2017 ePANDDA Hackathon: Difference between revisions

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===Tuesday, 6 June 2017===
===Agenda: Tuesday, September 19, 2017===
Wireless link: http://its.umich.edu/enterprise/wifi-networks/wifi
Twitter: #ePANDDA
 
{| class="wikitable" style="background-color:#FFF8DC;"
{| class="wikitable" style="background-color:#FFF8DC;"
!colspan="5" style=background-color:#FFEBCD;|  Day Two
|-
|-
|colspan="5" style="vertical-align:top; text-align: center; background-color:#FFEBCD;"|'''Breakfast (On your own) 7:00 - 8:00 a.m.'''
|-
|-
|colspan="5" style="text-align: center; background-color:#eed1a9;"| '''Light Breakfast & Coffee outside BEES classroom 3rd floor (8:15)'''
|-
|-
|colspan="5" style="vertical-align:top; text-align: center; background-color:#FFEBCD;"|'''Registration 7:00 - 8:00 a.m.'''
|-
|-
! colspan="1" style="background-color:#FFEBCD; text-align:center;" |     Time 
! colspan="2" style="background-color:#FFEBCD; text-align:center;" | Title
! colspan="2" style="background-color:#FFEBCD; text-align:center;" | Presenter(s)
|-
|-
|colspan="5" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|<b>'''Plenary Session - The League Ballroom (8:00 - 10:15 a.m.)<br>[http://idigbio.adobeconnect.com/pbkhy6j7a7kk/ Session Recording]<br>Moderator: Katelin D. Pearson'''
|-
|-
| colspan="1" style="vertical-align:top; text-align: left;"|9:00-9:15
| colspan="2" style="vertical-align:top; background-color:#FFF8DC;"| Q+A session about Day 1 progress
| colspan="2" | Jocelyn Sessa
|-
|-
! style="background-color:#eed1a9;" | Time
! style="background-color:#eed1a9;" | Title
! colspan="3" style="background-color:#eed1a9;" | Presenter(s)
|-
|-
| colspan="1" style="vertical-align:top; text-align: left;"|9:15-10:45
| colspan="2" style="vertical-align:top; background-color:#FFF8DC;"| Hackathon resumes
|-
|-
|style="vertical-align:top; text-align: left;"|8:00-8:30
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Summers_iDigBio_2017.pdf|Big Data, Museum Specimens, Access and Archiving - Lessons from #scanAllFish]]
|Adam Summers, University of Washington
|-
|-
| colspan="1" style="vertical-align:top; background-color:#FFEBCD;"|10:45-11:00
| colspan="4" style="vertical-align:top; background-color:#FFEBCD;"|'''Break'''
|-
|-
|style="vertical-align:top;"|8:30-9:00
|colspan="3" style="vertical-align:top; background-color::#eed1a9;"|[[Media:Brainerd_iDigBio2017.pdf|Video Data and Motion Analysis in Comparative Biomechanics Research]]
|Beth Brainerd, Brown University
|-
|-
| colspan="1" style="vertical-align:top; text-align: left;"|11:00-12:00
| colspan="2" style="vertical-align:top; background-color:#FFF8DC;"| Hackathon resumes
|-
|-
|style="vertical-align:top;"|9:00-9:30
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:AdrianaDePalmaJune2017iDigBio_(A.De-Palma@nhm.ac.uk).pdf|The PREDICTS Project: Projecting Responses of Ecological Diversity]]<br>In Changing Terrestrial Systems
|Adriana De Palma, Natural History Museum, London
|-
|-
|colspan="5" style="text-align: center; background-color:#eed1a9;"| '''Lunch - location dependent on weather (12:00)'''
|-
|-
|style="vertical-align:top;"|9:30-10:00
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Contreras_IDigBio_Michigan_June2017_ver3.pdf|Field Collections to Digital Data: A Workflow for Fossils and the Use of Digital Data for Reconstructing Ancient Forests]] 
|Dori Contreras, University of California Museum of Paleontology
|-
|-
| colspan="1" style="vertical-align:top; text-align: left;"|1:30-3:15
| colspan="2" style="vertical-align:top; background-color:#FFF8DC;"| Hackathon resumes
|-
|-
|style="vertical-align:top;"|10:00-10:15
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Natural_History_data_pipelines_-_Bentley.pdf|Natural History Data Pipelines:  The Good, the Bad, and the Ugly]]
|Andy Bentley, University of Kansas Biodiversity Institute
|-
|-
| colspan="1" style="vertical-align:top; background-color:#FFEBCD;"| 3:15-3:30
| colspan="4" style="vertical-align:top; background-color:#FFEBCD;"|'''Break'''
|-
|-
|style="vertical-align:top; background-color:#FFEBCD;"|10:15-10:45
|colspan="4" style="vertical-align:top; background-color:#FFEBCD;"|'''Break -  The League Second Floor Concourse'''
|-
|-
| colspan="1" style="vertical-align:top; text-align: left;"|3:30 - 4:30
| colspan="2" style="vertical-align:top; background-color:#FFF8DC;"| Demos of tools, code created<br>Discussion of next steps
|-
|-
|colspan="5" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|'''Concurrent Session III - The League Ballroom (10:45 a.m. - Noon)<br>[http://idigbio.adobeconnect.com/pe7pi9wvcwj9/ Session Recording]<br>Moderator: Katelin D. Pearson'''
|-
|-
| colspan="1" style="vertical-align:top; background-color:#FFEBCD;"| 4:45
| colspan="4" style="vertical-align:top; background-color:#FFEBCD;"|'''Group photo in front of the panda diorama'''
|-
|-
|style="vertical-align:top;"|10:45-11:00
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:1Esquivel-iDigBio_stat_analysis.pdf|Using Statistical Analysis to Calculate the Size of Biodiversity Literature]]
|Alicia Esquivel, Chicago Botanic Garden
|-
|-
|-
| colspan="5" style="vertical-align:top; text-align: center; background-color:#eed1a9;"|'''Simon Goring (Earthcube) and Alex Thompson (iDigBio) will be presenting at DataPhilly (7:00) OPTIONAL<br>Arrangements for group transportation can be made'''
|style="vertical-align:top;"|11:00-11:15
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:2Reznicek-Illustrating_value_added_in_databasing_historical_collections_Entered,_proofed,_and_done.pdf|Illustrating Value Added in Databasing Historical Collections: Entered, Proofed, and Done (or Not!)]]
|Tony Reznicek, University of Michigan Herbarium
|-
|-
|style="vertical-align:top;"|11:15-11:30
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:3IDBD_Hammock.pdf|The Encyclopedia of Life v3: Constructing a Linked Data Model]]
|Jennifer Hammock, Smithsonian National Museum of Natural History
|-
|-
|style="vertical-align:top;"|11:30-11:45
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:4IDBD_Schulz.pdf|Encyclopedia of Life Version 3: New Tools for the Exploration of Biodiversity Knowledge]]
|Katja Schulz, Smithsonian National Museum of Natural History
|-
|-
|style="vertical-align:top;"|11:45-12:00
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:5Michigan-Delaunay.pdf|How do People see Biodiversity? Using a Digital Identification Key in a Citizen Science Program]]
|Mathilde Delaunay, Muséum national d'Histoire naturelle, Paris, France
|-
|-
| colspan="1" style="vertical-align:top;"|12:00-12:15
| colspan="2"  style="vertical-align:top; background-color:#FFF8DC;"|[[Media:6Damerow_DDConference_2017.pdf|Taxonomic Data Quality in GBIF: A Case Study of Aquatic Macroinvertebrate Groups]]
| colspan="2" | Joan Damerow, Field Museum of Natural History
|-
|-
|style="vertical-align:top;"|12:15-12:30
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Pearson_Digital_Data_Presentation.pdf|Hole-y Plant Databases! Understanding and Preventing Biases in Botanical Big Data]]
|Katelin D. Pearson, Florida State University
|-
|-
|colspan="5" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|'''Concurrent Session IV - The League Hussey Room (10:45 a.m. - Noon)<br>[http://idigbio.adobeconnect.com/pb5kzjrwob25/ Session Recording]<br>Moderator: Priscilla Tucker'''
|-
|-
|style="vertical-align:top;"|10:45-11:00
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Punyasena_IDigBio_Conference_2017_v2.pdf|Reconstructing the Extinction Dynamics of ''Picea critchfieldii'' – The Application of Computer Vision to Fossil Pollen Analysis]]
|Surangi Punyasena, University of Illinois
|-
|-
|style="vertical-align:top;"|11:00-11:15
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|The Application of Optical Supperresolution Microscopy to the Study of Pollen Morphology
|Michael Urban, University of Illinois - Urbana Champaign
|-
|-
|style="vertical-align:top;"|11:15-11:30
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Developing_Entriprise_GIS_Kost.pdf|Developing an Enterprise GIS to Support Collections Management, Teaching, and Research]]
|Michael Kost, University of Michigan, Matthaei Botanical Gardens and Nichols Arboretum
|-
|-
|style="vertical-align:top;"|11:30-11:45
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|How Digitizing and Tagging Helped Solve the Tully Monster Mystery
|Paul Mayer, Field Museum of Natural History
|-
|-
|style="vertical-align:top;"|11:45-12:00
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|Open Source Tools for Digitization Workflows
|Mark Metz, USDA ARS SEL
|-
|-
|style="vertical-align:top;"|12:00-12:15
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Flannery_iDigBio.pdf|iDigBio and the Digital Humanities]]
|Maura Flannery, St. John's University, NY
|-
|-
|style="vertical-align:top;"|12:15-12:30
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:SandallDigitalData2017.pdf|Importance of Life Stage Capture in Dragonfly Specimen Digitization]]
|Emily Sandall, Frost Entomological Museum, Penn State University
|-
|-
|style="vertical-align:top; background-color:#FFEBCD;"|12:30-1:45
|colspan="4" style="vertical-align:top; text-align:center; background-color:#FFEBCD;"|'''Lunch (On your own) - See page 3 of [[Media:logisticsUM.pdf|logistics]] document for restaurant suggestions'''
|-
|-Digital Curation of Botanical Specimens from Isle Royale National Park
|colspan="5" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|'''Poster Session - The League Vandenberg Room (1:45 - 3:30 p.m.)'''
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|Widespread Sampling Bias in Herbarium Collections Identified from Comprehensively Sampled Mobilized Herbaria
|Barnabas H. Daru<br>Harvard University Herbaria
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|Digital Curation of Botanical Specimens from Isle Royale National Park
|Helen DeMarsh<br>Johns Hopkins University
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|Sharing Research Data: “I need to store and share data, and get recognition”
|Danielle Descoteaux, Publisher, Ecology & Biodiversity<br>Elsevier
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Esquevel_iDigBio_poster.pdf|Visually Representing a Biodiversity Literature Collection Using Metadata and Full Text Analysis]]
|Alicia Esquivel<br>Chicago Botanic Garden
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|Consider the Source: A Case Study Using GBIF Data for Research on Entocytherid Ostracods
|Raquel A. Fagundo<br>North Carolina Museum of Natural Sciences
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Hackett_et_al_2017_iDIGBIO_Digital_Data_Conference.pdf|Research and Management Applications of Online Collection Data: A Case Study of Prairie Fen Biodiversity]]
|Rachel Hackett<br>Central Michigan University
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:BioBeacon_Poster_Revised.pdf|BioBeacon: An Online Field Guide to Digital Biodiversity Information Resources]]
|Jarrett Blair, Bob Hanner, University of Guelph<br>Biodiversity Institute of Ontario
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Geodeepdive_small.pdf|Identifying, Cross-referencing, and Extracting Dark Data using GeoDeepDive]]
|Erika Ito<br>University of Wisconsin-Madison
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:TaxonomicConceptMapping_Jaster_etal.pdf|Taxonomic Concept Mapping in Support of Floristic Studies]]
|Thea Jaster<br>Oregon State University
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:PotentialWithinAFlora_Jaster_etal.pdf|The Potential Within a Modern Flora]]
|Thea Jaster<br>Oregon State University
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|Imago: Building a Biocollections Repository for Digital Preservation and Scientific Reproducibility
|Jennifer Laherty and Gary Motz<br>Indiana University
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:NLC_Digital_Data_poster.pdf|Exploring the Untapped Potential of CT Scanning in the Quantitative Analysis of Brachiopod Long Loops]]
|Natalia Lopez Carranza<br>University of California, Davis
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|Kurator: A scientific workflow tool for data quality improvement of natural science collections data
|James Macklin<br>Agriculture and Agro-Food Canada
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:KaylinMartin_iDigBio_poster_final_pdf.pdf|Digitizing Archival Data: Ecoinformatics in the Alcohol House]]
|Kaylin Martin<br>Carnegie Museum of Natural History
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|Biodiversity Literacy in Undergraduate Education (BLUE): Opportunities for Collaboration
|Anna Monfils<br>Central Michigan University
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Tdwg2016GloBIPoster_(1).pdf|Global Biotic Interactions: A Case Study in Ecological Data Aggregation]]
|Jorrit Poelen<br>Global Biotic Interactions
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:ShireyV36x48Unmounted_(1).pdf|Big Data Opportunities in Ecological and Biodiversity Informatics: A Functional Trait Perspective]]
|Vaughn Shirey<br>The Academy of Natural Sciences of Drexel University
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|The Value of Digital Morphology for Understanding Plant (Paleo) Biodiversity
|Selena Smith<br>University of Michigan
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|Automatic Generation of Herbarium Labels from Spreadsheet Data using LaTeX
|R. Sean Thackurdeen<br>New York Botanical Garden
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Wildbook-poster-2017.pdf|Wildbook: Computer-assisted Identification of Crowd-sourced Wildlife Imagery]]
|Jon Van Oast<br>Wild Me
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Westeen_poster_mockup_iDigBio.pdf|Patterns and Processes in the Evolution of Opisthoglyphous Fangs in Colubrid Snakes]]
|Erin Westeen<br>University of Michigan
|-
|-
|colspan="4" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Yapuncich_et_al_2017_DLC_cadavers.jpg|Digitization of Strepsirrhine Primates from the Duke Lemur Center]]
|Gabriel Yapuncich<br>North Carolina State University
|-
|-
|style="vertical-align:top; background-color:#FFEBCD;"|3:30-4:00
|colspan="4" style="vertical-align:top; background-color:#FFEBCD;"|'''Break -  The League Second Floor Concourse'''
|-
|-
|colspan="5" style="text-align:center; vertical-align:top; background-color:#eed1a9;"|'''Capstone Session<br>[http://idigbio.adobeconnect.com/pd8z98sahwgk/ Session Recording]<br>Moderator: Gil Nelson'''
|-
|-
|style="vertical-align:top;"|4:00-4:30
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:Donoghue_Michigan_slides_final.pdf|Prospects for the Use of Digitized Specimens in Studies of Plant Diversity and Evolution]]
|Michael Donoghue, Patrick Sweeney, and Beth Spriggs, Yale University
|-
|-
|style="vertical-align:top;"|4:30-5:00
|colspan="3" style="vertical-align:top; background-color:#FFF8DC;"|[[Media:McCartneyDigitalDataBiodiversity.pdf|A Vision for a National Cyberinfrastructure for Biodiversity Research and what NSF can do Enable it]]
|Peter McCartney, National Science Foundation
|-
|-
|}
|}

Revision as of 17:18, 23 August 2017

Welcome Info

Welcome packet will be available shortly.

For questions about Philly, The Academy, or other logistical matters, please contact Monet (Academy administrative coordinator) or Vincent (Drexel senior & Academy bioinformatics and collections assistant). For questions about the hackathon itself, please contact Jocelyn or any of the other ePANDDA PIs.

Venue

Travel and Lodging

Costs supported through ePANDDA funding from NSF. The hackathon will be two full days in length, both 18 and 19 September. Travel should be planned for Sunday (17th) and Wednesday (20th).

Participants are responsible for booking your own airfare/ground transport (to be reimbursed after the workshop). When booking airline travel, be sure that:

  • you arrive and depart from the Philadelphia International Airport (PHL).
  • your flight arrival and departure times allow you to participate ALL DAY on Monday September 18th and until 5pm ET on Tuesday September 19th.
  • you book only economy class, as economy is the only class that can be reimbursed.
  • you pay with a credit card, as frequent flyer miles can not be reimbursed.
  • all receipts show proof of payment (i.e. last four digits of credit card shown on receipt).

Participants can make reservations (hotel or Airbnb) on your own, and submit for reimbursement following the hackathon, or, we have reserved a block of rooms at nearby hotels, which will be paid directly by ePANDDA. If you want one of these rooms, please fill out the form here by August 31.

Wireless Connectivity

A sponsored guest user id and password will be assigned for the duration of the hackathon and shared by all participants, which will extend the function of the guest network. These credentials are shared, and cannot be published on the web. They will be emailed just prior to the event, and distributed on-site.

Collection Tours

Check back soon for sign-ups. Tours will be approximately 10 minutes long.

  • Botany collections with Jordan K. Teisher, Ph.D. Collections Manager, and Rick McCourt, Ph.D. Curator.

Agenda: Monday, September 18, 2017

Twitter: #ePANDDA

Registration at 19th St. entrance of Academy (8:30-9:15)
Light Breakfast & Coffee outside BEES classroom 3rd floor (8:30)
    Time  Title Presenter(s)
9:30-9:45 Hackathon Opening Remarks
Introductions 		Jocelyn Sessa
9:45-11:00 Introduction to ePANDDA API
Q+A session 		Seth Kauffman
11:00-11:15 Break
11:15-12:00 Additional discussions and group formation Jocelyn Sessa
Lunch - location dependent on weather (12:00)
1:30-4:30 Hackathon continues within strategic groups Jocelyn Sessa
4:30 - 5:15 ANSP Collection Tour #1 (OPTIONAL) Botany Collections
5:30 - 6:15 ANSP Collection Tour #2 (OPTIONAL) Botany Collections
Dinner Reception in Dinosaur Hall (6:30)
Cash bar (accepts cash only!) will be available

Agenda: Tuesday, September 19, 2017

Twitter: #ePANDDA

Light Breakfast & Coffee outside BEES classroom 3rd floor (8:15)
    Time  Title Presenter(s)
9:00-9:15 Q+A session about Day 1 progress Jocelyn Sessa
9:15-10:45 Hackathon resumes
10:45-11:00 Break
11:00-12:00 Hackathon resumes
Lunch - location dependent on weather (12:00)
1:30-3:15 Hackathon resumes
3:15-3:30 Break
3:30 - 4:30 Demos of tools, code created
Discussion of next steps
4:45 Group photo in front of the panda diorama
Simon Goring (Earthcube) and Alex Thompson (iDigBio) will be presenting at DataPhilly (7:00) OPTIONAL
Arrangements for group transportation can be made
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