Resources
Biodiversity Informatics Training Workshop 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.
Tutorial Scripts
Quantum GIS 1.8.0
R 3.0
RStudio Desktop
Open Refine
MaNIS/HerpNet/ORNIS Georeferencing Guidelines
Georeferencing Best Practices
Georeferencing Quick Referencing Guide
Georeferencing Spreadsheet Template
Georeferencing Resources
How Do I Do That In Quantum GIS?
DIVA-GIS 7.5
ArcGIS 10.1 (Evaluation copy provided)
R SNIPPETS
Calc_species_richnessfrompolys.r
Geolocate.r
Geonames_lookupSnippet.r
RasterClipSnippet.r
Tues.Acquiring&Exploring_species.r
Tues.IntroductionR.r
SDM_Bioclim_maxent.r
ENMTools.zip
(Test_ENMTools.R has the syntax for each of the commands)
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.