BioTapestry Frequently Asked Questions (FAQ)
ISB Logo BioTapestry Caltech Logo

BioTapestry Frequently Asked Questions (FAQ)

Version B: released 03/19/09

Back to Home Page

Getting Started

What's involved in getting BioTapestry running?

What's a fast way to learn how to use BioTapestry?

Can I install the software on my computer?

Do I have to be online to run BioTapestry?

Why do I have to always accept the security certificates?

I'm not getting the most recent version. What do I do?

I'm using a Mac with a one-button mouse. What's a right-click?


How do I draw links?

How do I reorganize links after moving nodes around?

Why won't BioTapestry allow me to draw a link a certain way?

Can I change an existing link to another source or target node?

How can I make sure my links get drawn orthogonally?

The Model Hierarchy and Submodels

What's the relationship between all these different views of the network?

Can I use BioTapestry without having to build a model hierarchy?

How do I create submodels?

How do I get colored background squares to appear in my model?

How do I build the network in a submodel?

Is there a way to build submodels without having to set up tables of experimental data?

What do I need to do to get an interactive time slider control?

I've built a dynamic model, but I don't have a time slider control!

My dynamic model just has light grey region blocks in it!

Can I copy and paste networks?

Can I move models around in the model hierarchy?

Can I create a subset submodel with all components included at the start?

Modeling Issues

What names can I use for genes, nodes, and regions?

Can I use greek characters in gene and node names?

How do I create embedded regions like the mesoderm and endoderm in the sea urchin endomesoderm network?

How do I display a 2D view with each network model?

Can nodes and links be set to values between on and off?

How can I add text notes to a model?

Can I set experimental evidence levels for links in the comma-separated value (CSV) input file?

A comma-separated value (CSV) file exported from Excel won't load. What's wrong?


What are the various zoom options?

My model has become too large to fit the workspace! What do I do?

When I click the "Zoom As Needed to Show Current Model" button, things are not centered correctly. What's wrong?

I want to see a different model on startup. What do I do?

Can I set the zoom level used at startup?

Can I set the zoom behavior moving between models?

How can I find specific nodes in a model?

How do I select nodes, genes, and links?

Can I define a tour of models to visit in a specified order?

Visual Appearance of the Network

How do I grey out inactive nodes and links?

How can I change the colors assigned by BioTapestry to the regions, genes, and links?

Can I change lots of gene/link/node/region colors at once?

How can I change the fonts? Can I change the font used for an individual gene?

Can I change the color/thickness/style of only a part of a link tree?

I have a ton of links inbound to a node. Where can I put them all?

How do I make my gene (signal, slash node, ...) point a different way?

Can I increase the size of link arrowheads and repression feet?

How can I eliminate link crossing ambiguities?

Can I change the size of the colored region rectangles?

Automatic Layout Tools

What automatic network layout tools are there?

Are there tools to just layout links?

Why am I getting link layout failures? What can I do about it?

Is there a way to improve the result of my link-only automatic layout?

Are there any other tools to help with network layout?

My best layout is in a submodel. Can I duplicate it to the top-level model and/or other submodels?

Experimental Data Entry and Presentation

Can BioTapestry support my form of raw data?

Do I have to enter all the experimental data by hand?

What experimental data can I display for a gene?

Are there limitations on the time units I can use for my experimental data?

What graphical symbols are available for indicating confidence levels or experimental evidence?

Export Options

How do I get model images for publication?

Is there a quick way to get images of all the models at once?

Can I export my network to Adobe Illustrator?

What else can I export?

What is the format used when I export a network model to a SIF file?

How do I set up a web-hosted BioTapestry viewer like the one for the sea urchin endomesoderm model?

Network Simulation

How can I run network simulations with BioTapestry?