Download the original photo
CJ Grady
Software Developer
Informatics
Biodiversity Institute

Contact Information

Office Phone: 
785.864.7792
Building: 
Dyche Hall

CJ came to the Biodiversity Institute as a Student Software Tester for the Specify Project in 2004.  After graduating in 2006, he transitioned into a developer role and joined the Lifemapper team.  His interests include process metadata and standards, scientific workflow systems, web services, and parallel computing.

Recent Blog Posts

February 4, 2011
We have combined Lifemapper and VisTrails software to create an intuitive and...
Process Metadata, Parallel Computing, Open Source Software, Web Services
February 4, 2011

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. 

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/clients.shtml

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.

 

0 comments
There are no additional posts.

From the Biodiversity Insitute blog

September 28, 2012
Please congratulate Dr. Matthew Gimmel on his acceptance of a 2.5 year European Social Fund postdoctoral fellowship to work on beetle systematics in the lab of Dr. Milada Bocakova, Department of...
September 28, 2012
The Chaboo lab hosted Sara López from the Ciudad Universitaria (UNAM) and the Departament of Zoology, National Collection of Insects, Mexico City, Mexico. Sara is conducting M.Sc. research on a...
August 22, 2012
The Aug. 6 edition of the Proceedings of the National Academy of Sciences  included a large-scale analysis of bony fishes using DNA sequencing. One of the major conclusions is that tarpons, eels...
August 17, 2012
The Biodiversity Institute was well represented at the 7th World Congress of Herpetology held on August 8–13 in Vancouver, Canada. Among the 1700+ delegates from 41 countries were Rafe Brown,...
August 4, 2012
From Andrew: After a day of rest back in Paramaribo after our Voltzberg adventure, we loaded up the trucks today and headed for Brownsberg Nature Park, which sits atop a 1500 ft. mountain a few...
July 31, 2012
From Clay: Last night was our final night at the research station at the base of Voltzberg. After breakfast, we packed our hammocks and made a pile of the food and gear the porters were going to...
July 30, 2012
From Clay: We woke up at 4 o’clock this morning and we’re on the trail shortly before 5 a.m. We were planning to reach the summit of Voltzberg to watch the sunrise. Of course,...
July 24, 2012
 I caught a glimpse of the mountains as I left the field team, two days ago.  Over the last 48 hours Dr. Tess Sanguila and I drove back and forth along the north coast of Mindanao, visiting...
July 16, 2012
Funny, just after I waxed cathartic about figuring out that one species was actually two, today I experienced a kind of reversal.  Shrub frogs of the genus Philautus in the Philippines are, in...
July 12, 2012
 Today was a cathartic day in my own personal journey in studies of Philippine biodiversity.  The story starts in 1991 when, as an undergraduate student at Miami University, I joined my...