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William Longabaugh and Hamid Bolouri, Institute for Systems BiologyDavidson Lab, California Institute of Technology |
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Running BioTapestryClick 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:
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. BioTapestry in ActionBioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks. Here are some uses of BioTapestry:
Interactive Web Models from the Davidson Lab
Other Interactive Web Models Around the Web
Papers and Books Using BioTapestry
Please let us know if you are using BioTapestry for your research! DescriptionBioTapestry is designed around the concept of a developmental network model, and is intended to deal with large scale models with consistency and clarity. It is capable of representing systems that exhibit increasing complexity over time, such as the genetic regulatory network controlling endomesoderm development in sea urchin embryos:
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:
DocumentationBioTapestry Frequently Asked QuestionsIf 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 TutorialsA 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 ListQuick 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 DocumentationThe 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 DocumentationThe original Version 1 documention is still available on this page for obsolete documentation. Alternative Launch OptionsFor Java 1.4 UsersClick 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 VersionClick 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 VersionA Gaggle-enabled instance of BioTapestry can be launched from this page. See the BioTapestry for Gaggle section below for the link and more information. What's NewVersion 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:
Older release notes are also available for Version 4, Version 3, Version 2 and for even older versions. PublicationsPlease cite BioTapestry using [Longabaugh et.al. 2005] or [Longabaugh et.al. 2009] if you use BioTapestry in your research.
RoadmapWith 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 changes in the network state over time. Work is ongoing to create a version that will analyze experimental spatial/temporal expression data and raw perturbation data, guide the user through the process of deciding what network connections should be included in the network diagram, and then automatically creating the full dynamic network hierarchy. Other planned enhancements include:
If you have suggestions for other enhancements that would make BioTapestry more useful to you, please let us know. Problems Running It?
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 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 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. Supported PlatformsBioTapestry 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. BioTapestry for GaggleA 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. Developer's NotesBioTapestry supports user-written plugins for creating a customized experimental data display. There are example plugins in the source code tree (see below) that can serve as a starting point. If you need any guidance on building plugins, feel free to contact us.
Starting with Version 4.0, BioTapestry can be called in batch mode from
within another Java program to generate images from a comma-separated-value
specification coming from a provided InputStream. A small example is provided
in the source code tree (see below) in the
Source CodeA tar file of the current version of the source code is available here.BioTapestry ViewerThe 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! Send FeedbackWe are eager to receive any feedback you wish to send us, such as questions, bug reports, feature requests, and usability issues. The best place to do this is in the BioTapestry-users Google group. However, you can also email us privately at:
BioTapestry-users Google GroupThis group is intended to give BioTapestry users a place to discuss the program, get help with questions, ask for program enhancements, provide feedback, and share tips with each other on using the software. The group home page is:
CreditsBioTapestry is a joint project of the Institute for Systems Biology and the Davidson Lab at Caltech. Primary contributors are:
BioTapestry is supported by a grant from NIH General Medical. License and DisclaimerThis 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. |
Last updated: May 19, 2011
biotapestry at systemsbiology dot org