View source for Advances in Digital Media Workshop Series: Yale

== Workshop at Yale Peabody Museum: June 2024 ==
<strong>When:</strong> June 10-11, 2024<br>
<strong>Where:</strong> Yale Peabody Museum in New Haven, CT<br>
<strong>Organizers:</strong><br>
<strong>Expected Number of Participants:</strong> <br>

== Logistics Information ==
'''Lodging''': Omni Hotel (155 Temple St, New Haven, CT 06510)

'''Parking''': On campus parking is challenging. Please use public parking at or near the Omni.

'''Travel from Airport to New Haven''':

'''From Hartford''': There are multiple options traveling between Hartford and New Haven. The Hartford Line can bring you from Windsor Locks Station to New Haven Station, but an additional shuttle service would be needed to get from the airport to the train station, then the train station to the Omni. An Uber/shuttle to New Haven is another option. If possible, please reference the rideshare document to see if sharing a ride with another workshop attendee is possible.

'''From JFK''': JFK to Train route – At JFK you hop on the Airtrain which takes you to Jamaica Station (20-30 min). There you hop on the Long Island Railroad to Grand Central Station (20-30min). At Grand Central you hop on the Metro North Train to New Haven Union Station (about 2 hours). Airtrain you can just swipe your credit card ($8.50) to get through the turnstyle.  For the Long Island Rail Road (about $5) and the Metro North ( $18.25 (off-peak)-24.50 (peak)), you can buy tickets right before boarding using the MTA Train Time app. Once at New Haven Union Station, it’s a short 5-10min Uber to the Hotel.  For first timers, I would plan 4 hours in case you miss a train. 
Advanced tip- There is also a combo ticket from the LIRR station that is a bit cheaper during peak travel, but requires you buy tickets using the train time app while at the station (uses your phone's gps).

Additional travel information and options from both airports can be found here: https://your.yale.edu/work-yale/campus-services/travel/air-travel/airport-shuttle

'''[https://docs.google.com/spreadsheets/d/18tvM8pt8s6qqHdvsDkURh4NTI9yxuTZ5D5xYhKZmm58/edit?usp=sharing Rideshare doc to self-organize with other attendees.]'''

'''Workshop Location''': Yale Peabody Museum (170 Whitney Ave, New Haven, CT 06511)
The museum is an easy 18-minute walk from the Omni. Cross Chapel street directly in front of the hotel and follow Temple St or Church St all the way to Whitney Ave, then continue straight to the museum. Use the side entrance on Sachem St. 
Workshop participants interested in walking as a group should meet in the Omni lobby by 8:00am to walk to the museum. 

'''Start Time''': Please arrive to the museum no later than 8:30am! Presentations will be streamed to a virtual audience. We need to start the day promptly at 9:00am.
 
'''Submitting your presentation''': Please add your slides to this folder prior to the start of the workshop

'''Reimbursement''': You will be reimbursed for associated expenses following the workshop. UF will only reimburse meals at a per diem rate - you do not need to save meals receipts. Receipts will be needed for any other associated fees (transportation, lodging, luggage, etc.)
<br>
If you have any additional questions or encounter any problems during travel, please reach out to 
Nelson Rios (New Haven local) 504-723-2085 or Jill Goodwin 508-887-6043

<strong>Wifi networks:</strong> If you are coming from an institution that uses <strong>eduroam</strong> that will be available on the Yale campus. If that is not the case, then you can connect via the Yale Guest wifi.<br>

<strong>Meals:</strong> Lunch will be provided at the Yale Peabody Museum on both workshop days. Breakfast and Dinner are not provided, but you will be reimbursed for meals not provided following the workshop.<br>

=Resources=
* [https://www.idigbio.org/wiki/images/6/61/Media2_Yale_Workshop_Scenario.pdf Activity Prompt]
* [https://docs.google.com/presentation/d/1JlyTYTxmJyDAsKj3I5hCiQCpm390m7jtVniTVgkX0Ho/edit#slide=id.g1f4a8a06bfd_0_536 Google Slides]

=Agenda=
{| class="wikitable"
!  !! Day 1: Virtual Showcase Highlighting AI and Digitization Considerations to Optimize use of data <br>
Topics include: Rapid specimen digitization, Storage, Management, and Sharing, Information ecosystems/pipeline, Linking traits			
|-
| 8:00 || Breakfast on your own ||
|-
| 9:00 || Morning Welcome || Nelson Rios, Yale Peabody Museum and Austin Mast, Florida State University
|-
| 9:10 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=466 Multi-view text detection for LightningBug]''' || Mark Hereld, Senior Scientist, Argonne National Laboratory
|-
| 9:20 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=939 Virtual Label Reconstruction for LightningBug]''' || Nicola Ferrier, Senior Computer Scientist, Argonne National Laboratory
|-
| 9:30 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=1619 Multi-modal imaging for next-generation heritage science]''' || Hugo Reyes-Centeno, Assistant Professor, University of Kentucky
|-
| 9:40 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=2380 Q&A]''' || Whole Group
|- 
| 9:50 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=2730 Preserving and Sharing Museum CT Scans at an Institutional Data Repository]''' || Peter Cerda, Associate Librarian, Data Curation Specialist, University of Michigan 
|-
| 10:00 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=3156 Let the Records Show: Attribution of Scientific Credit in Natural History Collections]''' || Rebecca Dikow, Director of Computational Methods and Data, Yale Library
|-
| 10:10 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=3763 MorphoSource: A Community 3D Data Repository for Representational Media]''' || Julie Winchester, Technical Director, MorphoSource 3D Data Repository, Duke University
|-
| 10:20 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=4780 Q&A]''' || Whole Group
|-
| 10:40 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=5616 Interoperability of Information Ecosystems: Envisioning Collaboration between Biodiversity Informatics, Remote Sensing, and Ecology]''' || Kit Lewers, PhD Student, University of Colorado Boulder
|-
| 10:50 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=6355 Increasing Accessibility to museum digital collections]''' || Ed Stanley, Florida Museum of Natural History
|-
| 11:00|| '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=7516 Recent advancements in the Audiovisual Core standard for biodiversity multimedia]''' || Steve Baskauf, Data Science and Data Curation Specialist, Vanderbilt University (retired)
|-
| 11:10 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=8285 Q&A]''' || Whole Group
|-
| 11:30 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=8725 Expanding LeafMachine2: new training data, models, and methods for processing herbarium specimens]''' || Will Weaver, PhD Candidate, University of Michigan
|-
| 11:40 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=9431 Large-scale, research-ready herbarium trait extraction with confidence-based deep-learning]''' || Quentin Bateux, Postdoctoral Associate, Yale Institute for Biospheric Studies
|-
| 11:50 || '''[https://youtu.be/EWVL9PnEoyM?feature=shared&t=10375 Challenges linking traits and harmonization for big data research]''' || Rob Guralnick, Curator of Biodiveristy Informatics, Florida Museum of Natural History
|-
| 12:00 || Q&A || Whole Group
|-
| 12:20 || Lunch provided || 
|-
| 1:30 - 4:30 ||Group Activity: Compiling Resource Summary of Day 1 (Rooms 118, 107) - Need to be out by 5:00 ||
|-
|-
|}
{| class="wikitable"
!  !!Day 2, June 11: Virtual Showcase Highlighting Innovative Technologies for downstream data use
Topics include: Harmonizing data for research, Innovation, Big Data, Non-conventional technologies to promote research and increase visibility ||
|-
| 8:00 || Breakfast on your own  ||
|-
| 9:00 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared Welcome back]''' || Austin Mast
|-
| 9:10 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=600 Image Informatics for Metadata Extraction and Verification of Museum Specimen Images]''' || David E. Breen, Professor of Computer Science, Drexel University
|-
| 9:20 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=1131 FishAIR as a model system for AI-Readiness and skipping the data pre-processing]''' || Yasin Bakış, Sr Manager of Biodiversity Informatics and Data Science, Tulane University
|-
| 9:30|| '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=1838 Knowledge-guided Machine Learning for Discovering Biological Traits from Images]''' || Anuj Karpatne, Associate Professor of Compute Science, Virginia Tech (Virtual)
|-
| 9:40 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=2713 Extracting phenological information from specimen images]''' || Daijiang Li, Assistant Professor, LSU
|- 
| 9:50 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=3261 Q&A]''' || Whole Group
|- 
| 10:05 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=3965 IIIF: Standards, Communities, and Tools for Sharing High-Quality Attributed Digital Objects at Scale]''' || Julie Winchester, Technical Director, MorphoSource 3D Data Repository, Duke University
|-
| 10:15 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=4743 An AI infrastructure for Natural History collections]''' || Arthur Porto, Curator of AI, Florida Museum
|-
| 10:25 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=5538 Mapping out phenotypic diversity in a large family of butterflies]''' || Moritz Lürig, Postdoctoral Researcher
|-
| 10:35 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=6280 Q&A]''' || Whole Group
|-
| 10:50 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=6847 Data Sharing Policies and Considerations Must Influence Machine Learning Research Directions in Ecological Applications]''' ||  Neha Hulkund, PhD student, Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology
|-
| 11:00 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=7431 Enabling Novel Scientific Discovery With Multimodal AI]''' ||  Eddie Vendrow, PhD student, Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology
|-
| 11:10 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=8024 Q&A]''' ||  Whole Group
|-
| 11:25 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=8779 AI Based 3D Modeling Methods Capture Complex Subjects in Uncontrolled Environments]''' || Alex Adkinson, Researcher, Florida State University, iDigBio  
|-
| 11:35 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=9536 From fossils to footsteps: reconstructing dinosaur locomotion with computer animation]''' ||  Armita Manafzadeh, Postdoctoral Fellow, Yale Institute for Biospheric Studies
|-
| 11:45 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=10146 Recent Advances in 3D modelling – Machine learning, Morphometrics and Conservation tools]''' ||  Duncan Irschik, Professor, UMASS Amherst
|-
| 11:55|| '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=10799 Q&A]'''
|-
| 12:10|| '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=11071 A link between biomedical and natural history research]'''  || Matteo Fabbri (remote), Assistant Professor, Johns Hopkins University
|-
| 12:20 || '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=11931 Using Specimen Media and Machine Learning for Research and Engagement]''' ||  Mike Webster, Director, Macaulay Library, Cornell University
|-
| 12:30|| '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=13010 The 'museum philosophy', digitization, and the Macaulay Library]''' ||  Glenn Seeholzer, Curator, Macaulay Library, Cornell Lab of Ornithology
|-
| 12:40|| '''[https://youtu.be/MfAWDKuHDiA?feature=shared&t=14178 Q&A]''' ||  
|-
| 1:00 || Lunch provided ||  
|-
| 2:00-4:30|| Group Activity: Compiling Resource Summary of Day 2 (Rooms 118, 107) ||
|}