Biodiversity Informatics Training Workshop 2012

BITW I Students and Instructors. © Vijay Barve. 2012
BITW I Students and Instructors. © Vijay Barve. 2012

The Biodiversity Informatics Training Workshop (BITW), June 25-29, 2012, 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)
10:35 Data Basics - Geographic Concepts
(Nelson Rios)
10:55 Getting Data - Data Sources
(Nelson Rios)
11:15 Introduction to Georeferencing
Point-Radius Method, Georeferencing Calculator (Manual),
Georeferencing for Dummies, Locality Descriptions, and Best Practices
(Carol Spencer)
12:00 LUNCH
13:00 Georeferencing - Online Resources (Quick Reference)
Georeferencing Template
(Carol Spencer)
13:30 Georeferencing - Semi-Automated Tools
Batch Processing
(Nelson Rios)
14:15 Georeferencing - Paper Maps
Georeferencing for Dummies,
Paper Maps Handout, and Point-Radius Method
(Dave Bloom)
15:00 BREAK
15:15 Georeferencing - Exercises
16:10 A Word About Data Organization
Lab Exercises: Acquiring Data, Validation and Modeling in DIVA-GIS (tutorial)
(Michelle Koo)
18:00 REST
Hour Activity
9:00 Introduction to R - The R Environment and Basics
FishNet Sample Query
(Nelson Rios)
9:30 Introduction to R - Workspace and Tools
Niche Demo, A Beginner's Guide to R
10:00 GIS Basics
(Michelle Koo)
12:00 Lunch
13:00 GIS Basics - Continued
ArcGIS: Model Builder, Mask Creation
QuantumGIS: Raster, Vector, Plugins
fTools, GDALTools, OpenLayers
(Michelle Koo)
14:00 Niche Modeling Concepts - Conceptual Framework of Modeling
(Rob Guralnick)
14:45 BREAK
15:00 Niche Modeling - Maxent Tutorial (.zip, .doc)
Maxent Data Files
Fish Data for Maxent
16:15 Breakout Session
17:10 Virtual Talk
Dan Warren, University of Texas, Austin (.ppt)
Pascal Title, San Diego State University (.ppt)
17:30 REST
Hour Activity
9:00 Workshop Project Introduction, Group Organization
(Rob Guralnick)
9:30 Work Session - GIS and Modeling
12:00 LUNCH
13:00 Statistical Analysis and Validation of Models - Tutorial and Demonstration
More on Maxent
Displaying Results
Species Distribution Modeling References
15:00 Work Session - Individual or Group Projects
(Instructors available for tutorials and guidance)
17:10 Virtual Talk
Michael Denslow, Appalachian State University (.ppt)
Hour Activity
9:00 Post-Processing of Niche Model Results
(Michelle Koo)
10:00 Work Session - Individual and Group Modeling
11:00 Data Trends - Species Richness, Phylogenetic Connections
(Rob Guralnick)
11:20 GIS/Cartography - Demonstration
(Michelle Koo)
12:00 LUNCH
13:00 Work Session - Individual or Group Projects
(Instructors available for tutorials and guidance)
17:10 Virtual Talk
Marie Studer, EOL
Tanya Dewey, Animal Diversity Web
17:30 REST
Hour Activity
9:00 Data Trends - 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
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
15 minutes each, Q&A included
Summary of research, question(s) answered, methods, and results
Group Jared
Group KC
Group Brian
Group Jenna
Group Joe D
Group Kerri
Group Pika Joe
Group Brad
Group Ramon
Group Bernardo
Group Rick
17:00 Evaluations and Reimbursement Documentation
(Dave Bloom)
17:40 Closing Statements
18:00 END


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



David Bloom. USA. VertNet Coordinator, Museum of Vertebrate Zoology, University of California, Berkeley. dbloom[at]
Rob Guralnick. USA. Associate Professor, EBIO, and Curator, CU Museum, University of Colorado, Boulder. robert.guralnick[at]
Michelle Koo. USA. GIS and Informatics Specialist, Museum of Vertebrate Zoology, University of California, Berkeley. mkoo[at]
Nelson Rios. USA. Manager of Collections and Bioinformatics, Tulane University Museum of Natural History. nelson[at]
Carol Spencer USA. Staff Curator of Herpetology, Museum of Vertebrate Zoology, University of California, Berkeley. atrox[at]

Guest Lecturers:

Dan Warren. Texas, USA. University of Texas, Austin.
Pascal Title. California, USA. San Diego State University.
Michael Denslow. North Carolina, USA. Appalachian State University.
Marie Studer. Massachussetts, USA. Encyclopedia of Life.
Tanya Dewey. Michigan, USA. Animal Diversity Web.


Umilaela. West Java, Indonesia. School of Life Sciences & Technology-Institut Teknologi Bandung.
Kerri Ackerly. New York, USA. Adelphi University.
Vijay Barve. Kansas, USA. University of Kansas.
Ileana Betancourt. New York, USA. Cornell University.
Bernardo Blanco-Martin. Queensland, Australia. Australian Institute of Marine Science.
Kevin Bracy Knight. Colorado, USA. University of Colorado, Boulder.
Mariel Campbell. New Mexico, USA. Museum of Southwestern Biology.
Steven Dilliplane. Pennsylvania, USA. Academy of Natural Sciences of Drexel University.
Joseph DeVeer. Massachussetts, USA. Harvard Extension School, Harvard University.
Nicholas Famoso. Oregon, USA. University of Oregon.
Ramon Gallego. Auckland, New Zealand. University of Auckland.
Rachel Golden. Maryland, USA. University of Maryland, College Park.
Jared Grummer. Washington, USA. University of Washington.
Christy Hipsley. Berlin, Germany. Museum fur Naturkunde Berlin.
Kiki Martial. Oueme, Benin. Faculty of Agronomic Sciences, University of Abomey-Calavi Benin.
Richard Levy. Colorado, USA. University of Colorado, Boulder.
Juan Andres Martinez Lanfranco. Montevideo, Uruguay. Faculty of Sciences, University of the Republic of Uruguay.
Jenna McAleer. Colorado, USA. Colorado State University.
Matthew McElroy. Washington, USA. University of Washington.
Brian Rankin. Alberta, Canada. University of Calgary.
Brad Ruhfel. Massachussetts, USA. Harvard University.
Kassandra Semrau. Michigan, USA. University of Michigan.
Jeff Shi. North Carolina, USA. Duke University.
Joseph Stewart. Nevada, USA. University of Nevada, Reno.
Yanina Sulca Pereira. Heredia, Costa Rica. Instituto Tecnologico de Costa Rica.
Gerard Talavera. Barcelona, Spain. Universitat Autonoma de Barcelona.
Xiao Xiao. Utah, USA. Utah State University.