SPNHC 2014 DemoCamp

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Advancing Collections Care
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Quick Links for SPNHC 2014 DemoCamp Workshop
SPNHC 2014 DemoCamp Agenda
SPNHC 2014 DemoCamp Biblio Entries
SPNHC 2014 DemoCamp Report

This wiki supports DemoCamp at SPNHC 2014. The SPNHC 2014 DemoCamp is sponsored by iDigBio and organized by Amanda Neill.

DemoCamp provides a venue for promotion of technological solutions to advance the field of museum curation and specimen digitization, with broad applications for biology, ecology, and biodiversity informatics. Live demonstrations are welcomed in any technologies relevant to biologists, collections managers, or biodiversity information managers, as well as technologies that enable the broader use of data, or enable citizen scientist participation. Technologies demonstrated at past sessions have included collections/ transaction management software, georeferencing applications, robotic imaging equipment, automated label digitization tools, and programs for analysis of data/ images. DemoCamp presentations feature the latest developments in currently available products/ software/ applications/ tools as well as ongoing research projects and prototypes. DemoCamp sessions also provide a venue for idea exchange and feedback from potential users. --No powerpoints allowed!

Digitization Training Workshops

iDigBio Digitization Resources Home

SPNHC 2014 Conference website

SPNHC DemoCamp Report 2014

SPNHC DemoCamp Entries

  1. Abstract: Specify 7 for the Web, Specify Insight for the iPad, and other Novelties Bentley, A. & Specify Software Project http://specifysoftware.org
    • Purpose: To demonstrate the next generation of Specify--Specify 7 for the Web, the updated Specify Web Portal, and Specify Insight for iPad.
    • Intended Users: Biological collection managers, curators, and researchers working with biological specimen data (Specify 6), Collaborative groups wanting a shared network database (Specify 7), and museum directors who want insight into their collections' holdings (Specify Insight).
    • Classification: Specify 6.x is a thick client database application that runs on Mac OS, Windows and Linux. Specify 7 is a web application that runs in a browser. The Specify 6 Portal is an Apache based web server and browser application. Specify Insight is an iPad app.
    • Technology and Integration: MySQL, Java, PHP. Specify is a pluggable platform for extension of the rich client; uses various web services such as GeoLocate, Lifemapper, and Google Earth. The Specify 7 web app is implemented with Javascript, Python, Django, JQuery, and Apache. Specify Insight is written in Objective C and available from the Apple Store.
    • Licensing Model: GPL2, open source
    • Platform Requirements: Specify 6.x runs on all desktop platforms. It requires MySQL, and Java 7 JRE. Specify 7 is supported on Apache servers with MySQL using the same database schema as Specify 6 - which will allow concurrent web app and thick-client use. Specify Insight requires an iPad 2 or newer.
  2. Abstract: The Field Book Project: The Starting Point of Natural History Collections Russell, R., L. Parilla, & C. Sheffield http://www.mnh.si.edu/rc/fieldbooks/
    • Purpose: An aggregator of original source documentation covering field activities in the natural sciences. Documents the actual events that frame biodiversity information and collections.
    • Intended Users: Science historians, research botanists, collections managers, general public
    • Classification: Website; catalog of field books and related objects; images and transcriptions of individual field book pages; blog
    • Technology and Integration: Field book catalog data is managed in FileMaker Pro 12 and can be exported to MARC XML and CSV. The metadata schema employs existing standards from archives (EAC), natural history collections (TDWG-NCD), and libraries (MODS). Field Book Project content is loaded to the Smithsonian Search Center, and is ingested into both BHL and DPLA.
    • Licensing Model: Content avalable for personal, educational, and other non-commercial purposes.
    • Platform Requirements: Client: any modern standards-compliant web browser. Database: FileMaker Pro 12
  3. Abstract: Historical Expeditions Website (Botany) at the Smithsonian Russell, R. & S. Orli http://www.botany.si.edu/colls/expeditions/
    • Purpose: A catalog of historical expeditions resulting in botanical collections. Connects expedition information to herbarium specimens.
    • Intended Users: Science historians, research botanists, collections managers, general public
    • Classification: Website; specimen catalog
    • Technology and Integration:A series of web apps written in ColdFusion, linked to specimen records in an EMu database; specimen records include multiple resolutions (all .jpg) of specimen images; includes bios of principal participants, references/sources, illustrations, and maps.
    • Licensing Model: Content avalable for personal, educational, and other non-commercial purposes.
    • Platform Requirements: Client: any modern standards-compliant web browser. Database: Emu
  4. Abstract: GB3D Fossil Types Online Howe, M. & S. Harris http://www.3d-fossils.ac.uk
    • Purpose: Unified online database of British macrofossil type specimens, including information on taxonomy, provenance, location, stratigraphy, and references, plus high resolution images, stereo anaglyphs, and some 3D digital models
    • Intended Users: Academic palaeontologists & taxonomists, geoscience students, curators and collections managers, amateur fossil collectors, general public, 3D printing hobbyists
    • Classification: Web portal to database and image/3D model store
    • Technology and Integration: Web portal to Oracle database and linked large image (JPEG2000) and digital model (.PLY & .OBJ) stores. Type macrofossil records are exported from participating museum databases, or manually input through spreadsheets. High resolution images (Canon EOS5D) and stereopairs have been post-processed, including anaglyph production, and then converted to JPEG2000 format. Selected specimens digitally scanned with NextEngine HR Laser Scanners and made available in zipped .PLY and .OBJ format.
    • Licensing Model: Creative Commons - Attribution - NonCommercial - ShareAlike 3.0 Unported License
    • Platform Requirements: Any modern standards-compliant web browser. Red-cyan anaglyph glasses.
  5. Abstract: Infrared Thermal Imaging for Collections Management Larkin, N.R. http://www.flir.com/cs/emea/en/
    • Purpose: The analysis of the subtle - and not so subtle - variations in temperature (and therefore potential variations in RH) within a museum storage or display area, allowing a deeper understanding of the museum environment analysed and therefore better collections management within the area.
    • Intended Users: Collection managers, curators, and conservators
    • Classification: Digital infrared thermal imaging equipment (still and video) and software analysis of digital images
    • Technology and Integration: Various infrared thermal imaging cameras are available. All these cameras take normal digital photographs at the same time as taking digital infrared images; some also take digital infrared videos. Every single pixel in the image is a thermal datapoint and in the proprietary software the data can be analysed pixel by pixel. Shapes can be drawn within the image with the software and the data within the shapes can be averaged etc. All the digital infrared images can be saved in normal formats such as Jpeg etc. and used in normal software documents. The ‘FLIR E40bx’ demonstrated takes infrared still images and video, it has an image resolution of 160 × 120 pixels (providing 19,200 temperature data points in a single image), the working range is -20°C to 120°C, the thermal sensitivity is <0.045 °C, the built-in ‘normal’ digital camera is 3.1 megapixels, it has one LED spotlight, and it has wireless/Bluetooth technology.
    • Licensing Model: Proprietary software is included in the purchase of the infrared camera.
    • Platform Requirements: Proprietary software can be loaded onto a PC or Mac.
  6. Abstract: Symbiota (Crowdsourcing in LBCC) Thiers, B., E. Gilbert, C. Gries, & B. Brandt http://symbiota.org
    • Purpose: A virtual platform for creating voucher-based biodiversity information communities. The suite of integrated modules is designed to mirror the conceptual structure of traditional floras and faunas. Symbiota is exclusively web-based and employs a novel data model, information linking, and algorithms to provide highly dynamic customization.
    • Intended Users: Data contributors: collections managers, and authors for checklists, images and illustrations, identification keys, and specimen description; Data consumers: researchers, collections managers, general public
    • Classification: Web portal software package, including online data and web presence management
    • Technology and Integration: The modules are written in PHP accessing a MySQL backend. Symbiota is the software package that may be used to drive a taxonomically or georgraphically oriented portal. Each portal may be independently managed, however, software improvements are benefitting all portals via regular upgrades.
    • Licensing Model: The code is available from a public SVN repository http://sourceforge.net/projects/symbiota/. The technology framework of PHP, MySQL, and Apache webserver are also open source.
    • Platform Requirements:The technology framework of PHP, MySQL, and Apache webserver are open source. The portals may be accessed with any modern browser.
  7. Abstract: AnnoSys Tschöpe, O., L. Suhrbier, A. Güntsch, & W.G. Berendsohn https://annosys.bgbm.fu-berlin.de/
    • Purpose: Repository for complex and cross-linked data including back-end server functionality, web services, a message system, and an on-line user interface. Allows users to create and search for structured annotations of online records.
    • Intended Users: Scientists, curators, collection managers, collection users, citizen scientists
    • Classification: Web application
    • Technology and Integration: Web application providing a workbench oriented user interface based on Eclipse RAP technology. Annotations are stored according to Open Annotation Core Data model in RDF store, annotated records as XML documents. Public Repository access provided by web services supporting Linked Open Data, REST and SPARQL interfaces.
    • Licensing Model: Usage of web application, annotation data, and code is open source (Mozilla Public Licence V2.0)
    • Platform Requirements: Client access to web application through any modern standards-compliant web browser
  8. Abstract: FilteredPush Data Entry McCallum, C., P.J. Morris, J. Hanken, M. Kelly, D.B. Lowery, B. Ludaescher, J.A. Macklin, R.A. Morris, & T. Song http://sourceforge.net/p/filteredpush/svn/HEAD/tree/trunk/FP-DataEntry/
    • Purpose: The FP-DataEntry plugin speeds up data entry by helping you find records for items like those in your collection, and by copying those records to your own data entry web application, saving you transcription time and the trouble of copy-and-pasting or retyping. Use cases include botanical duplicates, literature citations, and paleontological localities. The idea is analogous to copy-cataloging in the library world.
    • Intended Users: Staff who transcribe and enter specimen records. Configuration of new instances requires input from collection managers or biodiversity informaticians, and some familiarity with the command line.
    • Classification: Can be used either as a lightweight browser bookmarklet (no changes to existing software are necessary), or for a tighter integration, as a javascript library (added to an existing application, similar to the Geolocate plugin service). In either case, the front end relies on a back end server which the software also provides.
    • Technology and Integration: Client: Javascript. HTML5 Web Messaging is used to communicate between an iframe and host application. Server: Java. Provided Bash scripts make deployment easier. Solr is used as the index by default, but you may implement a Java interface to use another data source. (GBIF API integration is provided as an example.)
    • Licensing Model: Code is available under GPL 2.0. Running server instances might be shared between institutions that share an interest in particular specimens or data sets.
    • Platform Requirements: Client: Any modern browser. (Have not tested against IE.) Server: Java 6 or above. Provided scripts deploy either with Jetty (requires a free port and appropriate firewall settings) or with Tomcat (requires appropriate file system permissions).

SPNHC DemoCamp Schedule

This was updated 2014-06-11 (these changes may not yet be reflected in the SPNHC PDF Program).

DemoCamp sessions will be held Thursday 26 June, Wales Millennium Centre, Weston Studio (WS).

2:00pm/ 14.00 (Demo1): Specify 7 for the web, Specify Insight for the iPad, and other novelties. Andrew Bentley* & Specify Software Project

2:20pm/ 14.20 (Demo2): The Field Book Project: The starting point of natural history collections. Rusty Russell*, Lesley Parilla, & Carolyn Sheffield

2:40pm/ 14.40 (Demo3): Historical Expeditions Website (Botany) at the Smithsonian. Rusty Russell* & Sylvia Orli

(posters & pastries break from 3-4pm)

4:00pm/ 16.00 (Demo4): GB/3D fossil types online – not only the largest collection of 3D digital fossils, but also major format, schema, and vocabulary conundrums. Mike Howe*

4:20pm/ 16.20 (Demo5): Infrared thermal imaging as a collections management tool. Nigel Larkin*

4:40pm/ 16.40 (Demo6): Crowdsourcing in LBCC using Symbiota. Barbara Thiers*, Edward Gilbert, Corinna Gries, & Benjamin Brandt

5:00pm/ 17.00 (Demo7): AnnoSys – an online tool to annotate biodiversity data. Okka Tschöpe*, Lutz Suhrbier, Anton Güntsch, & Walter G. Berendsohn

5:20pm/ 17.20 (Demo8): FP-DataEntry, a tool for bringing community knowledge into data transcription applications. Chuck McCallum, Paul J. Morris*, James Hanken, Maureen Kelly, David B. Lowery, Bertram Ludaescher, James A. Macklin, Robert A. Morris, & Tianhong Song

(*lead presenter)

DemoCamp Recordings

Remote Participation

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