Visual Interactive On-line Navigation Biomodeling Data Base



Intro Home / Visual Tutorial / Return to the Database

Welcome to VISION-BIOMODBASE, the Visual Interactive On-line Navigation Biomodeling Data Base, an internet-accessible biomodeling module to be included under the PIEallaMODE umbrella, coupled with its analytical functionality, and hosted on our Lab server. VISION's purpose is to provide end-users with a visually-pleasing and interactive means for facilely displaying, documenting, and updating biomodels, in any and all forms - cartoon, schematic, mathematical - with ready-access to all embedded supportive data and reference material, all in one place.

Modeling software connectivity has been embedded throughout the project. Users can directly access VisSIMTM and SAAM II files and perform simulations right on his/her own computing machine, aiding in real-time studies of the model. The hallmark of this capability is that users can alter parameter values and simulate these customizations in real-time (VisSIMTM Viewer does not allow saving of alterations to models). See below for a free download of VisSIMTM Viewer (VISION is currently looking into a similar program for SAAM II).

VisSIMTM simulation files throughout this site can be simulated directly on the user's machine via the VisSIMTM Viewer, a FREE view-only version of the program. A license is not required. Note that some browsers may not work with VisSIMTM Viewer and may require the user to download the VisSIMTM simulation file to the user's machine prior to simulation. Download the viewer here.

User navigation is via graphical mappings from the biosystem diagram (e.g. a cartoon or schematic of cell-signal interactions or compartmentalizations), and a menu that explains the linkages of the interactive interface. It should be quite useful for teaching as well as research. Users will be able to query the online biomodel databases, and also store new ones. Tools for building new biomodel databases are being provided, currently in HTML, and later in XML and other web-oriented authoring languages, including Flash animation. We are in the process of completing ver.1 of the first biomodel database, currently being installed for our new PK/PD model of mAb/FcRn/apoptosis dynamics. Navigation is possible through three methods as outlined below:

1 Graphical-mapping   This is the main navigation module of VISION. Contained on each page is a central area for user navigation via graphics and descriptive text. Images are clickable for navigating the biomodel. If pages contain subpages, click the yellow arrows to access them.
2 Menu-and-Layer  

On the upper righthand corner of most pages is this button . Click it to display a layer, or pop-up window, which sits "on top" of the browser window. A sitemap is displayed which outlines the entire site with a collection of hyperlinks. This layer functions as a second window for easy access to other parts of the site without leaving your current page. Layers can exist on top of other layers. To exit the layer, click on the "X" at the upper righthand corner.

3 Indexing  

On the upper lefthand corner is text separated by ">>". This indexes the user's current page in a hierarchical manner with access to upper levels via the hyperlinks.
Ex. Home >> FcRn and Apoptosis Dynamics >> Rituxan





Web Adaptation & Interface Concept: Jason Lee | Research Content & Original Design: Gregory Ferl, PhD
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