ENDOMESODERM GENE NETWORK

BioTapestry Interactive Network Viewer

The endomesoderm network model is best viewed using the BioTapestry Interactive Network Viewer, which is a Java application. BioTapestry was originally developed by William Longabaugh, Eric Davidson, and Hamid Bolouri, supported by a grant by NIH General Medical. Active development is continuing with support from NIH Child Health and Human Development. The most recent release is Version 6 (December 2012), with many new features to assist in drawing and laying out networks. (N.B. An alternative viewing method, which just displays static images in your web browser, is also available if you have difficulties with the Java version.)

Requirements for Running BioTapestry Viewer

The BioTapestry network viewer uses Java Web Start, which is bundled with any recent version of the Java Runtime Environment (JRE). If the above link does not launch the viewer, you will need to make sure you have installed Java on your computer. Java can be downloaded from here (click the "Free Java Download" button) or here.

Java was formerly factory-installed on Apple Macs; for newer Macs, use the above link as well. BioTapestry is designed to work with all versions of Java since 1.4.2.

If you have any problems launching the viewer, there is some relevant information concerning troubleshooting tips for the associated BioTapestry Editor program provided on the BioTapestry home page here and here. You can also visit the BioTapestry-users Google Group for assistance (note that first-time postings from new members are moderated).

About The BioTapestry Editor

BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks. The network viewer used here is a simplified version of the full-featured network editor, which is available from BioTapestry.org.

• With the current version of BioTapestry, the user can: 1) draw networks by hand, or 2) specify a list of interactions either in interactive tables or comma-separated value (CSV) input files and then have the network laid out automatically. Also, when provided with separate tables of experimental data, BioTapestry can automatically show hourly changes in the network state.
• BioTapestry development is ongoing, with continuing new releases that improve the functionality and ease-of-use of the software.

Levels of Network Models

BioTapestry organizes the network model into four levels that are outlined in a tree view on the left side of the window. You can choose the view you want by clicking on it in this tree view. The four levels are:

Level 1: The Full Genome. This top level view shows the View from the Genome (VfG). This view shows only one instance of every gene, and all its inputs and outputs, regardless of when or where they occur. For example, the Tgif gene in this view show inputs that are present in both the PMCs and Veg2 Endoderm.

Level 2: This level shows four different views of the developing embryo. The first is a summarizing overview, that combines some features from the other three views. This is view you see when you start the viewer. Each of the other three views is called a View from All Nuclei (VfA).

The three VfAs are for the PMC region up to 30 hours, the Endomesoderm from 6 to 18 hours, and the Endomesoderm from 21 to 30 hours. Note that endomesoderm development is depicted in two separate VfAs because of the increasing complexity of the separate territories over time, while PMC development can be represented in a single VfA.

Level 3: The third level can be thought of as a summation of all the hourly Views from the Nucleus (VfNs) that are located beneath it in the hierarchy. For example, the Mesoderm 21-30 Hours view is the superposition of the 10 Mesoderm Hourly VfNs below it. Note, however, that the PMC branch omits this level.

Level 4: The bottom level shows the View from the Nucleus (VfN), which depicts a a particular region at a particular hour. You can select the hour using the time slider, which is described below.

Time Slider  

Whenever an "hourly" view is selected (the lowest level in the hierarchy), the viewer displays a time slider in the lower left corner that allows you to select the hour you wish to view by dragging the slider. Clicking to the left or right of the slider also moves it, and the left and right keyboard arrows are active (allowing fast hour switching) if you first click on the slider with the mouse.

Viewer Toolbar

The BioTapestry Viewer toolbar provides several important functions. As shown in the picture at left, there are buttons for (going left to right) zooming out one step, zooming in one step, zooming to the selected items (only active if something is selected), zooming out to view the current model, zooming out to bound all the models in the hierarchy, searching for genes/nodes, clearing current selections (only active if something is selected), and viewing the about page.

Selecting Network Elements

To select a gene, node, or link segment, just click on it. For genes, make sure to click in the areas highlighted in orange shown in the picture at left: either the gene name or the gene itself. To select more than one thing, hold down the Shift key while clicking on each new item. Use the toolbar button to clear all current selections.