Resources
Biodiversity Informatics Training Workshop 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 GEOLocate BioGeomancer 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 (Guralnick/Koo) |
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 (Guralnick/Koo) |
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 (Guralnick/Koo) |
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 (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
Rob Guralnick.
USA. Associate Professor, EBIO, and Curator, CU Museum, University of Colorado, Boulder. robert.guralnick[at]colorado.edu
Michelle Koo.
USA. GIS and Informatics Specialist, Museum of Vertebrate Zoology, University of California, Berkeley. mkoo[at]berkeley.edu
Nelson Rios.
USA. Manager of Collections and Bioinformatics, Tulane University Museum of Natural History. nelson[at]museum.tulane.edu
Carol Spencer
USA. Staff Curator of Herpetology, Museum of Vertebrate Zoology, University of California, Berkeley. atrox[at]berkeley.edu
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.
Trainees:
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.