BioTapestry is an
open source
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...
software application for modeling and
visualizing gene regulatory network
A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the fun ...
s (GRNs).
[
]
History
BioTapestry was created at th
Institute of Systems Biologyin Seattle, in collaboration with th
at th
California Institute of Technology The project was initiated to support the ongoing development of the model of the GRN regulating the development of the endomesoderm in the sea urchin
Strongylocentrotus purpuratus
''Strongylocentrotus purpuratus'', the purple sea urchin, lives along the eastern edge of the Pacific Ocean extending from Ensenada, Mexico, to British Columbia, Canada. This sea urchin species is deep purple in color, and lives in lower int ...
. BioTapestry was initially made public in late 2003 as a web-based, read-onl
interactive viewer for the sea urchin network with the first fully functional editor released in August 2004 (v0.94.1). The current version, 7.0.0, was released in September 2014.
Development
Development work on BioTapestry is ongoing. For more information about version 7.0, see th
Usage
BioTapestry is an interactive tool for modeling and visualizing gene regulatory networks.
Interactive examples
from the Davidson Lab.
from the Davidson Lab.
Mouse ventral neural tube specificationfrom the McMahon Lab.
Environment And Gene Regulatory Influence Network (EGRIN) for Halobacterium salinarum NRC-1from the Baliga Lab.
from the Rothenberg Lab.
Zebrafish developmental gene regulatory networkfrom the Yuh Lab.
Limb Morphogenesisfrom the Vokes Lab.
Features
Input
* Gene Regulatory Networks can be drawn by hand.
* Networks can be built using lists of interactions entered via dialog boxes.
* Lists of interactions can be input using comma-separated-value (CSV) files.
* Networks can be built using SIF files as input.
* BioTapestry can accept network definitions via the Gaggle framework.
Visualization
* BioTapestry uses orthogonal-directed hyperlinks and a hierarchical presentation of models.
Analysis
* BioTapestry can create
Systems Biology Markup Language
The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of use ...
files for a subset of networks.
Documentation
* The BioTapestry home page has links to several tutorials for using the software.
See also
*
Gene regulatory network
A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the fun ...
*
Systems biology
Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological syst ...
References
{{Reflist
External links
BioTapestry site
Systems biology
Graph drawing software
Cross-platform software
Java platform software