William Longabaugh and Hamid Bolouri, Institute for Systems Biology
Davidson Lab, California Institute of Technology
A New Way to Run BioTapestry
We are now providing BioTapestry as a locally installable executable, available from the Download section below.
The BioTapestry Editor has traditionally been available as a Java application that is launched from your web browser using Java Web Start; this method is still available by clicking on the link below. However, some web browsers are beginning to disable default Java support due to security issues, particularly for older operating system versions. In those cases, it is not advisable to enable Java in your browser just to be able to run BioTapestry. Therefore, we are now providing standard downloadable executables, so that these ongoing browser support problems will no longer be an issue for using BioTapestry. Go to the Download section, get the appropriate file for your operating system, and install a local copy of the BioTapestry Editor program directly on your computer. If you go this route, please try to keep your version of BioTapestry up-to-date, as the automatic download of new versions provided by Java Web Start will not apply.
Running BioTapestry Online Using Java Web Start
As long as your web browser supports Java Web Start, the following link will launch the BioTapestry Editor without having to first download and install it.
Click HERE to run the BioTapestry Editor (version 6.0.0, released 12/17/12, REQUIRES Java 1.5 or above) using Java Web Start.
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.
NOTE: Your computer needs at least Java Version 1.5 installed to run using the above link. However, it is still possible to run a version that works with Java 1.4 if you use a launch link in the Alternative Launch Options section below; see the discussion there. NOTE: It is planned that Version 6 will be the last version of BioTapestry that can be run with Java 1.4.
If you need to use an older version of BioTapestry prior to Version 6, you can still download older versions of the executable from the Archived Executables page.
BioTapestry in Action
BioTapestry 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!
BioTapestry 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:
BioTapestry is written in Java, and can be run on your Windows, Mac, or Linux computer. Note that all these downloadable executables require that you first download and install the Java Runtime Environment (JRE), which 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 was already factory-installed on new all Macs prior to Version 10.7 (Lion). With newer Macs, you will need to go to the above download pages as well.
If you need to download and install previous versions of BioTapestry, they are available from the Archived Executables page. However, these versions are no longer supported. If you have a problem, please upgrade to the latest version and see if that fixes the problem before sending us a bug report.
BioTapestry Frequently Asked Questions
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.
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.
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.
The original Version 1 documentation is still available on this page for obsolete documentation.
Alternative Launch Options
For Java 1.4 Users
Click HERE to run the BioTapestry Editor (version 6.0.0, released 12/17/12, operates on Java 1.4 or above) using Java Web Start.
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. Note that Version 6 is the last version of BioTapestry that will support Java 1.4.
We no longer provide a Java Web Start link for the previous version of BioTapestry. If you need to run an older version, please download and install an archived executable from the Archived Executables page. Remember, BioTapestry .btp files created and saved using the current version are typically not readable by a previous version. If you are running into problems with the latest version that forces you to use an older version, please report the problem so we can fix it. Thanks!
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 6.0.0 was released on 12/17/12. It introduces a number of new features, mostly related to automatic layout and link drawing and layout helper tools. The Version 6 Release Notes provide complete details.
Of particular note is the new overlay-driven layout feature. The user can create a high-level organization of the network using a network overlay containing a set of network modules and module links. After adding nodes to the modules, the system will automatically create a layout conforming to the specified organization. Consider the following small example, where nodes have been added to a set of modules defined in a network overlay:
Using the overlay-driven layout feature, the network can be laid out automatically in a way that follows this organization:
Other new features include:
With 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.
Starting with version 5.0.3, the recommended way to run BioTapestry is by downloading and installing it on your computer. If you encounter problems with the Java Web Start method, consider a local install. If you are having problems with Web Start, 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:
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 (5.0.3) can still be dowloaded from the Archived Executables page.
The BioTapestry downloadable executables and Web Start version require a minimum of Java Version 1.5. There is a legacy version that still works with version 1.4.2 provided above in the Alternative Links section, but this is not recommended and will be discontinued after BioTapestry Version 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. To run BioTapestry, you will first need to install the Java Runtime Environment (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 was already factory-installed on new all Macs prior to Version 10.7 (Lion). With newer Macs, you will need to go to the above download pages as well.
BioTapestry is known to work on Windows, Linux, and MacOS X. If you are having problems getting it to launch, you can try installing more recent version of Java.
BioTapestry for Gaggle
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 6.0.0, released 12/17/12, 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.
BioTapestry 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
Starting with Version 6.0, the BioTapestry Viewer can be embedded as a visualization component inside another
Java program. An example of how to do this is shown in the class
Source CodeA tar file of the current version of the source code is available here.
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 (6.0.0) 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:
Windows executable created using the Launch4j Executable Wrapper by Grzegorz Kowal (http://sourceforge.net/projects/launch4j/).
BioTapestry development was previously supported by the National Institute of General Medical Sciences under Award Number R01GM061005. It is currently supported by the Eunice Kennedy Shriver National Institute Of Child Health & Human Development of the National Institutes of Health under Award Number R01HD073113. The content of this web site is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
License and Disclaimer
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.
The downloadable Windows executable is wrapped in code that is made available by Grzegorz Kowal under this MIT License.
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: December 17, 2012
biotapestry at systemsbiology dot org