Peter W. Brewer

openModeller: a generic approach to species' potential distribution modelling

Species’ potential distribution modelling is the process of building a representation of the fundamental ecological requirements for a species and extrapolating these requirements into a geographical region. The importance of being able to predict the distribution of species is currently highlighted by issues like global climate change, public health problems caused by disease vectors, anthropogenic impacts that can lead to massive species extinction, among other challenges. There are several computational approaches that can be used to generate potential distribution models, each achieving optimal results under different conditions. However, the existing software packages available for this purpose typically implement a single algorithm, and each software package presents a new learning curve to the user. Whenever new software is developed for species’ potential distribution modelling, significant duplication of effort results because many feature requirements are shared between the different packages. Additionally, data preparation and comparison between algorithms becomes difficult when using separate software applications, since each application has different data input and output capabilities. This paper describes a generic approach for building a single computing framework capable of handling different data formats and multiple algorithms that can be used in potential distribution modelling. The ideas described in this paper have been implemented in a free and open source software package called openModeller. The main concepts of species’ potential distribution modelling are also explained and an example use case illustrates potential distribution maps generated by the framework.

How global is the global biodiversity information facility

There is a concerted global effort to digitize biodiversity occurrence data from herbarium and museum collections that together offer an unparalleled archive of life on Earth over the past few centuries. The Global Biodiversity Information Facility provides the largest single gateway to these data. Since 2004 it has provided a single point of access to specimen data from databases of biological surveys and collections. Biologists now have rapid access to more than 120 million observations, for use in many biological analyses. We investigate the quality and coverage of data digitally available, from the perspective of a biologist seeking distribution data for spatial analysis on a global scale. We present an example of automatic verification of geographic data using distributions from the International Legume Database and Information Service to test empirically, issues of geographic coverage and accuracy. There are over 1/2 million records covering 31% of all Legume species, and 84% of these records pass geographic validation. These data are not yet a global biodiversity resource for all species, or all countries. A user will encounter many biases and gaps in these data which should be understood before data are used or analyzed. The data are notably deficient in many of the worlds biodiversity hotspots. The deficiencies in data coverage can be resolved by an increased application of resources to digitize and publish data throughout these most diverse regions. But in the push to provide ever more data online, we should not forget that consistent data quality is of paramount importance if the data are to be useful in capturing a meaningful picture of life on Earth.

TRiCYCLE: a universal conversion tool for digital tree-ring data

Abstract There are at least 21 dendro-data formats used in dendrochronology laboratories around the world. Many of these formats are read by a limited number of programs, thereby inhibiting collaboration, limiting critical review of analyses, and risking the long-term accessibility of datasets. Some of the older formats are supported by a single program and are falling into disuse, opening the risk for data to become obsolete and unreadable. These formats also have a variety of flaws, including but not limited to no accurate method for denoting measuring units, little or no metadata support, lack of support for variables other than whole ring widths (e.g. earlywood/latewood widths, ratios and density). The proposed long-term solution is the adoption of a universal data standard such as the Tree-Ring Data Standard (TRiDaS). In the short and medium term, however, a tool is required that is capable of converting not only back and forth to this standard, but between any of the existing formats in use today. Such a tool is also required to provide continued access to data archived in obscure formats. This paper describes TRiCYCLE, a new application that does just this. TRiCYCLE is an open-source, cross-platform, desktop application for the conversion of the most commonly used data formats. Two open source Java libraries upon which TRiCYCLE depends are also described. These libraries can be used by developers to implement support for all data formats within their own applications.

Biodiversity World: a problem-solving environment for analysing biodiversity patterns

In the Biodiversity World (BDW) project we have created a flexible and extensible Web services-based grid environment for biodiversity researchers to solve problems in biodiversity and analyse biodiversity patterns. In this environment, heterogeneous and globally distributed biodiversity-related resources such as data sets and analytical tools are made available to be accessed and assembled by users into workflows to perform complex scientific experiments. One such experiment is bioclimatic modelling of the geographical distribution of individual species using climate variables in order to predict past and future climate-related changes in species distribution. Data sources and analytical tools required for such analysis of species distribution are widely dispersed, available on heterogeneous platforms, present data in different formats and lack interoperability. The BDW system brings all these disparate units together so that the user can combine tools with little thought as to their availability, data formats and interoperability. We describe the architecture of the BDW problem solving environment (PSE) consisting of a number of components providing uniform access to heterogeneous resources and analytical tools. Architectural components of the BDW system include a workflow management tool, resource wrappers, a communications layer, BDW datatypes and a metadata repository.

Accessing biodiversity resources in computational environments from workflow applications

In the biodiversity world (BDW) project we have created a flexible and extensible Web services-based grid environment for biodiversity researchers to solve problems in biodiversity and analyse biodiversity patterns. In this environment, heterogeneous and globally distributed biodiversity-related resources such as data sets and analytical tools are made available to be accessed and assembled by users into workflows to perform complex scientific experiments. One such experiment is bioclimatic modelling of the geographical distribution of individual species using climate variables in order to predict past and future climate-related changes in species distribution. Data sources and analytical tools required for such analysis of species distribution are widely dispersed, available on heterogeneous platforms, present data in different formats and lack interoperability. The BDW system brings all these disparate units together so that the user can combine tools with little thought as to their availability, data formats and interoperability. The current Web Services-based grid environment enables execution of the BDW workflow tasks in remote nodes but with a limited scope. The next step in the evolution of the BDW architecture is to enable workflow tasks to utilise computational resources available within and outside the BDW domain. We describe the present BDW architecture and its transition to a new framework which provides a distributed computational environment for mapping and executing workflows in addition to bringing together heterogeneous resources and analytical tools.

Roman Barrows and their Landscape Context: a GIS Case Study at Bartlow, Cambridgeshire

This paper examines the landscape context of the Bartlow Hills, a group of large Romano-British barrows that were excavated in the 1840s but have been largely neglected since. GIS is employed to test whether it was possible to view the mounds from nearby roads, barrows, and villas. Existing research on provincial barrows, and especially their landscape context, and some recent relevant applications of GIS are reviewed. We argue that barrows are active and symbolically charged statements about power and identity. The most striking pattern to emerge from the GIS analysis is a focus on display to a local rather than a transient audience.

Annual radiocarbon record indicates 16th century BCE date for the Thera eruption

New annual radiocarbon calibration data offer a resolution to controversial dating of the Bronze Age eruption of Thera. The mid-second millennium BCE eruption of Thera (Santorini) offers a critically important marker horizon to synchronize archaeological chronologies of the Aegean, Egypt, and the Near East and to anchor paleoenvironmental records from ice cores, speleothems, and lake sediments. Precise and accurate dating for the event has been the subject of many decades of research. Using calendar-dated tree rings, we created an annual resolution radiocarbon time series 1700–1500 BCE to validate, improve, or more clearly define the limitations for radiocarbon calibration of materials from key eruption contexts. Results show an offset from the international radiocarbon calibration curve, which indicates a shift in the calibrated age range for Thera toward the 16th century BCE. This finding sheds new light on the long-running debate focused on a discrepancy between radiocarbon (late 17th–early 16th century BCE) and archaeological (mid 16th–early 15th century BCE) dating evidence for Thera.

Supporting the construction of workflows for biodiversity problem-solving accessing secure, distributed resources

In the Biodiversity World (BDW) project we have created a flexible and extensible Web Services-based Grid environment for biodiversity researchers to solve problems in biodiversity and analyse biodiversity patterns. In this environment, heterogeneous and globally distributed biodiversity-related resources such as data sets and analytical tools are made available to be accessed and assembled by users into workflows to perform complex scientific experiments. One such experiment is bioclimatic modelling of the geographical distribution of individual species using climate variables in order to explain past and future climate-related changes in species distribution. Data sources and analytical tools required for such analysis of species distribution are widely dispersed, available on heterogeneous platforms, present data in different formats and lack inherent interoperability. The present BDW system brings all these disparate units together so that the user can combine tools with little thought as to their original availability, data formats and interoperability. The new prototype BDW system architecture not only brings together heterogeneous resources but also enables utilisation of computational resources and provides a secure access to BDW resources via a federated security model. We describe features of the new BDW system and its security model which enable user authentication from a workflow application as part of workflow execution.