Physiological and Anatomical Visual Analytics (PAVA) version 1.0

In short, this animation employs PAVA to compare models describing two exposure route scenarios, in 7 different organs, on a female anatomy. Oral exposure is red; intravenous, or IV, exposure is blue. Here, PAVA is used to visualize the differences between two ethanol PBPK model outputs. A PAVA comparison of the two routes suggest: (1) the oral exposure route peaks in the liver before the other organs (indicated in a bright red liver). (2) Within 45 minutes, regardless of exposure route, the pharmacokinetic profile to the other tissues would remain similar for about 15 minutes (white peripheral tissues, with a red liver also), and (3) would switch by about 60 minutes to remain higher in all tissues via oral exposure (all tissues change to red). (4) Within about 180 minutes, the levels in both scenarios, tailing to zero, become similar as tissues all fade to white.

Background

The need to more efficiently analyze human chemical disposition data derived from in vivo studies or in silico physiologically-based pharmacokinetic (PBPK) modeling efforts, and to see complex disposition data in a logical and clearly engaging manner, has created a unique opportunity for visual analytics applied to physiologically-annotated data (PAD). For a quick explanation about PAVA, see: EPA Researchers combine science and visualizations to predict chemical exposures and manage risk.

What is PAVA v1.0?

Physiological and Anatomical Visual Analytics (PAVA v1.0) is an easily accessible, Web browser-based application that is used to visualize user-provided physiologically annotated data (PAD) from a variety of sources. PAVA v1.0 is the first stand-alone Web-based visual analytics tool that is freely distributed to the scientific community to support the development, validation, and communication of PAD.

Research scientists at the U.S. Environmental Protection Agency (EPA) have developed the PAVA v1.0 tool to enhance ongoing growth and application of physiologically-based pharmacokinetic (PBPK) models for chemical risk management.

PAVA v1.0 goes beyond fish and rat models, and advances visual analytics by rendering pharmaco- and toxico-informatics on a human anatomy. PAVA v1.0 capitalizes on open-source platform concept used in social visual analytics. ( e.g. F. B. Viegas, M. Wattenberg, F. van Ham, J. Kriss, M. McKeon. ManyEyes: a Site for Visualization at Internet Scale IEEE Transactions on Visualization and Computer Graphics In Visualization and Computer Graphics, IEEE Transactions on, Vol. 13, No. 6. (05 November 2007), pp. 1121-1128. )

There is no need for a license and the program is available free of charge. The software is menu-driven, using a Web-based Graphical User Interface, and therefore eases inputting of data, generating, evaluating, and exporting of results.

PAVA v1.0 does not create the data for models, and is not a modeling application itself. Currently PAVA v1.0 only includes representations of the human anatomy and physiology; future versions may contain additional genus or species.

How does PAVA v1.0 work?

PAVA v1.0 employs user-provided physiologically annotated data (e.g., tissue concentration) or their associated statistics (e.g., variance, median, maximum, etc.). The PAVA v1.0 tool then generates two visual representation formats: (1) a physiological matrix format, and (2) a time-series, multi-organ human anatomical animation in GIF format. PAVA v1.0 accepts physiologically annotated data (PAD) from:

experimental or modeled (simulated) chemical time-course data (dosimetry), and
epidemiological data and anthropometric data.

PAVA v1.0 uses a continuous color mapping scheme to cast spatial (organ shape and location) and temporal (time-course / kinetics) data onto an abstract, layered, 2-dimensional visual representation of the human anatomy and physiology.

PAVA v1.0 accepts both positive and negative values (for use in comparing two models, or two scenarios) to provide differential anatomy-based animations.

How can PAVA v1.0 be obtained?

IMPORTANT: PLEASE REGISTER FIRST before performing the download.

The PAVA v1.0 Quick-Start Guide included with the server-side installation package (below) provides details on how PAVA v1.0 must be installed, implemented as well as references to third-party open-source software package requirements, in addition to an example of product use.

With the exceptions of the PAVA v1.0 script installation, and the requirement of ImageMagick (http://www.imagemagick.org/script/index.php ), the task of accessing PAVA v1.0 on a network requires no other software on client systems other than a Web-browser (it can be installed on a Linux or OS X server and be accessed on multiple network nodes via Firefox or Safari; not Internet Explorer however).

System Requirements: PAVA v1.0 was written in PERL/CGI-script and MUST be:

installed as a server-side application from within a firewall on a Linux or OS X server,
accessed via Firefox or Safari exclusively (not accessible from Internet Explorer),
installed on a computer housing ImageMagick (http://www.imagemagick.org/script/index.php ).

Full installation details are found in the README file on the downloadable installation package, or in the Quick-Start Guide.

DOWNLOAD PAVA v1.0: PAVA_v1_INSTALL_AND_GUIDANCE.ZIP (1.6 MB)

PAVA install overview

PAVA 1.0 Server-Side Software Installation/Guidance Documents (1.6 MB) will include zip file for installation linked here.

Includes relevant scripts, images, and installation guide

PAVA v1.0 server-side HTML and images (required) (250kB)
PAVA v1.0 server-side PERL script (CGI) – required (5kB)

PAVA v1.0 Quick-Start Guide (PDF, 2 pages, 1 MB)
PAVA v1.0 movie (~2 minutes run-time)

Comments or questions on PAVA v1.0 or problems with the download should be sent to PAVA_Model@epa.gov. We welcome comments that would be useful in future improvements.

Future releases and development: Researchers and modelers at the EPA are currently working on PAVA v2.0, which they anticipate, will provide additional anatomies in a more compact and interactive format. The updated version will be posted here some time in late 2010, early 2011. Please refer back periodically to ensure that the most recent version of PAVA is used in your applications. Thank you.

Environmental Science Connector portal: Request access to the Physiological and Anatomical Visual Analytics - PAVA v1.0 application by emailing: PAVA_Model@epa.gov

Technical Contact

Rocky Goldsmith, Ph.D.
U.S. EPA
Office of Research and Development
National Exposure Research Laboratory
Human Exposure and Atmospheric Sciences Division

References / Publications:

1.Goldsmith, M.-R.; Transue T. R.; Chang, D. T.; Tornero-Velez R.; Breen, M.S.; Dary, C. C.; "Physiological and Anatomical Visual Analytics for mapping of tissue-specific concentration and time-course data" (Submitted to Journal of Pharmacokinetics and Pharmacodynamics, Dec. 1, 2009. Published online: 22 May 2010.) (http://www.springerlink.com/content/342t0312v2699372/) doi: 10.1007/s10928-010-9160-6

2. Title: "Whole-body mapping and visualization of physiologically-relevant data"
@ Duke Visualization Friday Forum, 9/11/2009 – Duke University http://vis.duke.edu/FridayForum/09Fall.html

Entire Lecture in multiple video formats (1 hr)
http://lectopia.oit.duke.edu/ilectures/ilectures.lasso?ut=193&id=21022

Mention of trade names or commercial products does not constitute endorsement or recommendation for use by EPA.

Human Exposure and Atmospheric Sciences

Research & Development | National Exposure Research Laboratory