Informatics

Monday, October 10, 2011

Specify Software Sustains 20% Growth

Specify logo

Specify is now the database management of choice for over 375 biological collections worldwide. The Project is sustaining a 20% annual growth in the number of supported biological collections. In addition to offering research community software helpdesk support, the Project has produced 11 software updates in 2011, many of them extending and enhancing features researchers have requested for more effective management and analysis of specimen information.  Recent research funding awards by the U.S. National Science Foundation's 'ADBC' initiative for accelerating the computerization of information associated with biodiversity specimens have stimulated additional research repository adoption of Specify for their project data management.

The Specify Project has a number of new capabilities and releases planned for 2011 and 2012 including: (1) a Specify web client for remote access (editing, querying, reporting, etc.) over the internet to remote Specify databases (being developed in collaboration with the Swedish Natural History Museum), (2) release of the new Scatter-Gather-Reconcile or "SGR" capabilities which allow researchers to look for specimens which are related or duplicative to their own (in collaboration with the University Autonoma de Barcelona), and (3) innovative data entry software for acquiring specimen images for digital archives and specimen label data computerization.

The ultimate goal of mobilizing the locality, species identity, and collection date information associated with biological specimens into databases and onto the web is to provide easy open access to the information for biodiversity documentation and analysis, and for forecasting the impacts of climate change on species ranges.

Friday, February 4, 2011

Lifemapper + VisTrails = Better Science

Lifemapper logo

We have combined Lifemapper and VisTrails software to create an intuitive and powerful new way to analyze species distributions. Lifemapper is our NSF funded species distribution mapping and modeling initiative. VisTrails is a scientific workflow management system developed by the Scientific Computing and Imaging Institute at the University of Utah.

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Workflow systems allow scientists to assemble complex computational pipelines consisting of sequential tasks which are stitched together using a single desktop software program. Typically an automated research workflow will start by inputting data from an external source, then dragging that data through one or more computational or modeling tasks, and then outputting the results in formats which can then be analyzed. LM3 LogoData output formats might include geographical maps, numeric data sets or statistically summarized results. Workflow management software is integrative by design and it is an excellent tool to connect internet data and computer processing services together across institutional and  discipline boundaries. VisTrails is particularly suited for our Lifemapper Project because of its capabilities for integration with internet-accessible data and services and because of its strength with capturing the metadata or 'provenance' information associated with research workflows.

We have developed software extensions that computationally integrate VisTrails' functions with our Lifemapper Project's web services for species distribution modeling. Technically, this integration includes interfaces to post and retrieve species occurrence sets from our installation of theVT Logo Global Biodiversity Information Facility's global database of museum specimen data points. This software integration allows biodiversity researchers to quickly compose and execute species niche modeling experiments, using VisTrails' drag-and-drop workflow creation software.  Our latest Lifemapper VisTrails software (version 1.1.0) introduces the following features:

Lifemapper Ecological Markup Language (EML) Reader Software

EML is a standard, XML-based language for describing and archiving all of the background information  or 'metadata' associated with research data sets in environmental biology.  The Lifemapper EML Reader software enables researchers who map and model species distributions to automatically store the metadata associated with a Lifemapper/VisTrails workflow (modeling experiment) in an EML archive file.  An EML file would include metadata on such things as sources and formats of input data, any pre-processing steps or data filters that might be used, parameters for the modeling algorithms, as well as information about the resulting output files. This new capability makes complex modeling experiments easier to manage, archive and reference.  Best of all, storing Lifemapper/VisTrails metadata in EML files, enables the species range modeling experiment to be easily re-executed by the same or other researchers.  Being able to fully reference, re-use, and repeat a complex computational niche modeling process directly results in more transparent and verifiable science.

Enabling VisTrails for OpenLayers Display 

OpenLayers is open source software product which enables the creation of sophisticated map displays with point and click manipulation functions such as panning and zooming.  With our latest LM / VT client release we have enabled VisTrails' output screens to provide these mapping functions.  These new capabilities in VisTrails greatly facilitate the research exploration of species distribution maps and model outputs produced by running VisTrails / Lifemapper workflows.

Simplified Algorithm Inputs 

In previous versions of our Lifemapper / VisTrails this integration, species model algorithm parameters had to be specified, even if using default values. While it is still possible to change model parameters, default settings are now automatically applied.

Simplified Inputs and Outputs 

VisTrails works with software modules that are selected from a screen listing and dragged and dropped into a workflow workspace.  Modules have data Inputs and outputs as data are brought into a workflow, streamed through various processing steps and then output for analysis.  In our latest software we have simplified input and output links for Lifemapper's species niche modeling components, which makes the creation of new workflows faster and easier.

Our Lifemapper / VisTrails client allows one to wield the power of the Lifemapper web services inside a desktop application.  Researchers can quickly connect elements together without worrying about the work behind the scenes.  No studying APIs.  No constructing HTTP requests.  Just click, connect, and go!  The Lifemapper / VisTrails client software can be downloaded from the Lifemapper Project web site at: http://lifemapper.org

For assistance with installing or using Lifemapper / Vistrails software for research, send e-mail to: lifemapper@ku.edu or call the helpdesk at 785.864.4400.