Data Management in the Cloud

Wildbook™ is an open source software framework to support collaborative mark-recapture, molecular ecology, and social ecology studies, especially where citizen science data needs to be incorporated and managed. It is developed by the non-profit Wild Me and is the data management layer of the broader IBEIS Project.

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 that supports the exposure of data in biodiversity databases (e.g., GBIF and OBIS)
  • provides a platform for animal biometrics that supports easy data access and facilitates matching application deployment for multiple species

Open Source with a Professional Support Option

Wildbook™ is always free and open source. We are a community of IT professionals and wildlife researchers maintaining and improving a 21st century platform. However, sometimes you may need extra help on a deadline. Our non-profit Wild Me offers professional hosting and customization to fit your project's requirements. This helps us fund our non-profit projects. Contact us if you need help!

Gateway to IBEIS

Wildbook is the data management layer for the Image-Based Ecological Information System (IBEIS). IBEIS computer vision components pull data from Wildbook servers to detect features in images and identify individual animals. IBEIS brings massive-scale computer vision to wildlife research for the first time.

Images have become the most abundant, available and cheap source of data. The explosive growth in the use of digital cameras, together with rapid innovations in storage technology and automatic image analysis software, makes this vision possible particularly for large animals with distinctive striped, spotted, wrinkled or notched markings, such as elephants, giraffes and zebras. This large number of collected images must be analyzed automatically to produce a database that records who the animals are, where they are, and when they were photographed. Combining this with geographic, environmental, behavioral and climate data would enable the determination of what the animals are doing, and why they are doing it. This is our vision of IBEIS: an Image-Based Ecological Information System.Learn more.

Get Wildbook

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Projects with Wildbook

People

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Jason Holmberg is the Information Architect for Wildbook. Jon Van Oast and Drew Blount are the primary software developers. Together we bring a wealth of professional programming experience in data management, computer vision, and machine learning to the project.

Dr. Scott Baker of Oregon State University designed the DNA-related components within the software and remains an active adviser on the project.

Integration with IBEIS and other computer vision components is done in collaboration with Chuck Stewart's lab at RPI.

Demo Site

We are happy to give demos of the software via webinars. We also have a demo site here:

http://www.wildbookdna.org/demo

Please email “services [at] wildme [dot] org” to receive access credentials for the demo site, which refreshes itself periodically, allowing you to run real world tests of Wildbook.

News

2016-07-22

Wildbook 6.0 beta testing has begun. We anticipate an August release. Flukebook.org is featuring the new code, which will also be migrated to other Wildbooks quickly. Wildbook 6 merges the IBEIS.org and Wildbook.org projects into a single project re-using the name “Wildbook”!

2016-05-21

Check out the new humpback fluke matcher developed with Wildbook under the IBEIS.org project! This is one of two matchers we have coming out.

2016-04-02

Wildbook 5.5 has been released!

New features and fixes in Wildbook 5.5 include:

  • MOD: Standardization of PostgreSQL as the required database for Wildbook and removal of Derby and other database support. While Wildbook can technically support a wide array of databases and J2EE servers, we're standardizing on Tomcat and PostgreSQL for Wildbook 5.5 and all versions moving forward. We are also now highly recommending running Wildbook on Ubuntu Linux servers in Amazon's EC2 service. This also means that PostgreSQL must be installed and preconfigured for Wildbook to run.
  • MOD: JavaScript library dependency reductions.
  • FIX/MOD: Broad database connection improvements and fixes to better manage and close multiple database threads under higher usage.
  • FIX: Switch to full support of Encounter.individualID as NULL (upgrade fix script required for previous Wildbooks)
  • NEW: Make Google Map on main landing page (index.jsp) fully responsive for better mobile display
  • MOD: Remove automatic date filtering on Encounter Search default display
  • FIX: Better exception handling in spot matching grid
  • FIX: Make email templates more generic (remove project-specific branding) for reuse across projects
  • MOD: Persistence layer upgrade to DataNucleus 4.2
  • FIX: Improve sub-object REST/JSON display for typed Collections
  • NEW: Google reCAPTCHA integrated to prevent spurious data submission (upgrade requires getting Google key for your web site)
  • MOD: Switch to wildbook_data_dir as default data directory (check your configuration on upgrade)
  • MOD: change default username and password for database connections (now wildbook/wildbook)
  • MOD: Set logging directory relative to POM artifact to help prevent startup log errors
  • NEW: Add alternateID support for top bar Site Search of MarkedIndividuals
  • MOD: Better Java collection typing (MantaMatcher code contribution from Giles Winstanley)
  • FIX: Many minor HTML and CSS fixes

Past news...

Sponsors

Ongoing support for Wildbook is funded by the National Science Foundation, Amazon Web Services, collaborative co-investment by users, and donations to Wild Me.

Past development work for Wildbook has been supported by:

Collaboration Model

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.

Is Wildbook right for you?

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?

Screenshots

Features

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
  • Easily map a TapirLink provider or Integrated Publishing Toolkit (IPT) to the underlying relational database for exposure of mark-recapture data to biodiversity frameworks
  • For species with marked individuals identified by unique spot patterning:
    1. Extract spot patterning from photographs and scan for matches across all patterns in library using two approaches to pattern recognition (I3S and Modified Groth).
    2. Share computing power among globally distributed machines.
    3. 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

Marked Individuals

  • 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)

Photos

  • 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)

General

  • 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).

API

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.

Donation

You can help move Wildbook forward by making a donation! Your donation is tax deductible in the United States.

Feedback

Please send feedback to jason at whaleshark dot org. Your ideas to improve Wildbook are most welcome!

History

Wildbook was started by Jason Holmberg 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 .

Publications

Design Influences

The following publications have influenced our design and development of Wildbook:

Wildbook is a registered trademark of Wild Me.

Wildbook is distributed under the GPL v2 open source license.