There was no dearth of enthusiasm or expertise at the recent Fluid-preserved Arthropod and Microscopic Slide Imaging workshop held at the University of Michigan September 16-18, 2013. For those whose interests span the gamut of cameras, lenses, microscopes, and the myriad gadgets and creative solutions that make it possible to capture images of difficult subjects, this workshop was the place to be.
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!
On Friday, September 6th, Nelson Rios from Tulane University and the FishNet2 project, presented a lecture covering advanced use of GEOLocate software and services available through the web-based Application Programming Interface (API). Using Adobe Connect meeting software, over 30 people came to find out what they can do with GEOLocate tools and services beyond the online public user-interface. The recorded meeting was IT-oriented, but those new to "just what is a service?" were also welcome. Many of the participants were from the recent iDigBio 2nd Train-the-Trainers Georeferencing Workshop and they were eager to pick-up where the TTT2 GEOLocate material ended. (TTT2 Workshop) (TTT2 Blog)
From across the continent, a diverse group of 26 participants, 10 remote participants, and five instructors gathered in Gainesville from August 12 – 16 for a week-long intermediate to advanced course on georeferencing natural history museum legacy specimen data, emphasizing how to present and teach these skills to others. Please see our TTT2 wiki, TTT2 participant list, TTT2 Course Topics Summary List, Training Videos on Vimeo, and photos on facebook for details.
iDigBio, Specify Software Project, and the Biodivesity Institute at University of Kansas joined forces the week of August 12–16, 2013 to offer its first “progressive” Specify workshop. The recent release of Specify 6.5 made the event a timely adventure. Twenty on-site participants representing 16 institutions were joined by up to 20 remote attendees for the occasion. The workshop began with basic installation of Specify, followed by four days of progressively advanced topics.
The Tri-Tropic Database Thematic Collection Network recently finished up an exciting course about present best practices for specimen-level data management.The two-week Short Course on Biological Specimen Informatics was designed as a first introduction to biological informatics with early career graduates students in mind.
Authors: Jeremy Frank (Short Course Participant) & Katja Seltmann (TTD Project Manager, AMNH)
The expansive scope of iDigBio’s activities places it in the forefront of national and international digitization and data aggregation efforts. Recognizing the importance of its numerous international partners and encouraged by the NSF to expand international collaborations, iDigBio accepted an invitation to join a digitization symposium featured at the 12th Pacific Science Inter-Congress held at the University of the South Pacific in Suva, Fiji, and to follow the symposium with a digitization workshop for the Commonwealth Scientific and Industrial Research Organisation (CSIRO), in Canberra, Australia.
Demo Camp live demonstrations are a highlight of the annual SPNHC conferences. This year, iDigBio took this great opportunity to show the natural history collections community all we've accomplished in two years’ time. iDigBio Principal Investigator, Pam Soltis, stepped up to show off the iDigBio Data and Image Portal.
On May 6th and 7th, 2013, in a barn 3 hours from the home of iDigBio at University of Florida in Gainesville, the entire staff of iDigBio from UF and Florida State University gathered at Tall Timbers Research Station just north of Tallahassee for a two day retreat. Getting together at one time and in one place to work together was a rare opportunity everyone appreciated. We shared stories, celebrated almost two years of our project, and worked on our strategic plan.
Chicago’s Field Museum of Natural History (FMNH) turned out to be the perfect venue for iDigBio’s April 23–25 (2013) Dried Insect Digitization workshop. Overlooking Grant Park and the Chicago lakefront, FMNH provided an exceptionally attractive and hospitable environment with outstanding amenities. About 50 entomologists and digitization professionals from the U.S., Australia, and the United Kingdom attended, bringing together a diverse assemblage of knowledge and skill to address the complex job of digitizing pinned insect collections.
Digitization was a hot topic at the 2013 Association of Southeastern Biologists’ (ASB) meeting held in Charleston, West Virginia the week of April 10. Well before the beginning of the ASB–iDigBio-sponsored digitization symposium and workshop, several conference goers had already offered important papers outlining strategies and successes in digitizing small herbaria and incorporating digitization into biodiversity field research.
iDigBio Announces the Second Train-the-Trainers Georeferencing Workshop (TTT #2)
UPDATE: Participants Selected, GWG Second Train the Trainers Workshop Agenda
NOTE: AdobeConnect set up for REMOTE participation. Join us!
Save the Date Now and Join us remotely! See you August 12th - August 16th.
Application submission deadline was Thursday May 9th, 2013.
- Application via Google Form: http://tinyurl.com/gwgttt2app
Natural history collections have always played a crucial role in organismal biology, serving both as repositories for biological specimens that document biodiversity in space and time and sources of materials for scientific study.
iDigBio is actively compiling a list of DNA banking facilities and genetic resources repositories in the United States... more
iDigBio, the National Science Foundation’s national HUB for Advancing Digitization of Biological Collections (ADBC), in collaboration with the University of Michigan's Museum of Zoology, is pleased to announce the fifth in a series of preparation-specific workshops focusing on biological collections digitization. The workshop announced here focuses on imaging techniques for fluid-preserved invertebrates and microscopic slides.
iDigBio, in collaboration with Yale Peabody Museum, is pleased to announce the fourth in a series of preparation-specific workshops focusing on organizing, launching, maintaining, and/or enhancing a collections digitization program. This new workshop will focus on digitizing paleontology collections, including invertebrates, vertebrates, and plants.
As part of an NSF-funded Thematic Collections Network award, in mid-May the American Museum of Natural History will be offering a 2-week course dealing with the fundamentals of specimen databasing and how the tools used in this process can facilitate research in biology.
When iDigBio announced an upcoming wet collections digitization workshop to be held in cooperation with the Biodiversity Institute at the University of Kansas, we had no idea what to expect. As it turns out, we must have hit a nerve. By the close of the application period, well over 50 people had responded - far exceeding our expectations.
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.
The Association of Southeastern Biologists (ASB), in partnership with iDigBio, is pleased to announce a symposium and workshop that focus on workflows in the digitization of biological collections to be held at our annual meeting in Charleston, West Virginia, in April 2013.
iDigBio is pleased to announce the third in a series of preparation-specific workshops focusing on organizing, launching, maintaining, and/or enhancing a biological collections digitization program. This workshop will focus on digitization of dried insect specimens, stored in drawers and trays, either pinned or in packets. The workshop will be held at The Field Museum, Chicago, Illinois April 24–25, 2013. We have funding to support travel and per diem for 24 participants. April 23 and 26 will be travel days, with a welcoming reception early evening, April 23. Those desiring to attend this workshop should complete the online application no later than February 15, 2013. For more information, contact Gil Nelson.(email@example.com).
iDigBio is pleased to announce the second in a series of preparation-specific workshops focusing on organizing, launching, maintaining, and enhancing a biological collections digitization program. This new workshop will focus on digitization of wet collections, to include specimen label databasing, specimen imaging, ledger and field book imaging, and digitization of legacy objects such as X-rays, CT scans, and 35mm slides.
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.
Thirty participants gathered at Valdosta State University September 16–18, 2012 for iDigBio’s first herbarium digitization workshop. About half of the diverse group represented institutions at the earliest stages of launching digitization programs. More experienced attendees sought strategies for refining their institution’s workflows, processes, and protocols. iDigBio extends special recognition and appreciation to Valdosta State for hosting the workshop, providing extensive on-site support, and for making technology available that ensured the workshop's success.
After a flurry of summer planning activities and software and workflow development, the New England Vascular Plant TCN (NEVP) officially kicked off with a meeting at Yale Peabody Museum of Natural History on September 6, 2012. NEVP plans to digitize collections from 15 herbaria across New England, with a focus on creating a dataset that can be used to study the impact of climate change and land-use history across this region.
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
The Georeferencing Working Group at iDigBio is pleased to host the first "Train-the-Trainers" Georeferencing Workshop to be held October 8-12, 2012, in Gainesville, Florida. Participants will learn the fundamentals of georeferencing best practices with a combination of lectures and hands-on exercises, including paper maps, the MaNIS Georeferencing Calculator, GEOLocate, BioGeomancer and online exercises. Special attention will be paid to the specific and unique georeferencing needs of the TCNs.
iDigBio's technology preview is the first release of a semi-annual release cycle for a specimen portal that will eventually contain over 1 billion vouchered specimen records. This technology preview contains sample datasets provided by Morphbank and the Florida Museum of Natural History, some of which is research quality specimen data. These datasets allow iDigBio to share its development efforts with the community for feedback and guidance. You can access the technology preview here: portal.iDigBio.org
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.
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.
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.