Research Spotlight: February 2021
by: Vaughn Shirey, Michael Belitz, Vijay Barve, Rob Guralnick
Blog Archives
A Diversity, Equity, and Inclusion Reading List, with Special Emphasis on Natural Sciences and Natural History Museums
As the hub for digitization of U.S. natural history collections, iDigBio aims to engage our community in promoting a more diverse, equitable, inclusive, and actively anti-racist community. To that end, the iDigBio team focused on issues of Education, Outreach, Diversity, and Inclusion has compiled this reading list to begin conversations in the classroom, in museum collections, and among colleagues.
February 2021 Biodiversity Spotlight
Photo courtesy of Jeffrey Weinell, University of Kansas Biodiversity Institute and Natural History Museum
iDigBio Update 2020
Dear iDigBio Enthusiasts,
I am delighted to report that iDigBio enjoyed an exceptionally successful and productive 2020 made possible in large part by contributions of the many collaborators whose consistent support, involvement, and input have been highly valued and much appreciated. We enter the new year eager to continue integral involvement in the biodiversity collections community.
The iDigBio US Collections List - Now Proudly in Collaboration with GBIF
After many months of hard work in collaboration with our partners at GBIF, we are excited to announce that the new and improved iDigBio US Collections List has officially launched as of this week.
This latest development for the first time enables shared data management across iDigBio and GBIF, in addition to facilitating a unified, more efficient, and more exhaustive list of US Collections.
WeDigBio 2020
Contributed by: Libby Ellwood, Austin Mast, Robert Bruhn and Kevin Love
Scientist in the Spotlight: Noé De La Sancha
In our series, "Scientist in the Spotlight" we’ll sit down with the ADBC (Advancing Digitization of Biodiversity Collections) program's best and brightest to learn more about what makes them tick. This month, we had a chance to speak with Noé De La Sancha. He is a part of the oVert TCN.
Where are you from?
2020 SACNAS National Diversity in STEM Conference
Contributed by: Molly Phillips
Research Spotlight: November 2020
Comparing the use of species occurrence data and information systems by academics and government professionals
Contributed by: Elizabeth Martín, Shari Ellis, Larry Page
Strategic Planning for Biodiversity Collections Online Course
Dear Colleagues,
iDigBio is pleased to announce a 7-week "Strategic Planning for Biodiversity Collections” online course.
Take this opportunity to introduce new purpose and excitement into your organization. Prepare to relate your collection’s compelling vision to stakeholders and discuss long-term goals and strategies with administrators.
Research Spotlight: October 2020
Unlocking the secret histories of bats in natural history collections
Article by: Caitlin J.Campbell, Graduate Assistant at the UF Department of Biology
October 2020 Biodiversity Spotlight
Contributed by Cat Chapman
Have you ever been out on a walk through nature, or even in your neighborhood, and saw what appeared to be a clump of tiny leaves, debris, or lichen… only to see it move?
Upon closer inspection of this mysteriously motile clump of detritus, you may see that it has tiny little legs underneath it. It’s alive!
Meet the trash bug!
2020 TCN and PEN Awards
Welcome to all of the newly NSF-funded Advancing Digitization of Biodiversity Collections (ADBC) projects.
Scientist in the Spotlight: Diego Barroso
In our series, "Scientist in the Spotlight" we’ll sit down with the ADBC (Advancing Digitization of Biodiversity Collections) program's best and brightest to learn more about what makes them tick. This month, we had a chance to speak with Diego Barroso. He works at the Botanical Research Institute of Texas as the project manager of the TORCH TCN.
Biodiversity Spotlight: September 2020
Written by Erica Krimmel.
Research Spotlight: September 2020
Contributed by: Kayce C. Bell, Assistant Curator of Terrestrial Mammals at the Natural History Museum of Los Angeles County
Biodiversity Spotlight: August 2020
Written by: Alnycea Blackwell and Cat Chapman
Biodiversity Spotlight: July 2020
Article by: Caitlin J.Campbell, Graduate Assistant at the UF Department of Biology
Research Spotlight: July 2020
Contributed by: Aaron Goodman, Graduate Student Department of Entomology, California Academy of Sciences.
Research Spotlight: June 2020
Article by: Zoliswa Nhleko, PhD candidate at the UF School of Natural Resources and Enviroment
May 2020 Biodiversity Spotlight
Article by: Nattapol Kraisitudomsook, PhD student from the Smith Lab at the University of Florida
Virtual Resources for Your Life During Social Distancing
Many things have changed rapidly and these are unprecedented and stressful times, but one positive for our team now all working remotely are all of the new coworkers!
Research Spotlight: April 2020
Contributed by Luis D. Verde Arregoitia.
Find him on Twitter @LuisDVerde or on his Website.
February 2020 Biodiversity Spotlight
Photo credit: David Haring, Duke Lemur Center
Aye-aye, Daubentonia madagascariensis
Biodiversity Next 2019: vision, inspiration, action for our collective future
Deborah L Paul, Capacity Development Manager
2019 TCN and PEN Awards
Welcome to all of the newly NSF-funded Advancing Digitization of Biodiversity Collections (ADBC) projects. This year we have three new Thematic Collections Networks (TCNs) and six Partners to Existing Networks (PENs) joining the community.
2019 TCNs:
oVert Workshop: 3D Vertebrates, From Museum Shelves to Classrooms
Article contributed by Julie Bokor (UF Center for Precollegiate Education and Training)
SoRo Mountain TCN Field to Digital Object Workshop introduces undergraduate students to museum careers
Contributed by: J Ryan Allen, Dina Clark and Erin Tripp (University of Colorado)
BioQUEST and QUBES Summer Workshop 2019
Contributed by: Molly Phillips, iDigBio's Education, Outreach & Diversity Coordinator
Images courtesy of Adam Fagen
American Society of Mammalogists (ASM) 2019
The 99th Annual Meeting and Centennial Celebration of the American Society of Mammalogists took place 28 June to 2 July 2019, at the birthplace of ASM, Washington, DC. iDigBio helped to mark this important milestone through organizing a session on broadening representation in mammalogy as well organizing the first ever Data Help Desk at ASM.
Research Spotlight: April 2019
Climatic Niche Modeling for Beetleweed
(Galax urceolata, Diapensiaceae)
Contributed by: Shelly Gaynor
iDigBio Hosts the Life Discovery Conference
Bioblitz group photo (Florida Museum Photo Department)
Research Spotlight: March 2019
Emerging frontiers in phenological research
Libby Ellwood, Katelin Pearson, and Gil Nelson
Research Spotlight: February 2019 (Phylogenetics)
Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates
November 2018 Biodiversity Spotlight
Wood-warblers, Parulidae
Image Credit: Joe Poston
Research Spotlight: November 2018
Augustus Fendler Herbarium Specimens: A Locality Improvement Project
A component of the Southern Rocky Mountain Flora Database Project
Lance J. Gloss and Timothy J. S. Whitfeld
Brown U. Herbarium (BRU)
Dec 2017 - May 2018
Introduction
Research Spotlight: October 2018
Metabolic rates, climate, and macroevolution: a case study using Neogene molluscs
Luke C. Strotz, Erin E. Saupe, Julien Kimmig and Bruce S. Lieberman
ADBC Summit 2018 Report
Summit 2018 group photo
Research Spotlight: September 2018
Utilising publicly available species occurrence records to generate contemporary estimates of medically important snake species distributions
Contributed by: Joshua Longbottom, Liverpool School of Tropical Medicine
August 2018 Biodiversity Spotlight
European honey bee, Apis mellifera
Image Credit: USGS Bee Inventory and Monitoring Lab
Drawers, Jars and Databases: A Workshop for North Carolina Educators
Workshop Group Photo
MyCoPortal helps save life!
Contributed by: Timothy J. Baroni & Andrew N. Miller
State University of New York, Cortland, NY and University of Illinois, Champaign, IL
Chlorophyllum molybdites (Image courtesy of Roy Halling)
July 2018 Biodiversity Spotlight
Rattails and Grenadiers (Family Macrouridae)
Images courtesy of NOAA Okeanos Explorer
Contributed by Randy Singer
Research Spotlight: July 2018
Digital Coyote; an online archive of skulls
Contributed by: Osrica Mclean and Declan McCabe
How can you provide an authentic opportunity for undergraduate students to study geographical variation without hauling them to major metropolitan museums and arranging access to valuable specimens? This question started a slightly obsessive odyssey that began with a single coyote skull and now stands at 125 skulls….and counting.
How to, and how not to, design a light box: A cautionary tale
by C. Skema, Anne Barber, and Tim Block
The Oldest Specimen in the MyCoPortal
The oldest specimen in the MyCoPortal is housed at Purdue and was collected in 1769 in Tierra Del Fuego at the southern tip of South America. It was collected by the Englishman Sir Joseph Banks and Dr.
March 2018 Biodiversity Spotlight
Sand Food (Pholisma sonorae)
Photo courtesy of Michael Carters
February 2018 Biodiversity Spotlight
Pacarana (Dinomys branickii)
David F. Schmidt, USNM Dinomys branickii, Smithsonian Institution, NMNH, Mammals
Research Spotlight: February 2018
From the Tropics to the Drawer and Back: Digitized New World Swallowtail Butterfly Specimens Inform Biodiversity Patterns
Contributed by: Hannah Owens from the Florida Museum of Natural History, University of Florida
iDigBio Update 2017
Dear iDigBio Enthusiasts,
Research Spotlight: January 2018
New Insights from Old Herbarium Specimens
Contributed by Richard B. Primack (Boston University; primack@bu.edu) and Charles G. Willis (Harvard University; charleswillis@fas.harvard.edu)
“Live in each season as it passes - breathe the air, drink the drink, taste the fruit & resign yourself to the influence of each.” Thoreau, in his Journal. 1835
The Momentum for Integrating Collections and Ecological Research: Expanding Collections Stakeholders and Imagining Future Data Needs
by Deborah Paul, Libby Ellwood, Christina Alba, Larry Page
with contributions from our speakers: Dave Tazik, Jennifer McGuire, Anna Monfils, Barry Sinervo, and Elizabeth Martin; and from some participants present at this symposium including (at least): Vince Smith, Mary Klein, Herrick Brown, and Jason Knouft
‘What do we need to leave behind today to position our future selves for success?’
Big Data and Bugs: How Massively Collected Biodiversity Data Are Changing the Way We Do Insect Science - Symposium at EntSoc 2017
by Deborah Paul, Ana Dal Molin, and Pam Soltis, with contributions from all symposium presenters. Symposium from iDigBio and Universidade Federal do Espírito Santo, Brazil
Natural History Collections as Primary Data in Ecological Research
Prologue: Many of us in the ADBC world look for ways to expand the community of users of museum collections data and to increase the ways in which collections data are used. Recently, in Trends in Ecology and Evolution (TrEE), an opinion piece was published by Scott A. Morrison, et al. titled "Equipping the 22nd-Century Historical Ecologist." In this paper, Morrison, et al.
Research Experiences for Undergraduates in Digitized Collections Data
Contributed by Pam Soltis and Adania Flemming
iDigBio supported five students in its inaugural mini-REU site program during summer, 2017. This program, modeled on NSF’s Research Experiences for Undergraduates Program, was developed to provide undergraduates with research opportunities using digitized natural history collection data.
Digitizing Mollusks Workshop Report
Participants in the iDigBio supported Digitizing Mollusks workshop.
The iDigBio supported “Digitizing Mollusks” workshop was held immediately prior to the American Malacological Society meeting in Newark, Delaware on July 15-17, 2017. Thirty-eight collections professionals from 24 established and developing mollusk collections gathered to discuss the status of Mollusk collection digitization in North America and abroad.
Digitization of the ETH Entomological Collection
Contributed by: Rod Eastwood Curator, Entomological Collection, Eidgenössische Technische Hochschule (ETH) Zürich, Institut für Agrarwissenschaften, Biocommunication & Entomology, Zürich, Switzerland
Connecting Collections and Ecology
by Libby Ellwood, Katelin Pearson, Katja Seltmann, Deb Paul and Shelley James
Research Spotlight: August 2017
Collections Data Reveals Complex Plant/Pollinator Network, Inspires Research
Contributed by Dylan Ricke and Annika Rose-Person, Archbold Biological Station
NMITA – using an illustrated taxonomic database of living and fossil corals to expand bioinformatics education.
What is NMITA?
iDigBio at the Ecological Society of America Meeting 2017
UPDATE!: Read all about our ESA 2017 bioblitz and booth experience: https://www.idigbio.org/content/connecting-collections-and-ecology
iDigBio heads to the Ecological Society of America, 102nd Meeting, in Portland, Oregon from August 5 - 11, 2017.
The theme of this year's ESA meeting aligns directly with iDigBio's focus on enabling use of collections data by researchers, and serves as a special opportunity to engage with the ecological research community. Theme:
July 2017 Biodiversity Spotlight
Manta Rays
The Evolution of Darwin Core Hour
From the Darwin Core Hour Team.
Research Spotlight: June 2017
Hole-y Plant Databases! Understanding and Preventing Biases in Botanical Big Data
June 2017 Biodiversity Spotlight
American Horseshoe crab (Limulus polyphemus)
Photo courtesy of: Florida Fish and Wildlife, Photo by: Karen Parker
Research Spotlight: July 2017
Data Curation Profiles—An Information Science framework for data managers
-- Contributed by Wade Bishop and Kelly White, The University of Tennessee, School of Information Sciences
Data curation profiles (DCPs). DCPs give scientists, researchers, and data managers an enhanced and detailed understanding of the “data story” from the perspective of the data. A DCP “captures requirements for specific data generated by researchers articulated by the researchers themselves” (http://datacurationprofiles.org/purpose) and provides data managers a framework to acquire an in-depth understanding of the particular data curation needs of producers and their intended users. Read more about Wade & Kelly's work with the iDigBio community here.
Bering Land Bridge and the MyCoPortal
Contributed by: Teresa Iturriaga, Rhianna Baldree, Alex Kuhn, Andrew Miller
Mycologists long to collect
areas remote to most men
where fungi today may thrive
keeping plants, trees, and cycles alive.
Research Spotlight: May 2017
Using specimens to create a pollinator community assessment of restored tallgrass prairie
-- Contributed by Heather Cray, Department of Environment and Resource Studies, University of Waterloo
Animal species need space – a place to forage, grow, and nest. This is especially true of Lepidoptera (butterflies and moths), whose caterpillars generally feed exclusively on one genus or species of host plant (think monarch butterflies and milkweed). For the 4,000 or so species of native bees in North America, required forage plants and nesting sites vary from common suburban offerings (e.g., patches of bare ground, maples, willows, clover), to specialized needs which are ecosystem-specific. Enter tallgrass prairie – a grassland ecosystem with high forb diversity that supports a dizzying array of invertebrate life. As our continent’s most endangered ecosystem, the 1-3% that remains is a mix of remnant and restored habitat, and restoration efforts-- both large and small, are ongoing. Read more here.
National Science Teachers Association Conference 2017
iDigBio staff members Bruce MacFadden, Libby Ellwood, and Molly Phillips attended the 2017 National Science Teachers Association National Meeting held on March 30-April 2 in the L.A. Convention Center in downtown Los Angeles. The conference was massive – attended by thousands of K-college science teachers from around the country and world.
Research Spotlight: April 2017
Publishing a new species? Add the unique identifiers!
Citation of voucher specimen data can be problematic. There are currently no formulated rules for how to cite a digital specimen in a publication, but data aggregators such iDigBio, GBIF, and VertNet offer suggestions. Pensoft is leading the way by providing efficient methods for publishing digital data (see their blog post here) - but it still rarely happens, or occurs in a non-systematic way. Recently, with my colleague Dr George Argent, a new species of Rhododendron from Mount Yule, Papua New Guinea was published in the February 2017 online volume of the Edinburgh Journal of Botany. The digital data for the isotype housed at the Bishop Museum is available through iDigBio and we wanted to cite this information in the published paper. As a test case, we added the Darwin Core occurrenceID and a link to the iDigBio record page. Read more here.
Strategic Planning for Herbaria Short Course
The Society of Herbarium Curators and iDigBio are pleased to announce a 6-week "Strategic Planning for Herbaria” short course.
Take this opportunity to introduce new purpose and excitement into your organization. Learn how to relate your collection’s compelling vision to stakeholders and communicate long-term objectives and strategies to administrators.
Portal Curiosities: Asa Gray and the quest for Shortia galacifolia – a case study for the importance of collections
Contributed by: Donald H. Pfister, Asa Gray Professor of Systematic Botany and Curator, Farlow Library and Herbarium, Harvard University, 22 Divinity Ave., Cambridge, MA 02138
AIBS Communications Boot Camp
The scientific view from behind the microphone
Imagine it. The sweaty palms, the nervous fidgeting. You're sitting in the waiting room of the radio station, the governors' office, or waiting to speak with the Chair of your Department. You begin question your preparation - What is the key message and main talking points? Is there an engaging and relevant story to highlight the science? Does it fit with the audience you will be engaging with? You begin cursing that you didn't have more practice!
Research Spotlight: March 2017
Collecting trends: how wars and human history influence biological collections
-- Contributed by Vaughn Shirey, The Academy of Natural Sciences of Drexel University
A large portion of my research in The Gelhaus Lab at The Academy of Natural Sciences of Drexel University relies heavily on digitized specimen data and metadata, specifically the who, when, and where of specimen collection. “Big data” research has risen in popularity since high-performance computing has made it easier for researchers to conduct analyses of groups of organisms overnight; however, additional considerations to the use of large datasets should be taken into account. My research focuses on the historical biases present in natural history collection data, including identifying collection bias and gaps in data due to human history. Read more here.
Research Spotlight: February 2017
Allocating more memory to OpenRefine - and other helpful information for handling large datasets
-- Contributed by Chris Evelyn, University of California - Santa Barbara, along with Deborah Paul and Shelley James, iDigBio
This month's Research Spotlight contribution resulted from a recent iDigBio workshop where participants learned the basics of OpenRefine. Finding a limitation to the size of the dataset that could be manipulated, Chris found the following solution to working with large datasets from iDigBio and other biodiversity data aggregators. OpenRefine (formerly Google Refine) is a powerful tool for helping with the cleaning of messy data - ideal for natural history collection managers, data managers, and researchers using biodiversity data alike. Read more here.
iDigBio's Big Data Methods Symposium at TDWG 2016
January 5, 2017
iDigBio Update for 2016
Dear iDigBio Enthusiasts,
Research Spotlight: January 2017
TDWG 2016: Highlights for biodiversity research
-- Contributed by Shelley James & Libby Ellwood, iDigBio
The Biodiversity Information Standards (TDWG) annual meeting in 2016 had the theme of "Standards Supporting Innovation in Biodiversity and Conservation". Understanding the use of biodiversity standards, and having clear and concise documentation, is essential for the creation, aggregation and downstream use of biodiversity data, and it is exciting to see the diverse TDWG community helping to clarify and expand on the already existing data standards. Read more here.
WeDigBio 2016
Contributed by Libby Ellwood and Austin Mast (iDigBio-Florida State University).
The Advancing Digitization of Biological Collections Annual Summit, hosted by iDigBio, took place in Chattanooga, Tennessee, at 
International Congress of Entomology
iDigBio had a blast at ICE XXV International Congress of Entomology, held September 25-30, in Orlando, Florida.. The event brought together thousands of scientists from around the world under the theme “Entomology without Borders.” iDigBio staff participated in two symposia, the Insect Expo, and hosted the iDigBio booth in the ICE Exhibit Hall.
Ghost Towns in MyCoPortal I:Nuttallburg and Lawrence William Nuttall
Contributed by: Teresa Iturriaga, Rhianna Baldree, Alex Kuhn, Andrew N. Miller
University of Illinois, Illinois Natural History Survey, 1816 South Oak Street, Champaign, IL 61820-6970
We forget because remembering everything is impossible.
We also forget because remembering can be painful and raise too many questions that have no clear answers.
Such is the case regarding many ghost towns. They remind us of the transience of everything.
Research Spotlight: November 2016
Mapping Life – Quality Assessment of Novice vs. Expert Georeferencers
-- Contributed by Elizabeth R. Ellwood, Florida State University, with Henry L. Bart, Jr., Michael H. Doosey, Dean K. Jue, Justin G. Mann, Gil Nelson, Nelson Rios, Austin R. Mast
Citizen scientists participate in a host of activities that advance scientific research. These individuals are not trained scientists, but their contributions to research enable scientists to scale up their research across taxa and geographies. Read more here.
Research Spotlight: October 2016
Bees, bees and more bees - or are there? Monitoring the status of US bee populations using biological collections.
-- Contributed by Jillian Goodwin, iDigBio, interviewing Sam Droege, USGS Patuxent Wildlife Research Center
Sam Droege heads the USGS Native Bee Inventory and Monitoring Lab based at the Patuxent Wildlife Research Center, Maryland, and is working with other researchers to assess the status of bees nationwide.
Research Spotlight: September 2016
Using island biogeography to investigate a weird and scenic landscape in southern Idaho
-- Contributed by Katie Peterson, PhD Student, Parent Lab, Department of Biological Sciences, University of Idaho
I am currently a third year PhD student at the University of Idaho in the Parent Lab. The Parent Lab studies the biodiversity and evolution of organisms that have recently colonized novel, “blank slate”, environments on islands....read more here.
iDigBio Hosts Workshop on Biodiversity Research Methods at Botany 2016 in Savannah, GA
For the third straight year, iDigBio hosted a full-day workshop on research methods using digitized herbarium specimen data at the annual Botany conference (Botany 2016, Savannah, GA), sponsored by the Botanical Society of America and its affiliated societies. After successful workshops on Georeferencing (
Researchers Use MyCoPortal to Track Down Specimens Lost for Over 100 Years
Specimens collected in Nicaragua by American mycologist Charles Leonard Smith in the late 19th century were thought to have been lost for over 100 years.Through records created on the MyCoPortal, Gregorio Delgado and Ondřej Koukol of EMLab P&K (Phoenix, AZ) and Charles University (Prague, Czech Republic), respectively, were able to
Island Biology and iDigBio - expanding the role of biological specimens in evolution, ecology, and island conservation research
Research Spotlight: August 2016
Preserving historic bee specimens to protect future bee biodiversity
-- Contributed by Joan Meiners, PhD Student, Ernest Lab, School of Natural Resources and Environment, University of Florida
For my PhD research in Dr. Morgan Ernest's lab at the University of Florida, I am using large datasets of occurrence records of native bees and their habitat associations to try to understand native bee biodiversity and foraging patterns...read more here.
iDigBio at Flora Malesiana 10
Who could resist a conference where the mascot is a giant bright red Rafflesia flower, where bagpipes serenade the participants, and kilt-wearing and traditional folk dancing are encouraged, along with stimulating science? The 10th International Flora Malesiana Symposium was hosted by the Royal Botanic Garden Edinburgh, Scotland between 11-15 July 2016.
PSC2016 - iDigBio at the 23rd Pacific Science Congress
The 23rd Pacific Science Congress, successfully hosted by Academia Sinica, Taipei, Taiwan brought together scientists from a broad range of fields to discuss progress being made towards a sustainable future in Asia and the Pacific.
Research Spotlight: July 2016
Jointweeds and Their Many Mating Systems!
-- Contributed by Lauren Gonzalez
I’m currently a graduate student in the Soltis Lab in the Florida Museum of Natural History, working on Polygonella(Polygonaceae), sometimes called the jointweeds....read more here.
Georeferencing for Research Use, a Short Course
UPDATE: Wiki in development https://www.idigbio.org/wiki/index.php/Georeferencing_for_Research_Use
From iDigBio - About the Cisco Pit Stop: Digitising the Natural History Museum’s collections
For optimum results, digitization of collections needs to go faster, right? Of course, this includes addressing data quality and completeness.
Research Spotlight: May 2016
Playing with biological specimen data in iDigBio – limitations and solutions for research
-- Contributed by Shelley A James
Puerto Rico – warm Caribbean seas, high biodiversity, and coqui frogs. iDigBio was invited to NatureServe’s Biodiversity without Boundaries 2016 meeting in April 2016 to share ideas and resources with members of the conservation community....read more here.
Biodiversity without Boundaries 2016: iDigBio meets the NatureServe conservation network
Conservation. Endangered and rare species. Species distribution maps. Habitat and landscape integrity analysis. Observational data.
Can iDigBio be my research data repository?
Got research data? Need to submit your important data and media associated with biological voucher specimens to a data repository as part of your data life cycle best practices workflow? Are you thinking iDigBio would be the ideal repository for your data?
Although iDigBio is a repository for recordsets of primary biodiversity data of vouchered natural history collections, it is not a "data repository" as defined by most journals. Accepting individual researcher datasets, even those consisting of vouchered, natural history specimen digitized data and media, currently falls outside of the Scope of iDigBio.
Software Carpentry: an iDigBio staff perspective
Ever wondered where to start with analyzing a large biodiversity data set you've downloaded from iDigBio's portal or the iDigBio API? Wondering what software tools are available for cleaning your collections dataset or running some interesting queries? Finding a local Software Carpentry course is an excellent first step.
Research Spotlight: June 2016
Polyploidy in ferns: biodiversity data documenting speciation!
-- Contributed by Blaine Marchant
My research for iDigBio addresses ecological and evolutionary questions by utilizing the enormous dataset provided by digitized natural history specimens from across North America. My current project is aimed at investigating the ecological differentiation of polyploid plant species from their diploid progenitor species....read more here.
Research Spotlight: March 2016
Using herbarium specimen data to understand native mint distribution, evolution, and ecology
-- Contributed by Andre Naranjo
I am a graduate student at the University of Florida, and a member of the Soltis Lab, working on a genus of scrub mints found only in the southeastern United States....read more here.
iDigBio @ the League of Environmental Educators (LEEF) Conference
iDigBio's Jillian Goodwin and Molly Phillips traveled to St. Marks, Florida, to participate in the League of Environmental Educators (LEEF) Conference at COAST Charter School from March 18-20, 2016.
PHOIBOS2 at Biosphere 2 - practical hacking on identifiers
Permanent, globally unique identifiers are increasingly critical for the efficient analysis, publishing, tracking and reuse of dig data, including biological, geological and ecological information. Practical Hacking On Identifiers at BiOSphere2 (PHOIBOS2) took place at The University of Arizona’s Biosphere 2, Oracle, Arizona, from Feb 17-19, 2016. The Biosphere2 was an ideal location for a workshop - remote, spiny vegetation,
Call for Abstracts for iDigBio Symposium at the Pacific Science Congress 2016
iDigBio is pleased to announce the upcoming Symposium "Data and digital images: progress, tools and scientific need for digitizing Pacific biological specimen collections" at the 23rd Pacific Science Congress: Science, Technology and Innovation, June 13-17, 2016 in Taipei, Taiwan.
We invite presentations from students and professionals about the digitization of natural history collections data in the Asia-Pacific region and the use of mobilized collections data for research.
Call for student abstracts for iDigBio workshop at Island Biology 2016
Are you a student attending the Island Biology 2016 International Conference on Island Evolution, Ecology and Conservation, to be held on Terceira Island, Azores, from 18-22 July 2016? Do you have a research project which involves the digitization of vouchered natural history collections data from island communities, or utilizes published natural history collections data to better understand island ecosystems?
WeDigBio 2016 Call for Participation
During its inaugural year, the Worldwide Engagement for Digitizing Biocollections Event, WeDigBio 2015, engaged thousands of citizen scientists from >50 countries in transcribing specimen labels over four days.
Research Spotlight: Using Museum Specimens to Refine Models of Species Distribution
Using museum specimens to refine models of species distribution
-- Contributed by Charlotte Germain-Aubrey
Using distribution models are crucial for estimating levels of biodiversity at the landscape level. Museum specimens are a significant source of information for these models as they witness current but also past habitats...read more here.
Call for Abstracts for SCNet Symposium at SPNHC 2016
iDigBio and the Small Collections Network (SCNet) are pleased to announce the upcoming Small Collections Symposium at SPNHC 2016, to be held in Berlin, June 20-25.
Call for Abstracts for Symposium on Mobilizing Collections Data at SPNHC 2016
Gehen Sie zu der SPNHC 2016 Konferenz? Are you going to the Society for Preservation of Natural History Collection's (SPNHC) 2016 Conference? It's in Berlin this year, from June 20 - 25, 2016.
iDigBio Update for 2015
Dear iDigBio Enthusiasts,
The Inaugural WeDigBio Event: Global Event Advances Digitization and Science Literacy
Hundreds of volunteers around the world transcribed >30,000 specimen labels at 25 events over four days (Oct 22–25, 2015) in the first Worldwide Engagement for Digitizing Biocollections (WeDigBio) event. Events spanned a range of formal and informal education
venues, from middle-school and undergraduate science classrooms to county libraries to museums, universities, and botanical gardens, such as the Smithsonian's National Museum of Natural H
iDigBio and Data Carpentry go to Africa
Location: BIS (TDWG) 2015 Biodiversity Information Standards:
An amazing 2 weeks in Nairobi, Kenya.
by Deb Paul, input from Libby Ellwood and Matt Collins.
iDigBio and the EMu NHSIG in Philadelphia
iDigBio was delighted with Axiell's generous invitation to present a half-day digitization workshop at the annual meeting of the EMu user group Natural History Special Interest Group (NHSIG), held October 7 at the Penn Museum in Philadelphia. After determining via survey what EMu users would be interested in hearing about, we fashioned the following well-received agenda:
A summer learning R to clean up data with the iDigBio portal recordset correction feature
by Heather Appleby, former undergrad intern, Tri-Trophic Thematic Collection Network (TTD-TCN).
Katja Seltmann (TTD-TCN), Deb Paul, Alex Thompson, and Matt Collins Eds.
ASU Hosts Managing NHC Data for Global Discoverability
from Deb Paul @iDigBio
Exploring unique values in iDigBio using Apache Spark
Data exploration for large datasets is always challenging. Often you are left with deciding between subsetting the dataset (randomly or on some facet), making slow progress waiting for results just to find that something needs to be fixed, or optimizing code for performance when you don't even know if the result is going to be interesting. Having a high-performance system capable of ad-hoc investigation has always been difficult and/or expensive.
iDigBio Hosts Ecological Niche Modeling Workshop at Botany 2015
On July 26, 2015, iDigBio hosted an all-day ecological niche modeling (ENM) workshop at Botany 2015, the joint annual conference hosted by the Botanical Society of America, Plant Canada, and their affiliated societies, in Edmonton, Alberta.
iDigBio API Hackathon Report
iDigBio API Hackathon Report Blog
Tales from the iDigBio Booth: American Society of Mammalogists Conference
We (D
eb Paul, Cathy Bester, and Molly Phillips) had a fun and productive time staffing the iDigBio exhibit at the 95th Annual meeting of the American Society of Mammalogists Conference in Jacksonville, Florida, June 12-15, 2015. We set up the 10’ exhibit with the TV displaying the iDigBio Explore Research video series (thank you to Kevin Love and Chris Baker for helping us set up!).
Reproducible Science Workshop at iDigBio
By François Michonneau, @fmic_ (with editorial suggestions from Judit Ungvari-Martin)
The Results of the 2015 iDigBio Community Survey are In!
Each year, iDigBio surveys its internal team and the collections community, broader scientific community, partners, stakeholders, and others interested in the national digitization effort to find out how we are doing. We use the feedback to inform our decision-making and to help us set priorities and determine next steps. We are grateful to the nearly 250 individuals who participated in this year’s survey!
iDigBio API Hackathon Integration Group Report
June 3-5, 2015 (iDigBio API Hackathon) – Team Integration blog, by Jorrit Poelen (Global Biotic Interactions), Dmitry Mozzherin (Global Names), Jon Lauters (U.
Florida State University Transcription Blitz with Florida Native Plant Society
On Friday, May 29, Florida State University held a transcription blitz for attendees of the Florida Native Plant Society Annual Conference. This was the third digitization blitz hosted by iDigBio, the Southeastern Regional Network of Expertise and Collections Thematic Collections Network, and FSU's Robert K. Godfrey Herbarium.
SPNHC 2015: Sowing the Seeds of Digitization
The Florida Museum of Natural History and partners hosted the 30th Annual Meeting of the Society for the Preservation of Natural History Collections (SPNHC) from May 17-23, 2015, at the Hilton University of Florida Conference Center in Gainesville, Florida. The theme of the conference was “Making Natural History Collections
Accessible Through New and Innovative Approaches and Partnerships”.
Steps in Georeferencing Specimen Locality Data - Community Examples
Georeferencing Procedure Outline - a guest blog by Michael Yost, Macrofungi Collection Consortium (MaCC) Project Assistant at the Denver Botanic Gardens
Greetings, fellow georeferencers!
Sustainability and Social Media Conference Report
UF CAIRES (Center for Adaptive Innovation, Resilience, Ethics, and Science) sponsored a two-day Sustainability and Social Media Conference on Friday, April 17-18 2015, at the Levin School of Law. iDigBio graduate student Randy Singer was fortunate enough to be invited as a panelist for a session on Digitizing Nature.
Field to Database (F2DB): field-data collecting trends and 21st century data skills
From Deb Paul, @idbdeb
This 4-day hands-on short course in March investigated current trends in collecting, and focused on best practices and skills development for supporting the collection and sharing of robust, fit-for-research-use data.
Rmarkdown + GitHub = Reproducible Research
-Guest blog enthusiastically provided by course participant Rick Levy, Database Associate, Denver Botanic Gardens
3 day collaborative task: create a Data Carpentry genomics lesson with assessment modules
By: Deb Paul, Shari Ellis, Andréa Matsunaga, Blaine Marchant
From Deb
Apply now for iDigBio's Fourth Biodiversity Informatics Workshop
Managing Natural History Collections Data for Global Discoverability is fourth in a series of biodiversity informatics workshops at iDigBio and we are currently accepting applications! Don't wait, space is limited.
Deadline to Apply is May 1st, 2015.
SPNHC 2015 30th Annual Meeting and Gala Celebration
SPNHC 2015 30th Annual Meeting and Gala Celebration
Making Natural History Collections Accessible through
New and Innovative Approaches and Partnerships
May 17, 2015 to May 23, 2015
Data Standards for Sharing & Hands-On Experience with the Integrated Publishing Toolkit (IPT)
From Deb Paul, on twitter @idbdeb
Call for Participation: Hackathon on iDigBio APIs/Services and Interoperability
Goal: Design, develop, implement, test and/or document uses of iDigBio data via its APIs
Location: University of Florida, Gainesville, FL
Dates and times: June 3-5, 2015; 8 am - 5 pm each day
To apply: https://ufl.qualtrics.com/SE/?SID=SV_6Wr1womZuY7O5o1 deadline February 28, 2015. Invited applicants will be notified by March 9th.
iDigBio Update For 2014
Dear iDigBio Friends and Family,
iDigBio at BIS-TDWG 2014: some digitization, crowd-sourcing, and data use too
by Deb Paul, with Libby Ellwood and Greg Riccardi as Eds.
iDigBio and Entomological Collections Network Team for Successful ECN Annual Meeting
Nearly 200 collections professionals attended this year’s Entomological Collections Network (ECN) conference, 15-16 November 2014 in Portland, Oregon.
iDigBio Summit IV Report
Summary
Data Carpentry - Please can we have some more?!
iDigBio and the American Museum of Natural History (AMNH) co-hosted a Data Carpentry Workshop on Monday and Tuesday, September 29 – 30, 2014.
Florida Museum of Natural History ButterflyFest 2014
iDigBio staff participated in the Florida Museum of Natural History’s annual event ButterflyFest “A Celebration of Wings, Wildlife and Biodiversity”. The event was held Saturday, October 4, at the Florida Museum of Natural History in Gainesville Florida.
iNaturalist Workshop Report
iDigBio and the Florida Museum of Natural History co-sponsored a half-day introductory workshop to the website/application iNaturalist on Friday, September 26, 2014, at the Florida Museum of Natural History.
A New Report of Recommendations for DNA Banking
The use of sequencing and other molecular data now plays a critical role in the majority of research across the fields of systematics, ecology, and evolutionary biology. In addition, DNA barcoding offers an efficient way to identify specimens for large efforts like biodiversity inventory projects or biological resource management.
iDig’dBio@ FSU’s Herbarium Imaging Blitz a Success!
By the numbers:
Data Modeling Workshop Report
A workshop on data modeling took place at the East-West Center in Honolulu, March 24-25, 2014. The workshop immediately preceded the Biological Collections Digitization in the Pacific workshop and focused on data modeling and requirements for biodiversity information repositories.
Undergraduates Learn About Careers and Graduate Study in Biology at the Field Museum
About 50 undergraduates and recent graduates attended the Careers and Graduate Studies in the Biological Sciences workshop in Chicago, 6 September 2014.
iDigBio meets ESA
August 2014
Written by Libby Ellwood, iDigBio Postdoctorial Associate, Florida State University.
Deb Paul and I attended the Ecological Society of America conference in Sacramento, CA to represent iDigBio with an exhibitor booth. We set up our table with computers, brochures, posters, videos, newsletter sign-up sheets and, of course, enticing candy.
SPNHC DemoCamp 2014 Report
Amanda Neill, Director of the Herbarium, Botanical Research Institute of Texas
August 15th, 2014
Larkin infrared thermal imaging demo-SPNHC 2014 DemoCamp
Writing a proposal for the ADBC program at NSF
August 2014
Often at iDigBio sponsored workshops, symposia, and outreach events, we are asked the question: “How can I write a successful ADBC proposal?”
Collections for the 21st Century Report
“Those millions of bugs on pins, pressed plants, preserved animals and fossils hold a wealth of information about the adaptive abilities of our natural world, not to mention the DNA and curative uses yet to be discovered.”
BIOSPEX—A Crowdsourcing Management System
The BIOSPEX Management System—Provision, Advertise, and Lead Crowdsourcing Projects
University of Texas Proves an Excellent Venue for Paleo Imaging Workshop
There may be no place better than the University of Texas to conduct a broad-based paleo imaging workshop. This certainly seemed the consensus the week of 29 April at the co-sponsored iDigBio and Jackson School of Geosciences imaging event.
iDigBio celebrates Earth Day with the Florida Museum of Natural History
The Florida Museum of Natural History hosted its Earth Day Exploration event on Saturday, April 19th 2014. An annual celebration of Earth Day, the event showcased specimens from the museum's research collections and provided activities for those in attendance.
Students Shadow Scientists at the Florida Museum of Natural History
Fifteen undergraduate students from seven Florida colleges and universities converged on the Florida Museum of Natural History April 17-19 for an all-expense-paid opportunity to shadow museum professionals and explore careers in the biological sciences.
Women in Science and Engineering Science Spring Camp
Studies show that as girls transfer from middle to high school, they can perceive science as ‘uncool’ and subsequently loose interest in scientific careers. iDigBio postdoctoral associate Dr. Charlotte Germain-Aubrey, external vice-president of the Women in Science and Engineering (WiSE) at the University of Florida, created the WiSE Girlz Spring Science Camp to contradict this notion.
An Outsider’s view inside NSF: Trends and Tips
This article was generated from a webinar presented as an addendum to the iDigBio Education & Outreach Workshop held in Gainesville, FL, January 15-17, 2014. Participants were interested in finding out more about applying for grants available through the National Science Foundation (NSF) for Education and Outreach.
If you are targeting the National Science Foundation (NSF) for Education and Outreach funding, you may be looking for money in all the wrong places. With creativity and knowledge you can find the right places.
Education & Outreach Workshop
The Education and Outreach Workshop, held in Gainesville, FL from January 15-17, 2014, brought together representatives from each TCN to broaden our knowledge of E&O opportunities, resources, and strategies. Education and outreach are critical components of iDigBio TCNs. These activities are as wide-ranging and diverse as the TCNs themselves, and have likewise engaged a variety of students.
CITSCribe Hackathon
The CITSCribe Hackathon, co-organized by Zooniverse's Notes from Nature Project and iDigBio brought together over 30 programmers and researchers from the areas of biodiversity research and digital humanities for a week to further enable public participation in the transcription of biodiversity specimen labels.
Mobilizing Small Herbaria Workshop Attracts Enthusiastic Participants
Any doubt about the importance of small herbaria or the enthusiasm of their curators was certainly dispelled at the recent Mobilizing Small Herbaria workshop held at Florida State University the week of December 9th. Co-sponsored by iDigBio, the Robert K. Godfrey Herbarium at Florida State, the North American Network of Small Herbaria, and the Small Collections Network (SCNet), the event brought together about 30 collections professionals from 25 institutions representing 16 states.
Empowering International eCollaboration for Sustainability: Symposium at Biodiversity Information Standards (TDWG) 2013
by Deborah Paul, on Twitter @idbdeb
iDigBio Summit III
The iDigBio Summit III was held in Tallahassee, Florida, at the Aloft Hotel, November 18-21, 2013. Sixty attendees from more than 31 institutions met and focused on shared goals, challenges and opportunities, and collaboration among stakeholders.
Science Writers Conference 2013 comes to Gainesville
The University of Florida, the Florida Museum and iDigBio hosted a visit from the attendees at the Science Writers Conference. Some 400 of the nation's top science writers were in town from November 1-5 for the annual meeting of the National Association of Science Writers and the Council for the Advancement of Science Writing.
Broadening Diversity in the Biological Sciences: A Workshop for Undergraduate Students
iDigBio, University of Central Florida, and the Florida Museum of Natural History are pleased to announce a workshop for undergraduate students focused on increasing participation of underrepresented populations in the biological sciences. The workshop will be held at the University of Central Florida, February 1, 2014 and is open to college freshmen, sophomores, juniors, and seniors as well as recent college graduates. The goal of the workshop is to share important highlights about career and graduate study opportunities in the biological sciences.
FLMNH curators and iDigBio PIs presented a seminar to the UF Biology Department
Florida Museum of Natural History (FLMNH) curators Larry Page, Pam Soltis, and Bruce MacFadden presented a seminar about iDigBio to the Biology Department last Tuesday, November 5, 2013. This seminar provided an opportunity for the department to learn what the iDigBio project is all about and what research and educational opportunities are available.
Florida Museum of Natural History Butterflyfest
On October 19-20, iDigBio was represented by iDigBio project staff Cathy Bester, Kevin Love, Joanna McCaffrey and David Jennings along with post doc Charlotte Germain-Aubrey and graduate student Claudia Segovia at the Florida Museum of Natural History’s “ButterflyFest” in Gainesville Florida.
iDigBio’s Paleo Digitization Workshop Draws more than 60 Attendees to New Haven
More than 60 paleontologists representing 41 institutions assembled in New Haven, CT the week of September 23rd, 2013 to share ideas, protocols, preferences, and strategies. This was iDigBio’s most populous workshop to date, with an assortment of excellent presentations and ample opportunities for rich discussion.
Welcome Libby Ellwood, New Postdoctoral Scholar with iDigBio
Austin Mast interviews Libby Ellwood, our newest postdoctoral scholar.
Mast: It's my pleasure to welcome you as iDigBio's newest postdoctoral scholar, Libby. Your research focus will be on broadening public participation in the digitization of biodiversity research specimens. This is a goal to which your previous research background is well suited. What do you see as the most relevant aspects of your previous graduate and postdoctoral research for this new position?
Ellwood: Thanks, I’m thrilled to be a part of iDigBio’s dynamic team. I learned quickly in my graduate career that there is a wealth of information contained in museum specimens and that they are extremely useful in contemporary scientific research.
I earned my PhD in Biology from Boston University where my research focused on the effects of climate change on plants and animals. The metric I used to assess how much plants and animals were affected was phenology, the timing of biological events. Phenology includes the timing of when plants flower, when insects emerge and when migratory birds arrive, and many of these annual activities are impacted by temperature. In order to evaluate whether an organism’s phenology has changed, I first needed to understand the historical phenology—the date that a certain plant was flowering a hundred years ago, for example. Old journals, including those of Henry David Thoreau, were invaluable for this research. Some of these resources I found digitized online, while many others were tucked away deep in the special collections of museums and libraries. These records, combined with modern-day observations of the same plants and animals, allowed me to track phenology over 160 years. Several interesting discoveries came from this research, including the finding that many plant species are now flowering up to three weeks earlier now than they were in the 1850’s when Thoreau was observing them!
Unlocking the Fossil Cabinet: The Value of Collections in the 21st Century by Austin Hendy, Ph.D., Florida Museum of Natural History
Amateur naturalists, such as the fossil club participants pictured here (Friends of the Calvert Marine Museum) are potential downstream users of iDigBio.
SPNHC 2013 - Special Feature: iDigBio all-day symposium sponsored by iDigBio and the Natural Science Collections Alliance
From June 17-21, seven members of iDigBio (Gil Nelson, Pam Soltis, Joanna McCaffrey, Larry Page, Bruce MacFadden, Kevin Love and Deborah Paul) participated in SPNHC 2013, which is the annual meeting of the Society for the Preservation of Natural History Collections (http://www.spnhc.org/), fondly referred to as “spinach.”
iDigBio Pamphlet Available
iDigBio has developed a pamphlet featuring brief descriptions about the aims of ADBC and iDigBio, with colorful, eye-catching digitization-related images. This material provides a simple and visual representation of iDigBio‘s mission, suitable for all audiences. We would love for you to distribute these within and beyond your institution in order to promote interest in iDigBio and digitization. If you would like one or more shipped to you domestically (no international), please send a request via this webform. You may also download a print-ready copy (22 MB PDF)
iDigBio Tours New UF CNS Data Center
Members of the iDigBio UF staff recently visited the new University of Florida Data Center at the Eastside Campus facility. The tour, led by Associate Director of Data Center Operations David Burdette, led visitors through the newly constructed $14M facility. The tour allowed visitors to see the complete operation, from the large server rooms, the monster backup power supplies, and the room chilling equipment.
SPNHC 2013 Registration Now Open
Registration for the 2013 meeting of the Society for the Preservation of Natural History Collections is now open. This meeting is being held June 17-22 on the campus of the South Dakota School of Mines and Technology in Rapid City, South Dakota, home of the Museum of Geology.
Hackathon and iConference Update Part II
iDigBio Augmenting OCR Working Group provides a detailed update on the recent Hackathon and presentations at iConference 2013, held in Forth Worth, TX, February 12-15.
Map of Life Collaboration Meeting
On Monday, February 25th, iDigBio PI's and project staff met with Walter Jetz,Ph.D. from the Map of Life project. Dr. Jetz shared with us how the The Map of Life assembles and integrates different sources of data describing species distributions worldwide. These data include expert species range maps, species occurrence points, ecoregions, and protected areas from providers like IUCN, WWF, GBIF, and more.
iDigBio.org New Release
On February 25, 2013 iDigBio launched a new design for http://iDigBio.org and a new set of features for our specimen portal at http://portal.iDigBio.org.
Meet our Graphic Designer
Update from the iDigBio Augmenting OCR working group
Over the past 16 weeks, the aOCR wg has successfully orchestrated multiple initiatives intended to address some key issues on the working group's Wish List. Here, we briefly report on our recent Hackathon, held February 13-14, 2013 in Fort Worth, Texas, and on our "BioBlitz" at the iSchools iConference 2013, which was held February 12-15 in Forth Worth. We also discuss planned papers and new interactions resulting from these events.
iDigBio Blitz at iConference 2013!
iDigBio Blitz at iConference 2013
February 12-15th, Forth Worth, Texas
The iDigBio Augmenting Optical Recognition Working Group (AOCR wg) is headed to iConference 2013 in Fort Worth, Texas.
Congratulations to Dr. Anna K. Monfils: iDigBio Visiting Scholar
Please join iDigBio in congratulating Dr. Anna Monfils on her selection as our 2012 Visiting Scholar. Anna is an Associate Professor at Central Michigan University and Director of the Central Michigan University Herbarium.
Dr. Monfils' winning proposal includes building generalized, web-deliverable specimen databasing protocols, designing web-based teaching activities focused on databasing, and organizing a workshop aimed at professional botanists, students and citizen scientists from throughout Michigan.
1st Annual iDigBio Augumenting OCR Hackathon: Fort Worth, Texas, February 13-14
iDigBio Augmenting OCR Hackathon
February 13-14, 2013, in Fort Worth, Texas
Be a part of helping to get "dark data" out of millions of museum cabinets and into online databases!
UPDATE! See Hackathon Wiki: http://tinyurl.com/aocrhackathonwiki and Participate Remotely!
iDigBio Summit II Report
Summary
The second annual iDigBio Summit was held on October 23-24, 2012, in Gainesville, Florida, and was completed with great success! The Summit promoted clarification of objectives, communication of progress towards achieving objectives, identification and discussion of challenges and opportunities, and collaboration among stakeholders.
Congratulations to Dr. Corey Toler-Franklin, iDigBio's 2013 Visiting Scholar
Corey Toler-Franklin is a University of California President's Postdoctoral Fellow in the Computer Science Department at UC Davis. She is investigating new methods for capturing and processing digital media formats and imaging modalities to create more comprehensive representations of biological specimens. Dr. Toler Franklin's project will take her to the collections of AMNH and Duke University's Lemur Center, where she plans to use non-invasive optical capture techniques to digitize recent and fossil primates.
iDigBio Poster Available
iDigBio has developed a poster that provides a simple and visual representation of iDigBio‘s mission. We would love for you to put one up in your institution in order to promote interest in iDigBio and digitization. If you would like one or more shipped to you domestically (no international), please send a request via this webform. You may also download a copy to print locally (65 MB PDF).
1st Annual iDigBio Augumenting OCR Hackathon: Fort Worth, Texas, February 13-14
iDigBio Augmenting OCR Hackathon
February 13-14, 2013, in Fort Worth, Texas
Be a part of helping to get "dark data" out of millions of museum cabinets and into online databases!
Bruce MacFadden, iDigBio Director of Education and Outreach
Dr. Bruce MacFadden is Curator of Paleontology at the Florida Museum of Natural History and Director of Education and Outreach for iDigBio. His responsibilities with iDigBio include oversight of educational and outreach activities and their assessment at iDigBio, the TCNs and at other digitization projects involving biological collections. Here, he discusses his early fascination with dinosaurs and paleontology, pivotal experiences in undergraduate and graduate school that helped shape his career, and then some of his professional accomplishments.
iDigBio's Train the Trainers Georeferencing Update II - Out of the Dark Ages
The intensive, week-long First iDigBio Train-the-Trainers Georeferencing Workshop ended on October 12th, 2012. After a week, we are family and were sad to have to go home - but everyone seems very excited to get back to their own institutions to share what they learned and put it to good use in their own georeferencing and digitization projects.
Accelerating Scientific Discovery through Public Participation
A special iDigBio Blog Contribution by:
Austin Hendy, Ph.D.
Florida Museum of Natural History
iDigBio's Train the Trainers Georeferencing Update
The First iDigBio Train-the-Trainers Georeferencing Workshop is well into Day 4 now! Day one, participants and instructors met iDigBio PI Pam Soltis, Project Manager David Jennings, Biodiversity Informatics Manager Joanna McCaffrey, Cathy Bester, iDigBio Program Assistant and Kevin Love, the iDigBio IT magician who keeps us all in touch with one another and connected to the internet. Shari Ellis, iDigBio Project Evaluator, shared results of the iDigBio Pre-Workshop Survey for this workshop with all the participants.
Public Participation in Digitization of Biodiversity Specimens Workshop Report
iDigBio’s Public Participation in Digitization of Biodiversity Specimens Workshop was held on September 28-29 in Gainesville, FL.
Topics included the role of citizen science, ways to engage the public in digitization, methods to build public participant virtual communities, and an overview of biodiversity informatics software to facilitate public participation. Visit the workshop wiki page for links to the final agenda, the GoogleDoc, and the presentations.
Meet Joanna McCaffrey, iDigBio Biodiversity Informatics Manager
iDigBio is very pleased to welcome Joanna McCaffrey, our new Biodiversity Informatics Manager!
Joanna comes to the iDigBio team from the Field Museum of Natural History, where she has spent the past ten years working in a variety of databasing, imaging, and collections positions.
iDigBio Augmenting OCR October 2012 Workshop & February 2013 Hackathon
Seeking participants for “iDigBio Augmenting OCR” workshop, October 1-2
SCAN TCN Kick-Off Meeting
Compiled from notes in the field from Deb Paul, iDigBio Digitization Expert:
The Southwest Collections of Arthropods Network (SCAN): A Model for Collections Digitization to Promote Taxonomic and Ecological Research kickoff meeting at Arizona State University.
August 15-16th 2012
Meet David Jennings, iDigBio Project Manager
iDigBio is very pleased to welcome David Jennings as our new Project Manager! David is an industrial/mechanical engineer with over 18 years of experience in project management and leadership and will be responsible for overseeing day-to-day operations, developing requirements, coordinating activities within iDigBio, and coordinating activities between iDigBio and other networks/collections.
2012 Year in Review
On 30 June 2012, iDigBio completed its first year of operation. As the national resource for the NSF-funded Advancing Digitization of Biodiversity Collections(ADBC), our first year required that we identify and overcome major organizational hurdles as we develop a national infrastructure for the ADBC institutions. We are pleased to report that our first year was highly successful. In this article, we enumerate some of our major activities and accomplishments.
Seeking Effective Efficient Digitization - ZooKeys Publishes iDigBio's 5 Task Clusters
All of us at iDigBio are excited to announce the publication of Five Task Clusters that Enable Efficient and Effective Digitization of Biodiversity Collections in a ZooKeys 209:19-45 (2012) Special Issue No specimen left behind: mass digitization of natural history collections. We look forward to your comments...
Meet Corinna Gries, PI and head of the North American Lichens and Bryophytes TCN
Dr. Corinna Gries is PI and head of the North American Lichens and Bryophytes Thematic Collections Network. An accomplished researcher and programmer, here she is interviewed by Jill Holliday and discusses some of the history of specimen databasing, the goal of the North American Lichens and Bryophytes TCN, and the importance of public participation and crowd-sourcing to the TCN databasing projects.
Holliday: Corinna, you are the head of the North American Lichens and Bryophytes TCN.
Public Participation in Digitization of Biodiversity Specimens Workshop
Public Participation in Digitization of Biodiversity Specimens Workshop
University of Florida, Gainesville, FL
September 28 - 29, 2012
iDigBio, the National Science Foundation’s national HUB for Advancing Digitization of Biodiversity Collections (ADBC), is offering a workshop focused on engaging the public in the digitization of the approximately one billion biodiversity specimens housed in collections across the U.S. The workshop will explore how to involve the public in ways that are interesting and educational but also efficient and reliable for the facilities managing the digitization.
Digitization Workflow Workshop Report
Members of the collections community gather in Gainesville, FL to produce optimized specimen digitization workflows at the Developing Robust Object-to-Image-to-Data (DROID) Workshop. Tremendous participant insight holds the promise for informative documentation that will benefit all collections conducting or initiating digitization activities.
Slide-Scanning Protocol
Protocols for Slide-Scanning/Digitization of Standard Microscope Slides
Paleocollections Digitization Workshop Report
Bruce MacFadden reports on the recent Paleocollections Digitization Workshop hosted by iDigBio and FLMNH. The workshop was held to assess the status and future of digitized collections within the paleontological community. Presentations, discussions and breakout sessions focused on three themes: 1) tools, datapases and portals, 2) digitization and workflows, and 3) research applications and Grand Challenges.
Updated: Digitizing Plant Collections Workshop
Digitizing Vascular and Non-Vascular Plant Collections
Valdosta State University, Valdosta GA
September 17th - 18th, 2012
iDigBio, the National Science Foundation’s HUB for Advancing Digitization of Biological Collections (ADBC), is offering a series of preparation-specific workshops focusing on organizing, launching, and maintaining a biological collections digitization program. The target audiences for these workshops include collections managers, curators, and directors in institutions that are in the initial stages of implementing or planning a digitization program, regardless of collection size.
InvertNet Digitization Workshop Report
The InvertNet TCN reports on the details and accomplishments of the InvertNet Spring Workshop, which was held at University of Illinois/Illinois Natural History Survey. Presentations and breakout groups covered topics including progress in digitizing collections, information on current database platforms, and public outreach and educational activities. Hands-on sessions afforded an opportunity for participants to learn about different software and hardware tools related to digitization workflows.
iDigBio Botany 2012 Digitization Workshop - Open Registration
Registration is open for the Specimen Digitization Tools and Practices Workshop at the Botany 2012 Conference. The workshop will introduce current and future biological and paleontological specimen collections staff to resources and workflows that can lead to greater efficiencies in the digitization of their collections. The workshop will be held from 8:00 AM – 5:30 PM on Thursday, July 12, the day after the conference at the conference facility. Note: you do NOT have to attend the conference to attend the workshop.
iDigBio Call for Community Appliances
An important activity of iDigBio is to deliver IT infrastructure and services for a highly coordinated biocollections digitization community.
Through the use of computer appliances, the community will interact with the iDigBio storage cloud and specimen database.
The iDigBio team seeks to team up with developers of tools to guide development, disseminate, and host virtual appliances that integrate such tools.
Workshop for Developing Robust Object to Image to Data (DROID) Workflows
It is our pleasure to announce the Developing Robust Object to Image to Data Workflows (DROID) Workshop to be held at the University of Florida in Gainesville, FL. The workshop is designed to identify existing optimal digitization workflows, as well as process and technology gaps that must be bridged in order to achieve the scope of digitization required to meet the Grand Challenge. The workshop is co-sponsored by Integrated Digitized Biocollections (iDigBio) and Software Infrastructure for Sustained Innovation (S2I2). It will be held on May 30th and May 31st. Additional details may be obtained from the workshop overview.
Up to five participant slots are available for applicants. Accepted participants will be provided with travel, lodging and meals to attend the workshop.
Streamlining Collaborative Digitization
Streamlining Collaborative Digitization: How to order and install multiple digitization work stations
By Melissa Tulig and Kimberly Watson
Congratulations to Dr. Anna K. Monfils, iDigBio's 2012 Visiting Scholar
Please join iDigBio in congratulating Dr. Anna Monfils on her selection as our 2012 Visiting Scholar. Anna is an Associate Professor at Central Michigan University and Director of the Central Michigan University Herbarium.
Dr. Monfils' winning proposal includes building generalized, web-deliverable specimen databasing protocols, designing web-based teaching activities focused on databasing, and organizing a workshop aimed at professional botanists, students and citizen scientists from throughout Michigan.
Dr. Larry Page: Documenting Diversity
Dr. Larry Page is the Project Director for iDigBio, where he is responsible for overall project management, oversight of the national resource activities, and implementation of the strategic plan. He is based at the Florida Museum of Natural History, where he is Director of the University of Florida Biodiversity Institute and Curator of Fishes. Here, Dr. Page is interviewed by Jill Holliday, executive editor of the iDigBio e-newsletter.
Workshop and Symposium at Botany 2012
It is our pleasure to announce the Specimen Digitization Tools and Practices Workshop at the Botany 2012 Conference. The workshop is designed to introduce current and future biological and paleontological specimen collections staff to resources and workflows that can lead to greater efficiencies in the digitization of their collections. The workshop is organized by iDigBio, the National Resource for Advancing Digitization of Biological Collections. It will be held from 8:00AM – 5:00PM on Thursday, July 12, the day after the conference at the conference facility. A dinner for workshop participants will follow.
Meet the iDigBio Staff: An Interview with Gil Nelson
Meet the iDigBio Staff: An Interview with Gil Nelson
3 February 2012
Gil Nelson is iDigBio’s digitization specialist, with a focus on developing and improving digitization workflows and providing digitization support for the Thematic Collections Network projects. He is based at Florida State University. Here, Gil Nelson is interviewed by Austin Mast, a collaborator with Nelson on prior projects and a member of iDigBio’s Steering Committee.
iDigBio Summit Wrap-Up
The 2011 summit to kick-off the iDigBio project concluded on December 1st, 2011. By all accounts, this endeavor was a tremendous success, and enabled us to initiate a detailed dialog with representatives from the Thematic Collections Networks (TCNs) and other Advancing Digitization of Biodiversity Collections (ADBC) projects. Participants provided user insight into ongoing activities, projected progress, and resources available to the community.
New Resources from iDigBio
The iDigBio team plans regular Blog and Wiki contributions that provide useful resources to TCNs and others who are in the process of imaging and databasing biological collections. The newest contributions, available now, include a blog post outlining important global issues and decision points to be resolved prior to initiating an imaging project, and three new glossaries that provide definitions of tools, projects and organizations, and terms important to the digitization effort. The glossaries are posted on the iDigBio wiki and are editable by registered users. Our intent is for the biological collections community to enhance these glossaries by making regular additions and contributions.
Digitizing Biological Collections: Global Issues and Decision Points
Imaging and databasing a biological collection seems like a straightforward task: procure the specimens, extract the data, take the image, and serve the image and data on the internet. However, in most cases there are numerous preliminary global issues and decision points to be resolved before actual imaging and data extraction can begin.
The Grand Challenge - Uniting the Nation’s Biodiversity Collections through Digitization
On any given evening, it is commonplace for the nightly news to refer to debt and spending amounts in the billions and trillions of dollars.
The use of these massive numbers is so ubiquitous that many of us have become numb to the true magnitude of what one billion objects represent.
Consider this: to count from one to one billion, one number per second, without breaks or sleep, would take you thirty one years!
Newly Announced Funding for Advancing Digitization of Biodiversity Collections (ADBC)
Program Solicitation NSF 11-567 The new solicitation is the successor to solicitation, NSF 10-603 and differs in the following ways:
