Biodiversity Informatics Training on Demand and no Fee-per-View
National Biodiversity Diagnoses Instructor Team in Uganda: (L to R) Kate Ingenloff, Town Peterson, Lindsay Campell, and Arturo Ariño.
Over the past four years, the University of Kansas Biodiversity Institute (JRS grant page), lead by Dr. Town Peterson and Co-Director Dr. Kate Ingenloff, has had the ambitious goal to build a comprehensive package of biodiversity informatics educational materials that would be accessible for free to anyone – literally anyone – who wanted to learn about how to gather, manage, and use biodiversity data. Now, they have announced that they have done just that. The JRS Biodiversity Foundation aims to increase the capacity for biodiveristy informatics in sub-Saharan Africa by investing in the institutions and people that create and share biodiversity data and information. By providing formal and experiential training, road tested in Africa, and making it widely and freely available, the University of Kansas team has demonstrated a fresh and a notably dedicated approach to biodiversity informatics capacity building.
In a paper in the journal Biodiversity Informatics, Peterson and Ingenloff introduce the Biodiversity Informatics Training Curriculum (BITC), version 1.2, the first complete training curriculum in biodiversity informatics – the discipline is so new that there are no degree programs or existing textbooks synthesizing and translating the field. Major advancements in data availability and computing power have, over the past decade, enabled the development of new and powerful approaches to answering questions about the earth’s biodiversity, from basic questions such as, “what plants and animals live where?”, and extending to more complex scenarios, envisioning the effects of future climate or land use change on habitat connectivity. This knowledge base, and the techniques to implement informatics, are often learned one at a time, drawn from disparate sources. The new curriculum steps logically through the informatics approach, from data collection and management, to analyses, and applications in conservation and public health.
Students and instructors from the Biodiversity Indices and Species Descriptions course workshops, held in Cameroon, March 2015.
This training curriculum is noteworthy, not only for meeting the need of a growing discipline, but also because it trains young scientists through online resources and experiential training. Rather than presenting the curriculum as a standard textbook, inert and destined to become outdated, the BITC is constructed as an online course series and academic community. Each topic in the series, such as Biodiversity Data Analysis, is a modular course, originally implemented as a series of training workshops for scientists in Africa. It can be taken as 12 stand-alone components or as part of the entire series. Online resources include a webinar series and an active Facebook community to take advantage of widely-available web platforms, such as YouTube, and together create a resource that is responsive to new ideas and technologies, and an interactive opportunity to support educational goals of young scientists and managers worldwide.
The BITC team is committed to accelerating the transfer and dissemination of new and more powerful tools in biodiversity informatics and conservation with particular emphasis on the developing world. The goal of the BITC is to make this information as accessible as possible. The team offers to mail the compiled information in a USB memory drive to anyone who cannot access it via YouTube and is developing a semi-automated workflow to translate lectures subtitles into as many languages as possible. Future plans include creating a certification or degree program built around the curriculum.
Capacity Building in biodiversity informatics is one of JRS’ three core grantmaking Programs, and underpins nearly all JRS-funded projects. Training courses like the BITC enhance the technical capacity of African countries to manage biodiversity for sustainable growth and promote communities of learning that will sustain the demand for biodiversity data.
By Emily Grason
Scientists in the field have collected voucher specimens since the 19th century. Today, most sit in research institutions around the world “dried, mounted, pickled, preserved, frozen and stuffed,” according to the creators of Lifemapper, an online species-distribution tool created at the University of Kansas.
Most specimens in natural history museums come with a label describing, among other things, where in the world it was collected. But where might these species migrate in the future in order to survive extreme weather, shifting seasons, invasive species, rising oceans and other threats linked to rapid climate change?
“Climate change is the most pressing problem of the 21st century, and Lifemapper provides tools to explore how climate change can impact individual species ranges as well as the species composition of communities,” said James Beach, assistant director for informatics with the Biodiversity Institute at KU. “Since human life and quality of life is dependent on the functions and services of ecosystems and natural communities, seeing how thousands and tens of thousands of species are being impacted by changing climate should be of interest to anyone interested in future generations' quality of life on planet Earth for future generations.”
To generate predictions, Lifemapper performs “species distribution modeling” based on records of where organisms have been spotted and collected, along with environmental layers such as elevation, precipitation and temperature. Then Lifemapper determines the preferred conditions for a species — and where those conditions are most likely to be found in the future under various climate settings.
“Lifemapper has an agreement with the Global Biodiversity Information Facility to use the species data they aggregate from natural history museums and collections worldwide,” said Aimee Stewart, who serves as lead software engineer on the project. “Lifemapper uses elevation and current climate data calculated from observation stations by the Worldclim project for modeling GBIF species data. For projected future climate scenarios, we use climate data predicted for the International Panel on Climate Change Assessment Reports.”
Other KU Biodiversity Institute personnel working on Lifemapper include software engineers CJ Grady and Jeff Cavner.
In development since the early 2000s, Lifemapper today can help individual researchers anywhere in the world who lack the computing power needed to estimate the future distribution of plants and animals.
“The time and computational resources needed to perform calculations on hundreds or thousands of species can be prohibitive for an individual researcher on even a powerful desktop computer,” Stewart said. “Researchers can submit their own species and environmental data with the Lifemapper plugin to the GIS package QGIS for single or multi-species analyses with online Lifemapper tools. Lifemapper distributes these requests to one or more high performance computing environments running Lifemapper software, including the Advanced Computing Facility here at KU, where a divide-and-conquer approach allows computations to complete far more quickly than is possible on a single machine.”
Moreover, high school students are using Lifemapper’s website to analyze changes in habitat under various climate-change conditions.
“More advanced students might use the simplest species prediction tools available through the website or download data for further geospatial analysis,” said Stewart. “The ChangeThinking project, a collaboration with the University of Michigan School of Education and their Animal Diversity Web Project, created curricula and an online workbook using Lifemapper web services to teach middle and high school students about the effects of climate change. In 2014, ChangeThinking curricula were used in 130 schools in Michigan, Kansas and other states.”
Most of Lifemapper’s funding has been collaborative, as the project partners with experts in the fields of biology, macroecology, cyberinfrastructure, computer science and education. Additionally, the National Science Foundation and NASA have provided most of the support for Lifemapper.
“As part of a partnership with UTEP’s Cyber-ShARE Center of Excellence, we have been encouraged to seek support to connect and integrate Lifemapper’s models and computational services to other earth-science modeling systems with metadata and computer semantics,” Stewart said.
The KU researchers also collaborate with the Pacific Rim Applications and Grid Management Assembly, an international collaborative framework of Pacific Rim institutions working on bringing together science applications and cutting edge computer science research.
“As part of PRAGMA, we are working with UCSD’s San Diego Supercomputer Center and UF’s Advanced Computing and Information Systems Laboratory to further modularize our systems and speed our data computation, storage and retrieval systems,” Stewart said.
With an NSF award recently recommended for funding, the Lifemapper team hopes to further refine its ability to predict shifting habitats to supply scientists and conservationists with the best data to protect species around the world.
“Tools created as part of the new grant will allow further analyses of landscapes, identifying habitat fragmentation and how it can change over time with climate change, providing managers with the ability to pinpoint areas most at risk,” Stewart said.
The National Science Foundation has recommended full funding ($800,000) of a research grant in biodiversity informatics led by Jim Beach, Jorge Soberón and Aimee Stewart of the Biodiversity Institute. This is a collaborative project with University of Texas El Paso, which will receive an additional $174K.
The term “biodiversity informatics” may not set the average person’s heart aflutter. Yet, this emerging field is revolutionizing conservation efforts, public health and agriculture in parts of the world. Now, a researcher at the University of Kansas is ready to bring comprehensive training in biodiversity informatics to students and scientists across Africa.
“Biodiversity informatics is about how to develop, integrate and use information about life on Earth,” said Town Peterson, University Distinguished Professor of Ecology and Evolutionary Biology and curator in the Biodiversity Institute. “We have a lot of raw data about biodiversity, which is to say we know places where particular species have been seen. But turning those raw data into usable information is a much bigger challenge.”
In Africa, as in much of the world, there is scant availability of training in this important discipline. This is about to change. With funding from the JRS Biodiversity Foundation, Peterson will lead multiple training sessions in four African nations: Ghana, South Africa, Kenya and Egypt.
“The people doing the training will come from around the world, and the trainees will be a range of people, from people in decision-making situations, such as a ministry of natural resources, to professors, graduate students and undergrads,” said Peterson. “We’re going to focus on people with the promise to take this training and put it to good use.”
What’s more, Peterson and his team will make videos of the training sessions, along with other learning materials, available on the Internet for anyone to access. He calls it a free online “biodiversity informatics university.”
“You have a field that’s relatively new,” said the KU researcher. “Being able to analyze biodiversity patterns worldwide is not something that’s been feasible in terms of data availability for very long. This field emerged just in the last 10 to 20 years. It requires a fair amount of technology and access to the Internet. So not just Africa, but people all over the world, including in the U.S., are looking for means of obtaining quality training in terms of how you learn these techniques. The in-person training will be in Africa, but the training materials will then be made available worldwide.”
The training could significantly enhance efforts in Africa and elsewhere in several important fields.
“Say a country has the will to protect its natural resources in biodiversity, but may not have good information about where protection should be focused,” said Peterson. “If you want to have maximum effect, you need to know where each species is. Think of the national parks in the U.S.: here you have the Rockies, the Appalachians, the Great Plains and California. But if you were starting from zero and setting up a national park system, where would you protect first? Take that question to any number of countries in Africa, and there are data out there, but they are raw. So you need to organize the data and have a framework for analyzing and interpreting the results.”
Peterson also said that public health officials could use biodiversity informatics to track transmission of infectious diseases such as malaria and dengue, while agricultural experts could know better what insects and weeds could pose a threat to crops.
This work is funded by a three-year grant from the JRS Biodiversity Foundation.
The National Aeronautic and Space Administration has announced a grant of more than $1 million to fund a collaboration that will bring together NASA remote sensing technology with predictive modeling applications to develop and maintain data about the effects of climate change.
The project is entitled "Earth, Life and Semantic Web (ELSeWeb): An Earth observation-driven, semantic web system for computational modeling of the impact of changing climate on ecosystems and human/environmental health systems." Partners in the grant include the University of Texas at El Paso, the University of New Mexico, and the University of Kansas.
At KU, the work will be led by James Beach and Aimee Stewart, who heads up KU's Lifemapper program (lifemapper.org).
The research team will seek to develop information systems that allow researchers to demonstrate potential changes in climate and ecosystem conditions. The project will link three existing information technologies, including Lifemapper, to model and analyze the ways that changes in climate will affect the distribution of animals and plants.
The Specify Software Project is enthused to announce a software co-development collaboration with the Swedish Museum of Natural History (NRM) to create extensions to Specify for the web. NRM scientists and software developers will share the design vision and engineering tasks with Project staff in the Biodiversity Institute to produce a Specify web client (program) for browser-based access to remote Specify databases. The web client will complement the three desktop software versions of Specify currently available for Windows, Mac OSX, and Linux computers. The web client will enable new kinds of collaborations among collections institutions--a single Specify installation will now be accessible over the internet for querying, data entry and other analytical functions with data from multiple collections and institutions. The effort will also produce a web portal for Specify which will be a more traditional web site for open access to specimen data held in Specify databases. The Specify web client and web portal will be available and supported as open source extensions to Specify in 2012.
The National Science Foundation has awarded a KU Biodiversity Informatics research team a $1.7 million grant. Funding for the proposal, "Collaborative Biodiversity Collections Computing," will allow Jim Beach, Informatics director, and Informatics staff to continue to elaborate and support biodiversity data management software for the processing, analysis and publication of the information associated with biological specimens. The grant also will allow them to provide Specify software and helpdesk support for museums and integrate their research with broader computational initiatives in environmental biology. Specify is a software environment used in over 300 biological collections worldwide to manage the information associated with biological specimens. For more information on the Specify Software Project, visit the project web site.