Click HERE to run the BioTapestry Editor (version 2.1.0) using Java Web Start.

NOTE: The above version 2.1.0 (released July 23, 2007) includes two significant new features: 2D model images and user-specified development paths (see What's New). If you haven't used BioTapestry before, you can get up to speed on the basics by going through the new online Quick Start Tutorial (released September 28, 2007), and the new BioTapestry Frequently Asked Questions (released November 5, 2007) is another good source of information. If you run into any difficulties, take at look at Problems Running It? and Supported Platforms below.

• S. purpuratus endomesoderm at the Davidson Lab at Caltech.
• Mouse ventral neural tube specification at the McMahon Lab at Harvard.

Papers and Books Using BioTapestry

• Vokes, S.A., Ji, H., McCuine, S., Tenzen, T., Giles, S., Zhong, S., Longabaugh, W.J.R., Davidson, E. H., Wong, W.H., McMahon, A.P. Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning. Development 134, 1977-1989, 2007.
• Wellmer F, Alves-Ferreira M, Dubois A, Riechmann JL, Meyerowitz EM. Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development. PLoS Genetics 2(7), e117, July 2006.
• Livi, C.B., Davidson, E.H. Expression and function of blimp1/krox, an alternatively transcribed regulatory gene of the sea urchin endomesoderm network. Dev. Biol. 293(2), 513-25, 2006.
• Davidson, E.H., Erwin, D.H. Gene Regulatory Networks and the Evolution of Animal Body Plans Science 311 (5762), 796 - 800, 2006.
• Davidson, E.H., The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, Elsevier, 2006.
• Levine, M. and Davidson, E. H. Gene regulatory networks for development. Proc. Natl. Acad. Sci. USA 102, 4936-4942, 2005.
• Stathopoulos A, Levine M. Genomic regulatory networks and animal development. Dev Cell. 9(4), 449-62, Oct 2005.

Other Systems

Another system that demonstrates BioTapestry's capabilities for representing systems that exhibit increasing complexity over time is the network for mouse ventral neural tube specification (Vokes et.al., 2007):

With Version 2, BioTapestry's auto layout templates and resizable workspace make it a good tool for working with much larger networks, such as this network for Halobacterium salinarum from the Baliga Lab at the ISB:

BioTapestry's framework for creating sets of submodels is well-suited for organizing such large networks in an understandable way, as this detail from the above Halobacterium salinarum network demonstrates:

Significant features include:

• Supporting data resulting from the perturbation of expression of specific genes, measured in any way (QPCR, genetics, etc.), can be easily accessed for each gene. Temporal and spatial expression results are also accessible.
• BioTapestry can portray hourly, localized views of the network during development based on data tables describing the network's local and temporal states.
• BioTapestry can automatically layout the set of network models from lists of interactions provided either through interactive dialogs or comma-separated value (CSV) files exported by spreadsheet programs.

If you have a question about how something works in BioTapestry, consult the new online BioTapestry Frequently Asked Questions list. If you have a question that isn't covered there, then please let us know so we can add it to the list.

New Online Tutorials

The original BioTapestry Tutorial was available as a single PDF download. The tutorials are now being presented as a series of smaller online tutorials that focus on different aspects of the software. For example, for newcomers, the new Quick Start Tutorial covers the minimum material you need to get started working with BioTapestry. There are other tutorials that build upon that introductory material and cover more advanced topics.

Current Online Tutorial List

Quick Start Tutorial: This is the best way to learn the basics for using BioTapestry. It covers the minimum material you need to draw a top-level network model and then extend that into a multi-level model hierarchy. If you a newcomer, this will be the best way to begin.

Dynamic Submodels Tutorial: This tutorial covers how to create dynamic submodels, where data tables are used to automatically determine the active network elements, and the user can manipulate a time slider to see a dynamic presentation of the network behavior. This is the approach used for the S. purpuratus endomesoderm model.

Tutorial on Building Networks from Interaction Tables: This tutorial covers how to build and layout networks automatically from lists of interactions, which are specified using interactive dialogs. It also covers how to use several tools that can help with common network layout tasks; these are useful even if you are drawing all your networks manually.

Building Networks from Comma-Separated Value Files: This tutorial covers how to build and layout networks automatically using lists of interaction commands that are created in a spreadsheet program such as Microsoft Excel, and then imported into BioTapestry as a comma-separated value (CSV) file.

Tutorial on Using and Creating Paths: This tutorial covers a new feature of BioTapestry Version 2.1 that allows you to define named paths through the model hierarchy. You may have situations where you have a complex model hierarchy, and you want to be able to easily progress through a series of closely related submodels that could be widely dispersed across that hierarchy. Paths allow you to do this.

Other Documentation

For more in-depth treatment of topics, the BioTapestry User's Guide (PDF format) is available. This guide provides the same information as the online BioTapestry help system. The current version is Revision A (August 16, 2005). It has not been updated yet to reflect Version 2. A better bet for finding out about the details of BioTapestry is to check the BioTapestry Frequently Asked Questions.

Obsolete Documentation

The documentation listed below is obsolete; it is based upon BioTapestry Version 1.

What's New

Version 2.1.0 was released on 7/23/07. It includes two new significant features: optional 2D model images, and user-specified paths through the model hierarchy. These features are highlighted in this screen shot:

Changes also include:

• Bug fixes

More in-depth discussion of these new features can be found in the revised

Version 2.0.2 was released on 6/14/07. Changes include:

• More robust error checking and diagnostics for file input and output
• User is asked before overwriting existing files on most output operations
• Added an "Open Recent Files" menu
• Added finer-grained zoom settings to optimize sizing with "Zoom to Model" action
• Bug fix for rendering intercellular nodes with variable activity levels
• Code is signed with new security certificates

Version 2.0.1 was released on 5/22/07. Changes include:

• Fixed problem reading and writing files on Windows with Java 1.6
• Changed URL to www.BioTapestry.org in the HelloWebPlugIn example
• Notes associated with expression profiles now appear in the experimental data window

Version 2.0.0 was released on 5/17/07. It includes many new enhancements and bug fixes, including:

• Improved Automatic Layout
• Improved Link Rendering
• Configurable Workspace Size
• User-Configurable Time Units
• New Node and Link Activity Level Features
• Improved Zoom Features
• Improved Navigation Options
• Many More...

Release Notes for earlier versions are available in the Old Release Notes listing

• Longabaugh, W.J.R., Davidson, E.H., Bolouri, H. Computational representation of developmental genetic regulatory networks. Dev. Biol. 283, 1-16, 2005.
• Longabaugh, W., Bolouri, H. Understanding the Dynamic Behavior of Genetic Regulatory Networks by Functional Decomposition. Current Genomics, Volume 7, Number 6, 333-341, 2006.

• Making the creation of submodels easier, more intuitive, and more flexible.
• Making the ties to experimental data more flexible, thus allowing BioTapestry to handle a wider range of experimental data types.
• Tying the abstract network representations to 3D models of the developing organism.
• Addressing scalability issues, including adding support for arbitrary groupings of network elements.
• Significantly improved support for Systems Biology Markup Language (SBML) export and ties to the Dizzy simulation engine.

If you have suggestions for other enhancements that would make BioTapestry more useful to you, please let us know.

Version 2 URL change: If you are running a previous version of BioTapestry using a desktop shortcut icon that was installed when you first downloaded it, that version will no longer work; the previous URL for the BioTapestry web site is being retired. You should delete your previous shortcut and launch the program from the link at the top of this page.

If you have previous BioTapestry files that are not loading into the new version correctly, or run into any other show-stopping bugs with the new version, the previous version (0.97.4) is still available HERE for the time being. PLEASE let us know if you are running into problems that require you to use this version, so we can resolve the issue.

BioTapestry is currently available as a downloadable application using Java Web Start, which is bundled with any recent version of the Java Runtime Environment (JRE). If you have problems launching BioTapestry, you will need to install the JRE. BioTapestry is known to work with JREs v1.4.1_01 and v1.4.2_02; there are known problems with some other versions v1.4.1_0x. It also works with JRE v1.5, though there have been some cases of the screen not refreshing correctly. Version 2 also appears to work correctly with JRE v1.6 on Linux and (with version 2.0.1) Windows. If you need to install a recent JRE on your computer, you can download it from here (click the "Free Java Download" button) or here.

BioTapestry is known to work on Windows XP and Linux (Red Hat 8.0 and Fedora Core Releases 1 & 3). While there are some known glitches with Mac OS X version 10.2, it appears these have been fixed in version 10.3, and it also works on 10.4. There have been reported problems with launching the application directly from a web browser (e.g. Safari) on Mac 10.3; the workaround is discussed above. In general, BioTapestry should function properly on most platforms for which the Sun JRE is available. If you run into any issues with getting the application to run on your computer, please send a report to biotapestry at systemsbiology dot org so we can address your problem.

A software release that can be installed locally is anticipated. In the meantime, the Java Web Start version can be run unconnected from the network. Also, Web Start provides you with the option of starting BioTapestry from an icon on your desktop, so it behaves very much like a locally installed application.

This software is licensed under the GNU Lesser General Public License (LGPL), which is a standard "free software" and "open source" license. A copy of the license agreement is available online here.

BioTapestry is under continual development, and despite our best efforts there are bugs in the software. Please be advised that, as stated in the license agreement, the Institute for Systems Biology and the authors disclaim any liability stemming from the use of this software.