ADBC Summit 2017: Difference between revisions

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===Friday October 6, 2017===
===Friday October 6, 2017===
        ====Harn Chandler Auditorium====
====Harn Chandler Auditorium====
        ;Natural History Seminar
;Natural History Seminar
        :http://idigbio.adobeconnect.com/pkcw3kts1esl/
:http://idigbio.adobeconnect.com/pkcw3kts1esl/
        ====Powell Classroom====

Revision as of 14:48, 6 November 2017


Digitizing the Past and Present for the Future
Summit-Banner-2017.png
ADBC Summit VII Quick Links
Calendar Announcement
PDF Program
Online Agenda

Join the leading researchers and professionals striving to digitize our nation's Natural History Collections! The annual ADBC Summit brings together representatives from TCNs, PENs, NSF, iDigBio, and other initiatives related to the U.S. National Science Foundation’s Advancing Digitization of Biodiversity Collections (ADBC) program. The Summit inspires collaboration and focuses discussions on shared goals, challenges, and opportunities.

General Information

Maps & Dining Information

Note: There is a restaurant in the Hilton. On maps, it is listed as "Albert's." It is now a "Shula's Steakhouse."

Area Information

Ground Transportation Options

Wireless Service

Wireless access for onsite iDigBio participants is provided by the University of Florida. Refer to iDigBio's Wireless Network Service wiki page for more information on how to connect.

Remote Access

To the extent possible, the Summit sessions will be broadcast and recorded using Adobe Connect. If you wish to listen to the meeting remotely:

  1. First, read the iDigBio Web Conferencing Wiki Page to get you started.
  2. Connect to the meeting:

Summit Program

Interactive PDF Summit program. We will be distributing a hard copy of this condensed program at the Summit.

Agenda

Monday, October 30, 2017 thru Tuesday, October 31, 2017 -- Data Carpentry

Time Location/Information
9:00-4:30 Data Carpentry Workshop

The UF Carpentries Club and iDigBio are offering a two day Data Carpentry Workshop to help participants in the 2017 ADBC Summit and the UF community get started learning R and common data management tools such as the spreadsheets, OpenRefine, and SQL. Need to learn some programming for a class? Have data you're scared to work with in Excel? Want to collaborate effectively with your peers? We were there once too. Come start learning with us! Visit the workshop website to learn more: https://idigbio.github.io/2017-10-30-iDigBio-Summit-UFII/

The workshop will be held at the UF Informatics Institute, which has generously volunteered space and resources for this workshop. iDigBio is providing staff support. All of the organizers, instructors, and helpers are volunteering their time to help ADBC, UF, and you!

Wednesday, November 1, 2017 -- Florida Museum Collections Tours

Time Location/Information
2:00-5:00

Wednesday, November 1, 2017 -- Pre-Summit Meetings

Time Harn Galleria Harn Chandler Auditorium Harn Classroom 1 Harn Classroom 2 Powell Classroom McGuire Classroom
Watch Live 		McGuire Director's Conference Room
Morning Breakfast on your own
8:00-10:00 Unavailable Unavailable Unavailable Unavailable Unavailable iDigBio-GBIF Whiteboarding Session on Worldwide Collections-Level Data (closed session) Open meeting space
10:00-10:30 Unavailable Unavailable Unavailable Unavailable Unavailable Setup Open meeting space
10:30-12:00 Unavailable Unavailable Unavailable Unavailable Unavailable Orientation - Welcome to ADBC by the iDigBio Core Team

Join us for an iDigBio and ADBC orientation session where we will present information-fit-for-use about the following:

  1. What ADBC and iDigBio are about, the acronyms, the scope
  2. How you can fire up your involvement by participating in interest and working groups, community surveys, and useful website content
  3. How to get specimen data to us, the first time and with every update
  4. Ways to interact with us - listservs, meet the staff
  5. Forum for suggestions to make all of this better

Everyone is welcome! Come to learn, to refresh, to meet your fellow digitizers!

EAB pre-meeting 11-12PM
12:00-1:00 Lunch on your own
12:30-1:00 Unavailable Unavailable Unavailable Unavailable Setup Setup Setup
1:00-5:00 Unavailable Unavailable Unavailable Unavailable Reserved for oVert Breakout Sessions oVert TCN Kickoff Meeting

oVert PIs and associated team members will discuss short-term and long-term goals related to standardized methods for CT-scanning and data deposition and interactions with both research and educational communities. We will also have breakout groups focused on selection of specimens and taxa, mechanisms for reporting and tracking, methods development, and community outreach and training.

IDigBio External Advisory Board (closed session)
5:00-5:15 Unavailable Unavailable Unavailable Unavailable Cleanup Cleanup Cleanup
Evening Dinner on your own
6:30-9:30 Informal welcome and meet & greet with iDigBio staff in the No Name Lounge inside the Hilton

Thursday, November 2, 2017 -- Summit Day 1

Time Harn Galleria Harn Chandler Auditorium Harn Classroom 1 Harn Classroom 2 Powell Classroom McGuire Classroom McGuire Director's Conference Room
Morning Breakfast on your own
8:00-9:00 Setup Setup Unavailable Unavailable Unavailable Review of iDigBio in Supporting Thematic Collection Networks (Neil Cobb)

Since 2011, the NSF-ADBC program has funded 20 Thematic Collection Networks (TCNs) and 24 Partners to Existing Networks (PENs). The role of TCNs is to mobilize a community of museums and herbaria to provide specimen related data and media to iDigBio. Additionally, they collaborate with each other and iDigBio to promote the use of digitization products for research and education. As part of its role in advising iDigBio, the IDigBio External Advisory Board (EAB) wants to better understand the relationship between iDigBio and the TCNs in order to assess how iDigBio is meeting community needs.

Every year the EAB meets with iDigBio and NSF at the ADBC Summit. For the upcoming 2017 meeting in Gainesville, the EAB would like to meet with TCN leaders to discuss the role of iDigBio in supporting TCN activities. The meeting will be held 8-9AM on Thursday morning (Nov 2) in the McGuire Classroom in the Florida Museum. There will be someone posted outside the museum to help people gain access to the meeting room and you can text Neil Cobb 928-607-4075.

Session Notes: https://goo.gl/mn5z8P

Open meeting space
9:00-9:30 Arrival, Summit check-in, coffee, networking Networking, getting settled Unavailable Unavailable Unavailable    
9:30-10:35 Unavailable
9:30-9:45 Opening & Welcome (Larry Page)
9:45-9:55 Logistics (David Jennings)
9:55-10:10 ADBC Program Update (Reed Beaman)
10:10-10:20 2017 TCNs
10:20-10:35 2016 TCNs
Unavailable Unavailable Unavailable    
10:35-10:55 Morning break Open meeting space (no food allowed) Unavailable Unavailable Unavailable    
10:55-12:10 Unavailable
10:55-11:05 2015 TCNs
11:05-11:20 2014 TCNs
11:20-11:35 2013 TCNs
11:35-11:55 2012 TCNs
11:55-12:10 2011 TCNs
Unavailable Unavailable Unavailable    
12:10-1:15 Unavailable Open meeting space (no food allowed) Box lunch provided     Open meeting space
1:15-2:30 Unavailable Group Discussion: Data Integration, Attribution and Interoperability (Andy Bentley)

Collections, aggregators, data re-packagers, publishers, researchers, and external user groups form a complex web of data connections and pipelines. This forms the natural history infrastructure essential for collections use by an ever increasing and diverse external user community. We have made great strides in developing the individual actors within this system and we are now well poised to utilize these capabilities to address big picture questions. We need to continue work on the individual aspects, but the focus now needs to be on integration of the functionality provided by the actors involved in the pipeline to facilitate the transfer of data between them with as few human interventions as possible. In order for the system to function efficiently and to the benefit of all parties, information, data, and resources need not only to be integrated efficiently but flow in the reverse direction (attribution) to facilitate collections advocacy and sustainability. For instance, there are benefits to collections from inclusion into aggregators and subsequent use by researchers and publishers that are not being realized. The Biodiversity Collections Network (BCoN) is planning a program of workshops in conjunction with other groups to perform a needs assessment to identify gaps and problems in the data pipeline and explore future steps in coordinating efforts, providing solutions and standardizing tools and methods. This talk will explore this landscape and highlight BCoN’s efforts in this regard while soliciting participation from actors in the pipeline and the community at large.

Session Notes: https://goo.gl/zPMfV9

         
2:30-3:00 Unavailable Open meeting space (no food allowed) Afternoon break     Open meeting space
3:00-4:15 Unavailable Meeting of the Symbiota Working Group (Neil Cobb, Andy Miller)
  1. The role of Symbiota in the ecosystem of biodiversity informatics platforms (Neil Cobb)
  2. Symbiota Tools & Restructuring:
    • Genetic Linking and new GenBank Sequence Submission Tool (Andy Miller)
    • NfN loader (Herrick Brown & Michael Denslow)
    • CoGe plugin (Herrick Brown and Michael Denslow)
    • iPlant Image Processor (Herrick Brown and Michael Denslow)
    • Skeletal Data Entry (Herrick Brown and Michael Denslow)
    • Symbiota2 – (Ben Brandt)
    • Spatial Module (Ben Brandt) Phenology Tracker (Will Pearse and Ben Brandt)
    • Phylogenetics Module (Will Pearse and Ben Brandt)
  3. Extending the functions of Symbiota - Examples:
    • FieldGuide Computer Vision– LepSnap, CVBatch & CVWidget (Andre Poremski)
    • Oregon Flora Project – focus on regional management & conservation (Ben Brandt with Linda Hardison virtual)
    • Documenting the Ethnobiology of Mexico and Central America (DEMCA) (Jonathan or Ben Brandt) Education & Outreach (Anne Basham)
    • SeedTrack – From seed to seed: tracking seed types in restoration treatments (Neil Cobb)
    • Education & Outreach (Anne Basham)
  4. Areas in Symbiota that need attention (Neil Cobb & Ben Brandt)
    • Data entry form, Data search fields
    • Best practices for sharing needs and providing solutions (Neil Cobb)
  5. Open Discussion Time permitting

Session Notes: https://goo.gl/wbj7km

WeDigBio Planning Meeting (Austin Mast and Libby Ellwood)

After a brief introduction to the annual Worldwide Engagement for Digitizing Biocollections (WeDigBio) event, participants will brainstorm new innovations for WeDigBio 2018, including the development of a virtual science festival (e.g., on the Sococo platform) and virtual reality collections tours and field experiences.

Session Notes: https://goo.gl/oyhDMW

Legal Issues with Collections (Linda S. Ford)

As biodiversity collections are increasingly available online, they will be under increasing scrutiny. The Nagoya Protocol – a supplementary agreement to the Convention on Biological Diversity – has important implications for the conduct of U.S. biological collections, especially those whose data are available digitally. Knowledge of the protocol is not widespread among researchers or institutions. This session will discuss legal concerns associated with digitized collections and mitigating these issues using digital means. Compliance with the Nagoya Protocol will be a test case to evaluate how institutions must respond to requirements for increased transparency and digital tracking.

Session Notes: https://goo.gl/B9V6od

oVert/MorphoSource Working Group (David Blackburn)

Hands-on demonstration of issues related to DOIs, iDigBio integration, etc.

Agenda and Details

Session Notes: https://goo.gl/oJZsfB

Meeting of the iDigBio student group (open to all students)

The iDigBio student group plans to write a review paper about use cases of natural history collection data, which will simultaneously summarize resources for using the iDigBio database. We hope to address some of the roadblocks that prevent digital data use and create a repository of codes/methods etc. that can be used and referenced to overcome these issues. In the process of creating the review paper we will in situ highlight the work that iDigBio students, researchers and other users have done thus far, and can do in the future with this rich database. Join us to discuss the process for creating the review paper (including formalizing the iDigBio student group, a discussion of individual responsibilities and deadlines etc.).

Open meeting space
4:15-4:30 Unavailable Transition to Auditorium for wrap-up Cleanup Cleanup Cleanup Cleanup Cleanup
4:30-5:00 Unavailable Day 1 Wrap-up (Shari Ellis) Unavailable Unavailable Unavailable Unavailable Unavailable
5:00-6:30 Unavailable Unavailable Unavailable Unavailable Unavailable Unavailable iDigBio meeting with NSF (closed session)
6:30-9:30 Evening program at the Florida Museum of Natural History (Powell Hall)
6:30-7:30 Arrival, heavy hors d'oeuvres, cash bar
7:30-7:40 Welcome by Roland Roberts, NSF Program Director and BIO Centers Science Advisor
7:40-8:00 Presentation about the Florida Museum's 100-year Anniversary by David Reed, Florida Museum Natural History Department Chair
8:00-9:30 Museum exhibits open for your enjoyment

Friday, November 3, 2017 -- Summit Day 2

Time Harn Galleria Harn Chandler Auditorium Harn Classroom 1 Harn Classroom 2 Powell Classroom McGuire Classroom McGuire Director's Conference Room
Morning Breakfast on your own
8:00-9:00 Setup Setup Unavailable Unavailable Setup Setup Open meeting space
9:00-9:20 Arrival, Summit check-in, coffee, networking   Unavailable Unavailable     Open meeting space
9:20-9:30 Logistics, Announcements   Unavailable Unavailable     Open meeting space
9:30-10:10 Unavailable DemoCamp (Matt Collins, Alex Thompson)

Live demos and talks of community-contributed software.

9:30-10:00 GUODA/iDigBio JupyterHub (Matt Collins)

Session Notes: https://goo.gl/gQcw1p

Unavailable Unavailable Workshop on Collections Data in Ecological and Conservation Research (Libby Ellwood, Chrissy Alba, Deborah Paul, Anna Monfils, Larry Page)

The ICER Working Group (Integrating Collections and Ecological Research), along with BCoN, will present a half-day workshop centered around ecologists who incorporate collections data in their scientific research and sharing a potential model program for integrating collections data in conservation efforts. Speakers invited will give talks representing community examples of museum specimen data integrated with other biodiversity data to enhance and inform efforts to address key ecological questions and support conservation efforts.

9:30-9:35 Introduction to ICER (TBD)
9:50-10:05 Predicting phenology, demography and extinction risk due to climate change from ecophysiology and museum records (Barry Sinervo)
9:50-10:05 Collections data as an historical experiment (Jenny McGuire)
10:05-10:10 Questions and Discussion

Session Notes: https://goo.gl/D4oK8Z

ICER Workshop Wiki

Changes/Improvements to the [https://www.idigbio.org/portal iDigBio Portal] (Richard Garand, Joanna McCaffrey, Shari Ellis)

Overview of the iDigBio Portal with emphasis on use cases, features introduced since last presentation and NSF survey results.

Session Notes: https://goo.gl/hVThKY

Three Insect Projects (Neil Cobb, Crystal Maier, Jen Zaspel, Catherine Hulshof, Akito Kawahra, Caitlin Chapman)

Agenda 1. Database Before You Label Protocol 2. Inselect and insect soups (Jen and Neil) 3. Puerto Rico Hurricane support: Developing a reference base for a re-survey of butterflies (Catherine)

Database Before You Label Protocol: Finalize workflow(s) for rapidly digitizing material from “collecting events”, especially where a large amount of material is brought into the collection from inventories. The workflow is database neutral (Arctos [Derek Sikes], EMu [Crystal Maier], institutional [Chris Marshall], Specify [AndrewShort], Symbiota [ Neil Cobb]), it will be scalable from small to large institutions, and it will be cross-phyla functional (e.g., plants/herbaria, insects/museums). Develop strategy to ensure all museums adopt workflow. Inselect: With the newer DSLR cameras that have 50 megapixel capacity it is possible that many museums might be able to use Inselect https://vimeo.com/160792078 can be used more widely. Puerto Rico: Catherine Hulshof (U. of Puerto Rico) will discuss a Puerto Rican-Caribbean Lepidoptera project to study butterfly (maybe some moths) recovery/recolonization of areas destroyed. We will develop a strategy to have museums digitize their holdings of Puerto Rican/Caribbean butterflies as a good reference data set. 'Session Notes' https://docs.google.com/document/d/1EhLZocIRZzsHkEcJIfG4hqcnLqFR6jO97_Cxg7k9dAY/edit

10:10-10:25 Morning break Open meeting space (no food allowed) Unavailable Unavailable Morning break   Open meeting space
10:25-12:30 Unavailable DemoCamp (continued)
10:30-11:00 MorphoSource (Julie Winchester)
11:00-11:30 TaxonWorks (Matt Yoder)
11:30-12:00 OntoPilot (Brain Stucky)
12:00-12:30 Index Herbariorum (Barbara Thiers)

Session Notes: https://goo.gl/gQcw1p

Unavailable Unavailable Workshop on Collections Data in Ecological and Conservation Research (continued)

10:25-10:40 Research and management applications of online collection data: a case study of prairie fen biodiversity (Anna Monfils)
10:40-10:55 The NEON Biorepository: Vision and Status (Dave Tazik)
10:55-11:10 Preliminary Results on Survey about Reuse of Species Occurrence Data and Use of Web-based Information Systems by Professionals (Elizabeth Martin)
11:10-12:30 Discussion and Break-out groups

Session Notes: https://goo.gl/D4oK8Z

iDigPaleo Meeting (Talia Karim)

This session will focus on current and future developments for iDigPaleo and how you can utilize the portal for your education and outreach needs. iDigPaleo was build as a proof of concept E&O portal for the Fossil Insect Collaborative. It currently hosts data for the FIC-TCN and the CW-TCN, with several other projects to be added this fall. Bring your ideas for the future of this portal (including any ideas you might have for a new name!).

Session Notes: https://goo.gl/JTN4j4

Open meeting space
12:30-1:30 Unavailable Open meeting space (no food allowed) Box lunch provided Open meeting space Open meeting space Open meeting space
1:30-3:15 Unavailable Building a Local Carpentries Community (Matt Collins, Deborah Paul)

The capacity to manage, manipulate, and analyze data is important to modern research programs. Ensuring research staff and students have access to the education and learning opportunities to maintain their development is the role of PIs, program heads, and institutional directors. Peer teaching and learning communities provide a learner-lead environment that is easy to foster and support in parallel with formal structures like academic curricula and professional development. We will describe our experiences at UF and FSU developing a community centered around the Data and Software Carpentry organizations to advance the informatics capacity of our organizations.

Session Notes: https://goo.gl/XhiGrs

Broadening Participation & Biodiversity Literacy in Undergraduate Education (BLUE) (Anna Monfils, Molly Phillips, Libby Ellwood)

This session is an introduction and invitation to participate in two new initiatives related to biodiversity education: Biodiversity Literacy in Undergraduate Education (BLUE) a newly funded RCN-UBE, and the Broadening Participation in Biodiversity Sciences Working Group. Following a brief presentation on the two project’s upcoming activities and opportunities, facilitators will lead participants in a discussion focusing on the following: 1) What core data skills do all undergraduate biology students need to access and interpret data from digital natural history collection archives? 2) What resources are currently available for introductory biology instructors wanting to use collections based digital data in the classroom? and 3) What resources are available to biodiversity scientists seeking to broaden participation of underrepresented groups in the biodiversity sciences.

Session Notes: https://goo.gl/PBJyWS

iDigBio Office "Hour" (Shari Ellis)

This session is an open forum to interact with iDigBio staff. Come ask questions and/or brainstorm about other topics related to iDigBio's interaction among ADBC.

Session Notes: https://goo.gl/6Gnauo

Specify meeting (Andy Bentley)

Specify software manages species and specimen data for biological research collections with a full suite of software: desktop, web, and iPad applications, as well as cloud-based hosting. With new versions of Specify 6 and 7 having just been released with additional features to support the GGBN data model as well as data publishing, this session will be a drop in session that will include a short status update of Specify, a quick overview of key features, and discussion of our future vision. There will be time for Q & A and help desk problem solving/support and an opportunity to discuss TCN issues with Specify.

Session Notes: https://goo.gl/QRVrwb

Open meeting space Open meeting space
3:15-3:30 Unavailable Transition to Auditorium for wrap-up Cleanup Cleanup Cleanup Cleanup Cleanup
3:30-4:00 Unavailable Summit Wrap-up (Gil Nelson)

Breakout Summaries: https://goo.gl/rCgN54

Unavailable Unavailable Unavailable Unavailable Unavailable
4:00-5:45 Natural History Seminar at the Harn Chandler Auditorium in collaboration with the Florida Museum's Department of Natural History, iDigBio, the FOSSIL Project, and the Paleontological Society
4:00-4:30 Arrival, refreshments
4:30-5:00 "The Digital Atlas of Ancient Life" presented by Dr. Jonathan Hendricks of the Paleontological Research Institution (Ithaca, NY)
5:00-5:15 Questions & answers
5:15-5:45 Chat, departure
5:45pm-6:00pm Unavailable Cleanup Unavailable Unavailable Unavailable Unavailable Unavailable
Evening Dinner on your own
7:00-9:00 Drink with the Extinct at the Florida Museum (optional activity)

Separate registration and payment is required, but a discount code will be available for Summit participants (contact us for details). Registration for this event opens Monday, September 25. Event details are available on the Florida Museum's website.

Saturday, November 4, 2017 -- Optional Activities & Field Trip

Self-Guided Activities

Guided Field Trip

Sweetwater Wetlands Preserve

Report and Evaluation

Photos

Recorded ADBC Summit Proceedings

Wednesday November 1, 2017

McGuire Classroom

Orientation - Welcome to ADBC by the iDigBio Core Team(1030am)
http://idigbio.adobeconnect.com/p6v806qo3c18/
oVert TCN Kickoff Meeting (part1)
http://idigbio.adobeconnect.com/pluovtn6xhto/
oVert TCN Kickoff Meeting (part2)
http://idigbio.adobeconnect.com/p5ou6qkqsnmo/

Thursday November 2, 2017

Harn Chandler Auditorium

Opening & Welcome, Logistics, ADBC Program Update, 2017 TCNs (930-1035)
http://idigbio.adobeconnect.com/pctp7difar85/
2017 TCNs,2016 TCNs,2015 TCNs,2014 TCNs,2013 TCNs,2012 TCNs,2011 TCNs (1055-1210)
http://idigbio.adobeconnect.com/pugdivq00dlf/
Group Discussion-Data Integration, Attribution and Interoperability (115-2)
http://idigbio.adobeconnect.com/ps9sdbsbo016/
Meeting of the Symbiota Working Group
http://idigbio.adobeconnect.com/p3v0f3kk4mmu/
Day 1 Wrap-up
http://idigbio.adobeconnect.com/pwwsomftrf0u/

Powell Classroom

oVert/MorphoSource Working Group
http://idigbio.adobeconnect.com/ph5zk1ws7c0i/

Friday October 6, 2017

Harn Chandler Auditorium

Natural History Seminar
http://idigbio.adobeconnect.com/pkcw3kts1esl/
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