Click HERE to run the BioTapestry Editor (version 3.0.5, released 11/11/08) using Java Web Start.

If you haven't used BioTapestry before, you can get up to speed on the basics by going through the online Quick Start Tutorial. The BioTapestry Frequently Asked Questions 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.

Other Interactive Web Models Around the Web

• Mouse ventral neural tube specification at the McMahon Lab at Harvard.
• Environment And Gene Regulatory Influence Network (EGRIN) for Halobacterium salinarum NRC-1 at the Baliga Lab at the Institute for Systems Biology.
• T-cell gene regulatory network, a collaboration between Ellen Rothenberg and Hamid Bolouri at Caltech.
• Zebrafish developmental gene regulatory network at the Yuh Lab at the National Health Research Institute, Taiwan.

Papers and Books Using BioTapestry

• Morley, R.H., Lachani, K., Keefe, D., Gilchrist, M.J., Flicek, P., Smith, J.C., Wardle, F.C. A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation. Proc. Natl. Acad. Sci. USA 106, 3829-3834, 2009.
• Tamplin, O.J., Kinzel, D., Cox, B.J., Bell, C.E., Rossant, J., Lickert, H. Microarray analysis of Foxa2 mutant mouse embryos reveals novel gene expression and inductive roles for the gastrula organizer and its derivatives. BMC Genomics 9:511, 2008.
• Materna, S.C., Oliveri, P. A protocol for unraveling gene regulatory networks. Nature Protocols 3(12), 1876-1887, 2008.
• Smith, J., Davidson, E.H. Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo. Proc. Natl. Acad. Sci. USA 105, 20089-20094, 2008.
• Nikitina, N., Sauka-Spengler, T., Bronner-Fraser, M. Dissecting early regulatory relationships in the lamprey neural crest gene network. Proc. Natl. Acad. Sci. USA 105, 20083-20088, 2008.
• Ririe, T.O., Fernandes, J.S., Sternberg, P.W. The Caenorhabditis elegans vulva: A post-embryonic gene regulatory network controlling organogenesis. Proc. Natl. Acad. Sci. USA 105, 20095-20099, 2008.
• Georgescu, C., Longabaugh, W.J.R., Scripture-Adams, D.D., David-Fung, E.-S., Yui, M.A., Zarnegar, M.A., Bolouri, H., Rothenberg, E.V. A gene regulatory network armature for T lymphocyte specification. Proc. Natl. Acad. Sci. USA 105, 20100-20105, 2008.
• Bolouri, H. Computational Modeling of Gene Regulatory Networks: A Primer, Imperial College Press, 2008.
• Kioussi, C., Gross, M.K. How to Build Transcriptional Network Models of Mammalian Pattern Formation. PLoS ONE 3(5), e2179, 2008.
• Niessen, K., Karsan, A. Notch Signaling in Cardiac Development. Circulation Research 102, 1169-1181, 2008.
• Hoffman, B.G., Zavaglia, B., Witzsche, J., Ruiz de Algara, T., Beach, M., Hoodless, P.A., Jones, S.J.M., Marra, M.A., Helgason, C.D. Identification of transcripts with enriched expression in the developing and adult pancreas. Genome Biology 9(6), R99, 2008.
• Bonneau, R., Facciotti, M.T., Reiss, D.J., Schmid, A.K., Pan, M., Kaur, A., Thorsson, V., Shannon, P., Johnson, M.H., Bare, J.C., Longabaugh, W., Vuthoori, M., Whitehead, K., Madar, A., Suzuki, L., Mori, T., Chang, D.-E., DiRuggiero, J., Johnson, C.H., Hood, L., Baliga, N.S. A predictive model for transcriptional control of physiology in a free living cell. Cell 131(7), 1354-65, Dec 28 2007.
• 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.
• Kühn, C., Kühn, A., Poustka, A.J., Klipp, E. Modeling development: spikes of the sea urchin. Genome Inform. 18, 75-84, 2007.
• Mori, A.D., Zhu, Y., Vahora, I., Nieman, B., Koshiba-Takeuchi, K., Davidson, L., Anne Pizard, A., Seidman, J.G., Seidman, C.E., Chen, X.J., Henkelman, R.M., Bruneau, B.G. Tbx5-dependent rheostatic control of cardiac gene expression and morphogenesis Dev. Biol. 297(2), 566-586, 2006.
• Wellmer, F., Alves-Ferreira, M., Dubois, A., Riechmann, J.L., Meyerowitz, E.M. 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.
• Koshiba-Takeuchi, K., Takeuchi, J.K., Arruda, E.P., Kathiriya, I.S., Mo, R., Hui, C-c., Srivastava, D., Bruneau, B.G. Cooperative and antagonistic interactions between Sall4 and Tbx5 pattern the mouse limb and heart. Nature Genetics 38, 175-183, 2005.
• 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.

Please let us know if you are using BioTapestry for your research!

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):

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 (Bonneau et.al., 2007):

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 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.

Online Tutorials

A series of short tutorials that focus on different aspects of the software are available online. For example, for newcomers, the 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 multi-level hierarchy of network models, and now (as of March 18, 2009) uses the latest Version 3 features that simplify network construction. If you are a newcomer, this will be the best way to begin.

(The original Revision A of the Quick Start Tutorial is still available here if you want to learn about how to build networks using the original "top-down" method.)

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 the feature of BioTapestry 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

The BioTapestry User's Guide (PDF format) provides the same information as the BioTapestry help system currently built into the Editor. However, the User Guide is Revision A (August 16, 2005), and has not been updated to the current version of BioTapestry. A better bet for finding out about the details of BioTapestry is to check the BioTapestry Frequently Asked Questions.

Obsolete Documentation

The original Version 1 documention is still available on this page for obsolete documentation.

What's New

Version 3.0.5 was released on 11/11/08. It is an incremental release on Version 3.0 (see below) that fixes bugs and adds a few new features:

• The Apple Mac 9/08 Java update issue was resolved
• The batch mode for generating images supports a new -compress option for CSV loads
• New Tools->Show count of network elements feature provides counts of genes, nodes, and links in a model
• There are now ten different evidence levels available for links (up from three)
• Significant improvements in memory footprint and execution speed for large CSV imports and network layout operations
• Several bug fixes, both for the Editor and the Viewer

Version 3.0 was released on 09/30/08. It includes several significant new features designed to make model creation more flexible, search more powerful, and long-term maintenance easier. The biggest change is that genes, nodes, and links can now be drawn at any level of the model hierarchy, where the user has the option of selecting from existing network elements or creating completely new ones:

Other new features include:

• It is now possible to change a link's source or target node in top-level models
• The user can globally add a gene or node using a single dialog
• There is now a global gene/node/linkage search and navigation tool
• There are several new region operations, including explicit region ordering, full network import, single-region compression and expansion, and region moving
• The Experimental Data display can now be stocked by specifying a list of URLs for simple web pages
• Layout synchronization has been improved and made more flexible
• The root model layout can be changed to match child model layouts
• The BioTapestry Viewer has been enhanced to include the search and network exploration tools available in the Editor
• The program supports a new batch mode, useful for generating network images on a server
• The automatic link layout algorithms have been improved
• Several efficiency improvements and bug fixes
• Lots more!

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

Older release notes are also available for Version 2 and for even older versions.

Please cite BioTapestry using [Longabaugh et.al. 2005] or [Longabaugh et.al. 2009] if you use BioTapestry in your research.

• 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.
• Longabaugh, W.J.R., Davidson, E.H., Bolouri, H. Visualization, documentation, analysis, and communication of large-scale gene regulatory networks. Biochim. Biophys. Acta, in press, 2009.

• Addressing scalability issues, including adding support for arbitrary high-level abstract groupings of network elements.
• 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.
• 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.

If problems arise due to the version of Java installed on your computer, see the section below to learn about obtaining a supported version of Java.

If the program is failing to run, or if you are not getting the correct version, it is a good idea to remove any locally cached previous versions of the software that are on your computer. You can do this by running the Java Web Start Applications Manager/Cache Viewer, and deleting the existing local copy of BioTapestry. Finding and running the Manager depends on your operating system and Java version. This section of the FAQ details how to find and run the Manager program:

and this section talks about deleting the current cache copy:

IMPORTANT: In addition to deleting the BioTapestry Editor, you should also delete the Sun JavaHelp Support library if it is listed and you are having problems getting BioTapestry to run.

Since the BioTapestry Editor needs to be able to load and save edited BioTapestry (.btp) files from your hard drive, you are asked if you want to allow this before running the application. The code consists of two packages, one signed by the Institute for Systems Biology, and one signed by Sun Microsystems. You must accept these certificates to be able to use the program. If you are running on a Mac and find you need to accept these certificates every time you run the program, consult this section of the FAQ to find out how to avoid this. Please e-mail biotapestry at systemsbiology dot org if you have any questions about this requirement to accept certificates.

If you have previous BioTapestry files that are not loading into the current version correctly, or run into any other show-stopping bugs with the new version, the previous version (2.1.0) is still available HERE. Note that .btp files created by the current version may not load correctly in this older version. PLEASE let us know if you are running into problems that require you to use this version, so we can resolve the issue.

URL change: If you are running an early (pre-v2) 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 was retired in 2007. You should delete your previous shortcut and launch the program from the link at the top of this page.

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 make sure you have installed the JRE. The JRE can be download from here (click the "Free Java Download" button) or here if you want to select from a wide variety of versions. On MacOS X, Java should already be factory-installed on new computers.

Please note that although BioTapestry is launched on your computer by connecting to the www.BioTapestry.org web server to download the program and check to make sure you have the latest updates, all of your files stay on your personal machine. In the future, we plan to provide a BioTapestry package that can be installed locally on your computer. 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.

BioTapestry is designed to work with all versions of Java available since ~2003, including Java versions v1.4.2, 1.5 and 1.6. If you encounter problems with a particular version of Java, please let us know about it; switching to a different version should solve any version-related problems.

BioTapestry is known to work on Windows (XP, Vista), Linux (many versions, including Red Hat 8.0, Fedora Core Releases 1 & 3, CentOS 5), and MacOS X (version 10.2 had some quirks, but versions 10.3 and newer should work fine).

NOTE for Mac users: There have been reports that launching BioTapestry from Safari in MacOS 10.3 may fail after the application has been downloaded; you get an incorrect error message saying that the correct version of Java is not present. If this occurs, you can still run BioTapestry from the Java Web Start control panel. Run Applications->Utilities->Java->Java Web Start, select BioTapestry Editor, and click the Start button.

The BioTapestry Viewer can be installed on your web server to provide a read-only interactive interface for sharing your network on the web. A ZIP archive distribution that contains both the stripped-down .jar file for the current version (now 3.0.5) of the Viewer, as well as all supporting files, and a step-by-step HOWTO of what is involved in deploying the Viewer, is available here. (NOTE: right-click & use "Save Link As..."). If the HOWTO doesn't answer all your questions, please post a message in the BioTapestry-users Google group, or contact us directly.

If your deployment is on a publically available web site, please let us know about it. We'd like to link to your viewer page off the BioTapestry home page. Even if you prefer not to be linked to, we appreciate being able to keep track of viewer deployments. Thanks!

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.