Collaborations
Biodiversity Informatics is a multidisciplinary research and development activity. It spans computer science, data networking, software engineering, environmental biology, and education. To solve significant research challenges, informaticists must integrate across disciplines at several levels—with theory, concepts, methods, and data.
Biodiversity Informatics has an additional constraint of working with research collections which are financially resourced as archival specimen repositories, but not at the level of leading-edge technology centers. Without research I.T. development at any but the most well-endowed institutions, scientists at zoological museums and herbaria profit from the open exchange of research software. Numerous examples in academia of low or no cost computer applications for data analysis, management, modeling, and visualization attest to the scalability and essential role of open source software within a science economy based on public support and cost efficiency.
In addition, compelling software must be based on a clear understanding of how researchers conceptualize their data, contextualize a problem space, prioritize tasks, and evaluate results. Adopting a scientist-centered software development process greatly increases the likelihood of research utility of cyberinfrastructure as well as its prospects for community buy-in and long-term sustainability.
For these three reasons, our informatics research activities are developed as multidisciplinary partnerships with a the goal of producing innovative, high research impact and sustainable cyberinfrastructure. Our major active collaborations are described below.
Specify Software
Specify is an NSF-supported, open source, biological collections data management platform for museums and herbaria.
Our Specify collaborators include researchers in more than 300 biological collections around the world. Institutions which use Specify as their primary data processing environment interact with our Project staff and provide feedback which keeps our coordination activities responsive and relevant to community needs. Specify clients provide specifications for the customization of Specify’s interface and for migrating their historical data to Specify. They also notify us of engineering defects and inform our priorities for new features and capabilities. We interact with Specify collections daily through our helpdesk, and we collaborate with institutions around the world with software training workshops and project planning meetings.
In addition to our client museums, we have ongoing partnerships with collection institutions outside of the U.S. These international partners contribute in-country and regional technical support and training to biological collections in other continents.
Recent Specify Support Partner highlights include the work of Dr. Willem Coetzer of the South African institute for Aquatic Biodiversity who has installed, trained and supported Specify in multiple institutions in several African countries. Dr. Rui Figuera of the Instituto de Investigação Científica Tropical, Lisbon, organized a massive translation effort to completely translate Specify into Portuguese in 2010 in addition to hosting a Specify training workshop for Portuguese collections in Lisbon.
Specify Development Partners collaborate on the design and implementation of extensions to Specify, including plug-in modules to add new research and collaborative cataloging capabilities. We are currently in discussion with staff at national museums and biodiversity initiatives in Australia, Sweden, and Brazil regarding collaborative open source software development.
Specify is also partnering in a two-year software integration collaboration with the Florida State University (Drs. G. Riccardi, A. Mast), and the U. of Texas (Dr. D. Miranker). This partnership will enable Specify users to upload specimen images and their associated data from Specify into the Morphbank image repository for phenotype markup using controlled vocabularies from biological specimen ontologies managed by Morphster software.
Lifemapper
Lifemapper is a set of projects organized around a core of computational and web services which compute environmental niche models that predict the geographic distribution of species based on known occurrences as vouchered by museum specimens. Lifemapper came online as an independent effort in 2000, it has since evolved into several research collaborations, including:
The cyberCommons, a three-year, NSF-funded collaboration focused on studying the impacts of changes in land use and of climate on biogeochemical cycles, ecosystem function, and on biodiversity composition and dynamics in the Central Plains of North America. Collaborators include environmental researchers and bioinformatics engineers at four universities: Oklahoma, Oklahoma State, Kansas State, and Kansas.
ChangeThinking is a collaborative five-year project to investigate how thinking and understanding develop in junior and senior high school students when they are presented with complex environmental issues. Using grade-appropriate web curricula, ChangeThinking will examine how student mental models develop about how species respond to climate change variables. This collaboration with the University of Michigan Museum of Zoology (Dr. P. Myers) and School of Education is led by Dr. N. Songer. Several postdoc and graduate students are also involved in this large effort. The KU Lifemapper team develops the underlying technology and predictive modeling web services that will integrate into web browser curriculum materials being developed by the Michigan team.
Lifemapper/SAM is an NSF-sponsored collaboration with Drs. R. Colwell of the University of Connecticut and T. Rangel of the Universidade Federal de Goias, Brazil. LM/SAM is a project to develop computational and web services for populating multispecies geospatial data grids for macroecological analysis. Macroecology is a subfield of ecology that investigates the evolutionary, genetic, and ecological determinants of species diversity and distribution on large spatial scales, typically at the level of continents or the entire globe.
Map of Life is an NSF-funded collaborative cyberinfrastructure development project among Yale U., U. of Colorado, U. of California-Berkeley, and the U. of Kansas to develop a cloud-based comprehensive archive of species ranges derived from research literature and museum data. Lead collaborators outside of KU are Drs. W. Jetz, J. Wieczorek, R. Guralnick.
DataONE
DataONE is a very large, five-year, multi-institutional cyberinfrastructure development and management collaboration focused on building a sustainable, distributed data repository for earth observation data. Its vision is to ensure the preservation of environmental science data from atmospheric, ecological, hydrological, and oceanographic sources and to provide secure long-term access to that data for scientists, land-managers, policy makers, students, educators, and the public. The University of Kansas is a founding partner and member data node. Dr. D. Vieglais (KU) is DataONE’s director for development and operations. Collaborators are too numerous to enumerate; jump over to the DataONE web site for additional information.