ISB Logo BioTapestry Caltech Logo

William Longabaugh and Hamid Bolouri, Institute for Systems Biology

Davidson Lab, California Institute of Technology


Contents
Running BioTapestry
BioTapestry in Action
Description
Documentation
What's New
Publications
Roadmap
Problems Running It?
Supported Platforms
Developer's Notes
Source Code
Send Feedback
Get on the Mailing List
Credits
License and Disclaimer

New Version 2.1 Now Available

Running BioTapestry

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.


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

Papers and Books Using BioTapestry

Other Systems

BioTapestry is also being used to support ongoing research in: Halobacterium salinarum, yeast, zebrafish, T-cell development, the pancreas, and other systems. Please let us know if you are using BioTapestry for your research!


Description

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:

Endomesoderm Screenshot

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):

Mouse Ventral Neural Tube Screenshot

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:

Halobacterium Network

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:

Halobacterium Network Detail

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.


Documentation

New BioTapestry Frequently Asked Questions

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.

Quick Start Tutorial Resource File (right-click & use "Save Link As...")
Completed BioTapestry ModelQuickStartModel.btp

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.

Dynamic Submodels Tutorial Resource File (right-click & use "Save Link As...")
Starting BioTapestry ModelTutorialModelV2.btp
Time Course Data FileTutorialExpressionDataV2.xml
Temporal Input Data FileTutorialInputDataV2.xml
Completed BioTapestry ModelTutorialModelV2-Finished.btp

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.

Interaction Tables Tutorial Resource File (right-click & use "Save Link As...")
Completed BioTapestry ModelFromDialogTutorial-Finished.btp

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.

CSV Tutorial Resource File (right-click & use "Save Link As...")
First-Pass CSV Input FileTutorialSpreadsheetVer2.csv
Second-Pass CSV Input FileTutorialSpreadsheetVer2Pass2.csv
Completed (First-Pass Only) BioTapestry ModelCSVTutorialModel-Finished.btp

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.

Paths Tutorial Resource File (right-click & use "Save Link As...")
Starting BioTapestry ModelPathTutorialInitialModel.btp
Completed BioTapestry ModelPathTutorialModel-Finished.btp

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.

Documentation Description File
User's Guide (Revision A: August 16, 2005)UserGuide.pdf
Comma-Separated Value (CSV) Input File Format DescriptionCSVGuide.txt

Obsolete Documentation

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

Obsolete Documentation Description File
Original PDF BioTapestry Tutorial (Revision C: July 12, 2005)BioTapestryTutorial.pdf
Time Course Data File for Original TutorialTutorialExpressionData.xml
Temporal Input Data File for Original TutorialTutorialInputData.xml
Completed BioTapestry Original Tutorial Network Model (Built by drawing)TutorialModel.btp
Completed BioTapestry Original Tutorial Network Model #2 (Built from interaction tables)TutorialModelFromTables.btp
Sample Comma-Separated Value Spreadsheet Output for Original TutorialTutorialSpreadsheet.csv


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:

New Version 2.1 Features Highlighted
Changes also include:
  • Bug fixes
More in-depth discussion of these new features can be found in the revised
Version 2.1 Release Notes

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...
A full listing of the new features can be found in the Version 2.1 Release Notes

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


Publications

DB Cover Art



Roadmap

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.

The Version 2 release in May 2007 includes many new features to improve the usability, scalability, and functionality of the program, and includes several features requested by BioTapestry's users.

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?

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 can e-mail biotapestry at systemsbiology dot org if you have any questions about this requirement.

NOTE for Mac users: Although the BioTapestry Editor runs on MacOS X, there have been reports that launching it from your web browser in 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.

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.


Supported Platforms

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.


Developer's Notes

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.


Source Code

A tar file of the current version of the source code is available
here.

Send Feedback

We are eager to receive any feedback you wish to send us, such as questions, bug reports, feature requests, and usability issues. Please send us email at:
biotapestry at systemsbiology dot org

Get on the Mailing List

If you want to receive announcements regarding BioTapestry development and releases, just let us know at:
biotapestry at systemsbiology dot org

Credits

BioTapestry is a joint project of the Institute for Systems Biology and the Davidson Lab at Caltech. Primary contributors are:
  • William Longabaugh
  • Eric Davidson
  • Hamid Bolouri
Also, Stephen Ramsey of the Institute for Systems Biology has provided valuable assistance with SBML output and simulation support.

BioTapestry is supported by a grant from NIH General Medical.


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.

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: November 05, 2007

biotapestry at systemsbiology dot org