercises
(Carol Spencer, Dave Bloom)
12:00 LUNCH
13:00 Data Sources - Data Portals and Other Data Sources
Exercise: Getting Data from a Portal
Testing the VertNet Portal
(Dave Bloom)
13:45 Data Organization
(Javier Otegui)
14:00 Introduction to Geographic Validation and Fitness for Use
(Initial checks, Intermediate/Advanced checks)
(Javier Otegui)
14:30 Lab Exercises
Introduction to Open Refine: Data Cleaning 1:
Routine geographic data quality checks
Open Refine Walkthrough
Open Refine Walkthrough (DMNS Mammals)
(Javier Otegui)
16:00 BREAK
16:30 Taxon Validation Introduction
Open Refine Name Validation
(Gaurav Vaidya, Victoria Tersigni)
17:00 A tutorial in taxonomic validation
Source Code
TaxRefine Project (comments welcome)
(Victoria Tersigni, Gaurav Vaidya)
18:00 Virtual Talk
Laura Russell, VertNet Programmer, University of Kansas (Slides)
18:30 REST
Hour Activity
9:00 Workshop Project Introduction, Group Organization
Sample Past Presentations 1, 2
(Dave Bloom, Rob Guralnick)
9:30 Introduction to R - The R Environment and Basics
Coursera Online Course, rOpenSci, rVertNet Tutorial
(Michelle Koo)
10:00 SPLIT SESSION
Beginners Tutorial and Refresher Exercises: Introduction to RStudio (Script)
Loops (.pdf)
Recommended: A Beginner's Guide to R
(Javier Otegui, Carol Spencer, Dave Bloom)

Advanced Users: Mind Blowing Exercises
Acquiring and Exploring Species
DISMO
(Michelle Koo, Michael Denslow, Rob Guralnick)
11:30 GIS Basics and Introduction to RS
(Michelle Koo)
12:15 Lunch
13:15 Introduction to Raster Data
LULC, Climate Models, Format Types, and More
QGIS Demo
USGS Earth Explorer, (grd .zip), (shp .zip), (csv+ .zip)
(Michael Denslow, Michelle Koo)
14:15 QGIS - Exercises
QuantumGIS: Raster, Vector
Acquiring WorldClim Data, Projecting Spatial Data (QGIS 1.8)
(Michelle Koo and the Gang)
15:15 BREAK
15:45 Environmental Data Layers - Exercises in QGIS
Data Sources
(All)
17:00 Work Session
Group Project Proposal Submission Deadline: 19:30pm
Send proposals to allgeoref[at]gmail[dot]com
18:00 Participants - REST / Instructors - PASS OUT
Hour Activity
9:00 Announcements and Day 3 Check-In
(Dave Bloom)
9:15 Niche Modeling Concepts - Conceptual Framework of Modeling
SDM Readings, MaxEnt Read Me
(Rob Guralnick)
10:00 Niche Modeling - MaxEnt Tutorial (Program .zip, Tutorial .pdf)
(Rob Guralnick, Michelle Koo)
10:45 GIS and Modeling - Exercises
(All)
12:00 LUNCH
13:00 Statistical Analysis and Validation of Models - Tutorial and Demonstration
More on Maxent
Africa ASCI Clips
(Rob Guralnick, Michelle Koo)
14:00 Work Session - Individual or Group Projects
(Instructors available for tutorials and guidance)
15:00 BREAK
15:30 Work Session - Individual or Group Projects
(Instructors available for tutorials and guidance)
16:00 DEMO: Ensemble Modeling and Biomod2
Using Biomod2 in R
(Rob Guralnick)
Exercise: Modeling in R
SDM_Bioclim_maxent.r
(Michelle Koo)
16:20 Work Session - Individual or Group Projects
(Instructors available for tutorials and guidance)
17:10 Virtual Talk
Dan Warren, Australian National University (.ppt)
ENMTools.zip (Test_ENMTools.R has the syntax for each of the commands)
Vijay Barve, University of Kansas (.pdf)
Hour Activity
9:00 Announcements
9:05 Projecting Models in Space and Time
Gunnison's Prairie Dog Example (.zip)
(Rob Guralnick)
9:20 Exercise: Modeling in R
SDM_Bioclim_maxent.r
Demo: Post-Processing of Niche Model Results in a GIS or R?
Displaying Results
(Michelle Koo)
10:05 Work Session - Individual and Group Modeling
11:30 Demo: Cartography - Demonstration in QGIS
(Michelle Koo)
12:00 LUNCH
13:00 Work Session - Individual or Group Projects
(Instructors available for tutorials and guidance)
17:10 Virtual Talk
Tanya Dewey, Animal Diversity Web (Q'vark)
Scott Loarie, iNaturalist
17:30 REST
Hour Activity
9:00 Data Trends and Projects
Google Earth, Map of Life,
and LifeMapper
(Rob Guralnick)
09:20 Communicating to the Public, Outreach, and Citizen Science
(Rob Guralnick)
10:00 Citizen Science Activity - iNaturalist
Apple AppStore, Android Market
(Carol Spencer)
10:30 Work Session - Individual or Group Projects
(Instructors available for tutorials and guidance)
12:00 LUNCH
12:50 Group Photo
Main Entrance to MCOL (double doors, East side)
13:00 Group Presentations
20 minutes each, Q&A included
Summary of research, question(s) answered, methods, and results

Squads:
Ratastrophii
Mongoose Meals
Team Flycatcher
Lethal Tree Rats
Scratch That Niche (Lemurs Suck!)
Split the Difference
Feral Cat-aloguers
We Like Our Caipirinhas Dry
Lizard Man Speaks
Your Megafauna Asplode!
17:00 Evaluations and Reimbursement Documentation
(Dave Bloom)
17:40 Closing Statements
(Instructors)
18:00 END

VENUE

University of Colorado Museum of Natural History
University of Colorado, Boulder
Boulder, Colorado, USA


PARTICIPANTS

Facilitators:

David Bloom. USA. VertNet Coordinator, Museum of Vertebrate Zoology, University of California, Berkeley. dbloom[at]vertnet.org
Michael Denslow. USA. Assistant Director of Scientific Research Corrections, NEON. mdenslow[at]neoninc.org
Rob Guralnick. USA. Associate Professor, EBIO, and Curator, CU Museum, University of Colorado, Boulder. robert.guralnick[at]colorado.edu
Michelle Koo. USA. GIS and Biodiversity Informatics Staff Curator, Museum of Vertebrate Zoology, University of California, Berkeley. mkoo[at]berkeley.edu
Javier Otegui. Spain. Research Scholar, Department of Ecology and Evolutionary Biology, University of Colorado, Boulder. javier.otegui[at]gmail.com
Carol Spencer. USA. Staff Curator of Herpetology, Museum of Vertebrate Zoology, University of California, Berkeley. atrox[at]berkeley.edu
Gaurav Vaidya. India. Graduate Student, Department of Ecology and Evolutionary Biology, University of Colorado, Boulder. gaurav[at]ggvaidya.com

Guest Lecturers:

Laura Russell. Kansas, USA. University of Kansas.
Dan Warren. Canberra, Australia. Australian National University.
Vijay Barve. Kansas, USA. University of Kansas.
Tanya Dewey. Michigan, USA. Animal Diversity Web. tdewey[at]umich.edu
Scott Loarie. California, USA. iNaturalist. loarie[at]gmail.com

Trainees:

Jessica Allen. New York, USA. New York Botanical Garden.
Thiago Andre. California, USA. University of California, Berkeley.
Nicole Angeli. Texas, USA. Texas A&M University.
Mele Avery. Colorado, USA.
Kayce Bell. New Mexico, USA. University of New Mexico.
Kali Blevins. Colorado, USA. NEON.
Stan Blum. California, USA. California Academy of Sciences.
Allison Byrne. Pennsylvania, USA. VertNet Intern, Drexel University.
Christopher Evelyn. California, USA. University of California, Santa Barbara.
Kathryn Everson. Alaska, USA. University of Alaska, Fairbanks.
Adam Ferguson. Texas, USA. Texas Tech University.
Benjamin Frable. Oregon, USA. Oregon State University.
Grant Hurley. British Columbia, Canada. University of British Columbia.
Adam Martin. Oregon, USA. Oregon State University.
Nicholas Mason. New York, USA. Cornell University.
Brianna McHorse. Oregon, USA. University of Oregon.
Jessica Rothery. California, USA. University of California, Berkeley.
Karen Rowe. Victoria, Australia. Museum Victoria.
Philip Shirk. Florida, USA. University of Florida.
Gisèle Koupamba Sinasson Sanni. Atlantique, Benin. Laboratory of Applied Ecology.
Victoria Tersigni. New Hampshire, USA. VertNet Intern, Dartmouth College.
Alison Vaughan. Victoria, Australia. Royal Botanic Gardens Melbourne.
Julian Velasco Vinasco. Distrito Federal, Mexcio. Instituto de Biología, Universidad Nacional Autónoma de México.
Anne Virnig. New York, USA. New York Botanical Garden.