Click HERE to run the BioTapestry Editor (version 5.0.2, released 02/02/11, REQUIRES Java 1.5 or above) using Java Web Start.

NOTE: Your computer needs at least Java Version 1.5 installed to run using the above link. Since Java 1.5 has been out since ~2004, this should not be an issue with most users, but:

• If you need to upgrade, information is provided below on getting the current version of Java.
• If you cannot or do not want to upgrade, and your computer only has Java 1.4 installed, you can still use a launch link in the Alternative Launch Options section below; see the discussion there.

NEW USERS: 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.

• 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.
• phiSITE: Database of Gene Regulation in Bacteriophages at the Institute of Molecular Biology of the Slovak Academy of Sciences. Enter a search term, e.g. "Enterobacteria" or "phage", to see entries with live BioTapestry links.
• The Pigment Cell Gene Network at the Pavan Group at The National Human Genome Research Institute.

Papers and Books Using BioTapestry

• Inoue, T., Sternberg, P.W. C. elegans BED domain transcription factor BED-3 controls lineage-specific cell proliferation during organogenesis. Dev Biol. 338(2), 226-36, 2010.
• Danielli, A., Amore, G., Scarlato, V. Built Shallow to Maintain Homeostasis and Persistent Infection: Insight into the Transcriptional Regulatory Network of the Gastric Human Pathogen Helicobacter pylori. PLoS Pathog 6(6), e1000938, 2010. (NOTE: Bundled .btp file provided in supplemental materials.)
• Baxter, L.L., Moreland, R.T., Nguyen, A.D., Wolfsberg, T.G., Pavan, W.J. A curated online resource for SOX10 and pigment cell molecular genetic pathways. Database (Oxford) (2010), baq025, 2010.
• Klucar, L., Stano, M., Hajduk, M. phiSITE: database of gene regulation in bacteriophages. Nucleic Acids Res. (38), D366-70, 2010.
• Pruszak, J., Isacson, O. Molecular and Cellular Determinants for Generating ES-Cell Derived Dopamine Neurons for Cell Therapy. Adv Exp Med Biol. 651, 112-23, 2009.
• Wahl, M.E., Hahn, J., Gora, K., Davidson, E.H., Oliveri, P. The cis-regulatory system of the tbrain gene: Alternative use of multiple modules to promote skeletogenic expression in the sea urchin embryo. Dev Biol. 335(2), 428-41, 2009.
• Kühn, C., Wierling, C., Kühn, A., Klipp, E., Panopoulou, G., Lehrach, H., Poustka, A.J. Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network. BMC Syst Biol. 3, 83, 2009.
• Sansom, S.N., Griffiths, D.S., Faedo, A., Kleinjan, D.-J., Ruan, Y., Smith, J., van Heyningen, V., Rubenstein, J.L., Livesey, F.J. The Level of the Transcription Factor Pax6 Is Essential for Controlling the Balance between Neural Stem Cell Self-Renewal and Neurogenesis. PLoS Genet 5(6), e1000511, 2009.
• Morohashi, K., Grotewold, E. A systems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors. PLoS Genet 5(2), e1000396, 2009.
• Su, Y.H., Li, E., Geiss, G.K., Longabaugh, W.J., Krämer, A., Davidson, E.H. A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. Dev. Biol. 329(2), 410-421, 2009.
• Chan, T.-M., Longabaugh, W., Bolouri, H., Chen, H.-L., Tseng, W.-F., Chao, C.-H., Jang, T.-H., Lin, Y.-I., Hung, S.-C., Wang, H.-D., Yuh, C.-H. Developmental gene regulatory networks in the zebrafish embryo. Biochim. Biophys. Acta, 1789(4), 279-98, 2009.
• 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.
• Bolouri, H., Computational Modeling of Gene Regulatory Networks: a Primer, Imperial College Press, 2008.
• 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.
• Huang, T.S., Hsieh, J.Y., Wu, Y.H., Jen, C.H., Tsuang, Y.H., Chiou, S.H., Partanen, J., Anderson, H., Jaatinen, T., Yu, Y.H., Wang, H.W. Functional network reconstruction reveals somatic stemness genetic maps and dedifferentiation-like transcriptome reprogramming induced by GATA2. Stem Cells 26(5), 1186-201, 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. Regulation of spblimp1/krox1a, an alternatively transcribed isoform expressed in midgut and hindgut of the sea urchin gastrula. Gene Expr. Patterns 7(1-2), 1-7, 2007.
• 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., 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):

Users can annotate network elements with the supporting experimental evidence, as is shown here for the T-cell gene regulatory network (Georgescu et. al., 2008):

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 or link. 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 (as of March 18, 2009) uses the 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 Revision A (August 16, 2005) (PDF format) provides the information that was formerly included in the BioTapestry Editor's Help System. Starting in Version 4.0, the bundled Help System was dropped due to ongoing compatibility problems with recently released Java versions. Also, the material was not being kept up-to-date, with all revision work dedicated to the online documentation . A better bet for finding out about the details of BioTapestry is to check the BioTapestry Frequently Asked Questions or the online tutorials.

Obsolete Documentation

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

Click HERE to run the BioTapestry Editor (version 5.0.2, released 02/02/11, operates on Java 1.4 or above) using Java Web Start.

The newer code-signing security certificates that are now available, and which the BioTapestry Editor requires to run using Java Web Start, are not supported by Java Version 1.4. This is why the mainstream BioTapestry version now requires at least Java 1.5. For those users who must use Java 1.4, the Java 1.4 link provided here will allow you to run exactly the same current version of BioTapestry, but you will be warned that the code has been signed by an expired security certificate.

Previous Version

Click HERE to run the BioTapestry Editor (version 4.1.0, released 12/03/09, operates on Java 1.5 or above) using Java Web Start.

This link is for the previous major release version of BioTapestry. If you encounter any problems with the new version, or have a particular reason not to upgrade just yet, you can use the above link. However, this version will not be kept online indefinitely. Remember, BioTapestry .btp files created and saved using the current version are typically not readable by this previous version. If you are running into problems with the latest version that forces you to use this link, please report the problem so we can fix it. Thanks!

Gaggle-Enabled Version

A Gaggle-enabled instance of BioTapestry can be launched from this page. See the BioTapestry for Gaggle section below for the link and more information.

Version 5.0.2 was released on 02/02/11. It incorporates a new feature for optionally tagging expression table entries as "Maternal", "Zygotic", or both, and then using this information to selectively activate nodes in a dynamic submodel. Also, bug fixes for the BioTapestry Viewer and ImageGeneratorApplication have been included. Consult the Version 5 Release Notes for more details.

Version 5.0.1 was released on 11/24/10. It incorporates improvements in rendering tables on the Mac, as well as bug fixes to the perturbation data management system. Consult the Version 5 Release Notes for more details.

Version 5.0.0 was released on 11/17/10. The significant new feature is the overhaul of the perturbation data framework. It has been upgraded to have improved usability, generality, and handling of user input errors. The new interface makes it easier to search, sort, and maintain the data:

Other new features include:

• Changing properties for multiple selections
• Support for perturbed spatial and temporal expression data
• Per-link specification of experimental data
• Main menu access to "right-click" popup menus
• Experimental data display improvements
• Spatial and temporal expression data export to CSV
• Bug fixes

Older release notes are also available for Version 4, Version 3, 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, 1789(4), 363-74, 2009.

• 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 you run into any issues with getting BioTapestry to run on your computer that you cannot resolve, or have a program crash, please send a report to biotapestry at systemsbiology dot org or post a message on the BioTapestry-users Google group so we can address your problem. Browsing the Google group is a good way of finding out about any recently identified compatibilty issues and what workarounds have been developed to addess them.

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:

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 BioTapestry code has been signed by the Institute for Systems Biology as a guarantee that the program you are running has not been tampered with or altered, and you must accept this certificate to be able to use the program. If you are running on a Mac and find you need to accept the certificate 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 the certificate.

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 (4.1.0) can be launched from the link provided above in the Alternative Links section. 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.

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 downloaded 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, though you will need to run the alternative start link provided above in the Alternative Links section to run with Java 1.4. 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. MacOS 10.2 had some quirks, but versions 10.3 and newer generally work fine. With the Ubuntu 8.0.4 Linux distribution with Firefox and Java 1.5, you will need to upgrade to Java 1.6 to get things to work correctly.

A brief introduction to using BioTapestry with Gaggle is provided here; you should read it first.

After first launching the Gaggle Boss, click HERE to run the Gaggle-enabled BioTapestry Editor (version 5.0.2, released 02/02/11, requires Java 1.5 or above) using Java Web Start.

The Gaggle is a framework, developed at the Institute for Systems Biology, "...for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data." The BioTapestry Editor supports Gaggle, and the above link will launch the program with the Gaggle feature enabled (species is set to "unknown"). IMPORTANT: As noted above, you MUST start the Gaggle Boss before launching the BioTapestry Editor; the Boss auto-start feature is not currently supported. Launch the Boss and other Gaggle-aware applications using the links on the Gaggle Blank Slate page.

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 5.0.2) 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.