The biological and statistical communities already support a number of excellent tools, such as Program MARK,GenAlEx, and SOCPROG for use in analyzing wildlife data. Wildbook is a complementary software application that:
- provides a scalable and collaborative platform for intelligent wildlife data storage and management, including advanced, consolidated searching
- provides an easy-to-use software suite of functionality that can be extended to meet the needs of wildlife projects, especially where individual identification is used
- provides an API to support the easy export of data to cross-disciplinary analysis applications (e.g., GenePop ) and other software (e.g., Google Earth)
- provides a platform for animal biometrics that supports easy data access and facilitates matching application deployment for multiple species
Wildbook started as a collaborative software platform for globally-coordinated whale shark (Rhincodon typus ) research as deployed in the Wildbook for Whale Sharks. After many requests to use our software outside of whale shark research, it is now an open source, community-maintained standard for mark-recapture studies.
- SPLASH Catalog for humpback whales (Megaptera novaeangliae)
- Wildbook for Whale Sharks for whale sharks (Rhincodon typus)
- University of Manitoba Polar Bear Library for polar bears (Ursus maritimus)
- MantaMatcher for manta rays (Manta birostris and Manta alfredi)
- Strandings of Oceania for cetacean strandings in the South Pacific
- Flukebook for multiple species of cetaceans
Jason Holmberg is the primary software developer and Information Architect for Wildbook.
Dr. Scott Baker of Oregon State University designed the DNA-related components within the software and remains an active adviser on the project.
We are happy to give demos of the software via webinars. We also have a demo site here:
Please email “jason [at] whaleshark [dot] org” to receive access credentials for the demo site, which refreshes itself periodically, allowing you to run real world tests of Wildbook.
2014-07-07 We released Wildbook 5.0.3 today with the following changes:
- FIX: occurrence.jsp would not display due to bad Java logic
- MOD: The Wildbook version number has been moved to the top bar of the application and centralized in the file contexts.properties. This allows for clearer display of the version and a link for others to follow to learn more about Wildbook.
2014-06-24 We released Wildbook 5.0.2 today with the following changes:
- FIX: confirmSubmit.jsp would display a blank page if an Encounter was submitted without an image. No data was lost however.
- NEW: scanTaskAdmin.jsp now defaults to showing only the current user grid tasks but allows the user to expand the list to see all in the queue.
Wildbook 5.0 is released! And we couldn't be happier. That was a big release, bringing some much needed cloud-scale improvements to Wildbook. New features include:
- FIX: Fix the Wildbook link in header.jsp
- MOD: Handle null values in Encounter.informOthers
- FIX: Adjust CSS used in servletResponseTemplate.htm
- FIX: Do not allow “View My Submissions” access before login.
- FIX: Github.com Issue #44 Fix: JDO exception in Individual Search when patterning code is one of multiple parameter selections
- FIX: Github.com Issue #36 Fix: Enounters → View Images does not increment with Next and Previous buttons
- NEW: Part 2: Create ShepherdResourceBundles for localization out of shepherd_data_dir, applying this to all .properties file references
- Upgrade: move all .properties files to shepherd_data_dir (or project equivalent)
- NEW: Multi-project support in a single Wildbook (GeneGIS)
- Upgrade: all Role objects need a context=context0 assigned
- MOD: Move “Find record” field from main page to top bar for global accessibility
- FIX: Prevent duplicate addition of the same Encounter in MarkedIndividual and Occurrence objects
- NEW: L10N consolidation part 1: centralize language determination and apply across JSP files.
- NEW: Support HTTP Basic Authentication to secure the REST URL by default.
- NEW: Change your own password (EMAIL PLUS SERVLET) for users with login privileges
- MOD: Finish branding and make more generic the Inerconnect and Grid Client apps bundled inside Wildbook
- NEW: Add User filtering to Encounter Search and the related pie chart to the results
- NEW: RESTful API documentation
- MOD: When editing Contact info, populate the form with the existing data
- MOD: Make minimum supported Java version 1.7
- MOD: Upgrade unit testing framework version
- NEW: TEST Tomcat 8 support
- FIX: SinglePhotoVideo.correspondingUsername not being correctly populated
- MOD: Change Encounter.releaseDate to long data type for broader database compatibility
- Upgrade: migrate from Encounter.releaseDate to Encounter.releaseDateLong
- NEW: Default SQL Server and SQL Azure support
- MOD: Upgrade to latest DataNucleus 3.x components
- Upgrade: new datanucleus JAR files
- NEW: Storytelling part 1: backend data persistence to support Wild Me Facebook app
- MOD: Support null values for Encounter.sex and MarkedIndividual.sex
- NEW: Release with default Spanish L10N
- NEW: Use UUIDs for Encounter numbers
- MOD: Change how encounter directories are created to support Encounter limits > 32000 (whaleshark.org)
- FIX: Individual Search filter on having photos does not work
We are wrapping up development on Wildbook 5.0! Only one new feature remains: drag and drop image upload. In the mean time, we are testing for quality by running the latest code on our production sites, such as whaleshark.org and flukebook.org. Feature development should wrap up this month with the release occurring in the first week of June.
Past development work for Wildbook has been supported by:
Wildbook is designed to produce successful, reproducible collaborations between biologists, biostatisticians, computer scientists, and citizen scientists by providing a Web-based software platform for collaboration.
If you answer yes to any of these questions, Wildbook may be a very good choice for your research.
- Are you trying to track individual animals in a wildlife population using natural markings or genetic identifiers?
- Are you collecting biological samples from a wildlife population and performing genetic or chemical analyses (e.g., stable isotope measurements, haplotype determination, etc.)?
- Are you looking to increase wildlife data collection through citizen science?
- Are you looking to build a collaborative, distributed research network for a species?
- Are you looking to develop a new animal biometrics solution (e.g., pattern matching from photos) for one or more species?
- Are you collecting behavioral and/or social data for a wildlife study population?
Using the web-based interface of Wildbook Framework, a research team can:
Encounters (a.k.a. “captures” or “sightings”)
- Record an encounter (individual animal at a point in time and location) through a standardized data collection form
- Search a database of standardized encounter data using predefined search criteria
- Receive automated email updates when encounter reports are assigned to new or previously identified marked individuals
- Receive RSS feeds of encounter identifications as they are made
- View all reported encounters
- View individual encounter reports
- View thumbnail catalogs of submitted images
- View adopters of individual encounters (a fundraising tool)
- Edit encounter data with all changes tracked and permanently logged
- Assign encounters to new or existing marked individuals
- Set a list of additional email addresses to be notified with status and sighting updates for submitted encounters
- View an on-line calendar of whale shark encounter reports
- Restore accidentally deleted encounters
- For species with marked individuals identified by unique spot patterning:
- Extract spot patterning from photographs and scan for matches across all patterns in library using two approaches to pattern recognition (I3S and Modified Groth).
- Share computing power among globally distributed machines.
- View pattern match reports and evaluate matches side-by-side, including direct spot remapping and statistical analysis of results.
- Record physical, acoustic, and satellite tag data deployed during an encounter
- Record tissue samples collected with an encounter
- Record the results of genetic sex, haplotype, microsatellite marker, stable isotope, and contaminant analyses performed on a tissue sample
- View all marked individuals
- View consolidated capture and sampling history of marked individuals
- Receive automated email updates when a marked individual is re-sighted
- Search a global database of marked individuals using predefined search criteria
- View consolidated mapping of sighting locations an individual
- View co-occurrence for the individual with other individual (e.g., social grouping)
- Define common photo keywords for your species (e.g. scarring types)
- Add/remove keywords to encounter photos
- Search across photographs using assigned keywords
- Search all images\video using encounter data to create customized albums of images
- View photo metadata (e.g. EXIF data)
- Search all encounters and marked individual data using Google Search (when deployed as a web server)
- Assign alternate identifiers to encounters and marked individuals
- View sighting locations with satellite imagery incorporated from Google Maps (encounters, amrked individuals, and Encounter Search results)
- Export sighting data as a KML file or an Excel spreadsheet for use in Google Earth and other mapping applications (Encounter Search).
- Create and edit animal adoptions for project fundraising.
- Review access security logs and track the source of individual logins.
- Use a variety of relational and non-relational database types to store data. The full list of supported databases in available from the DataNucleus web site (our middleware).
The framework is open source and meant for you to extend it for your specific project! If it doesn't have the feature you need, use some simple Java programming and create it. Some things we have used it to do on whaleshark.org are:
- Quickly generate open and closed capture history files for population modeling in statistical packages, such as U-CARE, CloseTest, and Program MARK
- Generate statistical reports
- Rely on spam filters to block spurious data submission
The development of additional functionality is currently underway.
You can help move Wildbook forward by making a donation! Your donation is tax deductible in the United States.
Please send feedback to jason at whaleshark dot org. Your ideas to improve Wildbook are most welcome!
Wildbook started as the software behind the Wildbook for Whale Sharks, which is a multiuser, web-based, research application for studying whale sharks (Rhincodon typus). The aim of WIldbook for Whale Sharks is to prevent individual “silos” of whale shark data and to promote a global, cooperative approach to whale shark research using the Web as a communications and research platform. The Library went on-line and began collecting whale shark encounter data from the web in January 2003. In early 2004, the pattern-recognition system that allows the Library to distinguish between individual whale sharks using natural spot patterning was integrated. Since its first line of code, this Wildbook has seen continuous feature additions, bug fixes, and performance enhancements. Our work to maintain and enhance the Library is ongoing and requires knowledge of Java, J2EE, JDO, PHP , Flash/Flex, HTML , XML , RSS , a wee bit of Python, and CSS .
The following publications have resulted from Wildbook-related work:
The following publications have influenced our design and development of Wildbook:
- Hochachka WM, Fink D, Hutchinson RA, Sheldon D, Wong W-K, Kelling S. Data-intensive science applied to broad-scale citizen science. Trends Ecol Evol. 2012 Feb. 1;27(2):130. 137.
- Michener WK, Jones MB. Ecoinformatics: supporting ecology as a data-intensive science. Trends Ecol Evol. 2012 Jan.;27(2).
- Schwarz, C. J. (2009). Migration and movement – the next stage. Pages 325-350 in Modeling Demographic Processes in Marked Populations Series: Environmental and Ecological Statistics , Vol. 3. Thomson, David L.;Cooch, Evan G.; Conroy, Michael J. (Eds.). Springer, New York.
- Williams BK, Nichols JD, Conroy MJ (2002) Analysis and management of animal populations. Academic Press, San Diego, CA.
- White GC, Burnham KP (1999) Program MARK: Survival estimation from populations of marked animals. Bird Study 46:120. 138.
- Whitehead, H. Analyzing Animal Societies: Quantitative Methods for Vertebrate Social Analysis (University of Chicago Press, 2008).
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