Category Cross-Omics>Pathway Analysis/Tools

Abstract BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks.

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 (GRN) controlling endomesoderm development in sea urchin embryos, etc.

Significant features/capabilities include:

1) 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.

2) BioTapestry can portray hourly, localized views of the network during development based on data tables describing the network's local and temporal states.

3) 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.

Many significant new features/capabilities in Version 3.0 are available --

1) Genes, nodes, and links can now be drawn at any level of the model hierarchy - Previous versions of BioTapestry required the user to first create a top-level network, and then select elements and propagate them into models lower down in the hierarchy.

With Version 3.0, users can simply draw new elements at any model layer. If a newly added element is Not present in the parent model(s), it is added automatically as needed.

2) Genes, nodes, and links can be "pulled down" from the top-level network - This is an additional enhancement to make it easier to create and populate models at 'all levels of the hierarchy'.

3) Change link source or target node - In the top-level model, the user can now choose to move links from one node another, which can be a common procedure as the understanding of a network changes over time, but can be challenging since these changes need to be applied to all models in the hierarchy.

The program takes care of changing all the sub-models to match the root-level change, and asks the user to clarify when there may be potential ambiguities that need resolution.

4) Global add of gene or node - Another feature that has been added to simplify the editing and maintenance of large models over the long term is the ability to select a gene or node and then choose the models and regions where it should be added through a single global listing of the candidates.

5) Global gene/node/linkage search and navigation - With large models, it is essential to be able to find every usage of a particular network element across all models and regions, then go and see that usage in context. Starting in Version 3.0, the user can get a window listing all the places the feature is used (in static models).

6) Explicit region ordering - Regions can now be explicitly assigned a drawing order, so that the user can ensure that one region color block is drawn in front of another.

7) Rapid stocking of a region - A region can be fully populated with the all the network elements present in the parent model using a single operation, allowing the user to build sub-models much faster.

8) Networks can be expanded or compressed on a per-region basis - Previously, network geometry could only be expanded or compressed for an entire model. These operations can now be done on the granularity of regions.

9) Other new region functions - Regions can now be moved as a unit; also, region names can now be hidden.

10) The Experimental Data display can be driven using web pages - The Experimental Data display has been customizable in previous versions using small code plug-ins. To make this customization easier, the user can now stock the page by simply specifying a list of URLs for (simplified) web pages.

11) Improved layout synchronization - The ability to flexibly synchronize network layouts between models is crucial. Starting in Version 3.0, the root layout can be propagated to only a subset of regions and models in the hierarchy; previous versions synchronized everything.

In addition, the layout synchronization algorithm has been improved to do a better job of retaining the existing region positions and cross- region link layouts.

12) Modify root layout to match child model layouts - In those cases where the user changes the layout of the networks below the top-level root model, it is very useful to be able to modify the root model layout to match those changes. This feature has been added in Version 3.0.

13) Enhanced BioTapestry Viewer - The BioTapestry Viewer has been enhanced with many features that were previously only available in the Editor, such as search, finding sources and targets of nodes, exploring alternate network paths, and zooming to selected elements.

14) New headless batch mode - When using BioTapestry at the end of a computational pipeline for generating images of networks, it is very useful to be able to run it in batch mode. Version 3.0 adds this new mode.

15) Improved automatic link layout algorithms - There have been improvements to the automatic link layout algorithm to reduce link layout failures, provide better layout paths, and handle multiple link inputs into a single target pad.

Also, the link layout algorithm used in 'child models' to handle cross- region link layout tries to do a better job of retaining the existing link arrangement while doing incremental layout, layout synchronization, and network expansion or compression.

16) Per-embryo RNA counts can be imported and displayed - At this time, this data can be imported from an XML file and displayed in the Experimental Data window. There is No user interface for editing these data.

17) Support for Gaggle version 2007-04 has been added (see G6G Product Number 20222).

BioTapestry includes extensive documentation -- BioTapestry Frequently Asked Questions and Online Tutorials.

Current Online Tutorial List includes - Quick Start Tutorial; Dynamic Submodels Tutorial; Tutorial on Building Networks from Interaction Tables; Building Networks from Comma-Separated Value Files; and Tutorial on Using and Creating Paths.

System Requirements

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).

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).


BioTapestry is a joint project of the Institute for Systems Biology and the Davidson Lab at Caltech.

Manufacturer Web Site BioTapestry

Price Contact manufacturer.

G6G Abstract Number 20385

G6G Manufacturer Number 104022