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BioTapestry specifications

Information


Unique identifier OMICS_19344
Name BioTapestry
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Version 7.0.0
Stability Stable
Source code URL http://www.biotapestry.org/webclient/BTWebViewerV700.zip
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/BioTapestry

Maintainer


  • person_outline William Longabaugh

Information


Unique identifier OMICS_19344
Name BioTapestry
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 7.1.0
Stability Stable
Source code URL http://www.biotapestry.org/src/BioTapestry-7.1.0-src.tar.gz
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/BioTapestry

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Maintainer


  • person_outline William Longabaugh

Publication for BioTapestry

BioTapestry citations

 (13)
library_books

The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium

2017
PLoS Genet
PMCID: 5400277
PMID: 28388635
DOI: 10.1371/journal.pgen.1006726

[…] ne regulatory network (GRN; Figs and ) that acts during early gynoecium development. To verify that this network fits the experimental data, we made a GRN Boolean model using the computational tools BioTapestry [] and GeNeTool [] (), and we confirmed that the wiring of this network gives a stable output (i.e., fixed steady state for each gene) (). Note, we modeled TAA1 and PIN3 regulation by SPT […]

library_books

The Gene Regulatory Network of Lens Induction Is Wired through Meis Dependent Shadow Enhancers of Pax6

2016
PLoS Genet
PMCID: 5137874
PMID: 27918583
DOI: 10.1371/journal.pgen.1006441

[…] Previous studies have shown that the GRN of mammalian lens induction is governed by a multitude of mutual cross-regulations, including the transcription factors Pax6, Six3 and Sox2 (summarized in the BioTapestry visualization ). Six3 appears to regulate the onset of Pax6 expression in the PLE while Pax6 subsequently maintains Six3 levels [, , ]. Only a small fraction of Six3 f/del;Le-Cre embryos, […]

call_split

Activation of a T box Otx2 Gsc gene network independent of TBP and TBP related factors

2016
PMCID: 4852510
PMID: 26952988
DOI: 10.1242/dev.127936
call_split See protocol

[…] Regulatory interactions of the mesendoderm specification network () were visualized using BioTapestry (). For analysis of T, Vegt, Eomes, Gsc, Lhx1 and Otx2 binding, ChIP-seq data (; ) was mapped to X. tropicalis assembly 7.1. Peaks were called using MACS2 () with q0.001. To obtain high-co […]

library_books

Developmental gene regulatory networks in sea urchins and what we can learn from them

2016
F1000Res
PMCID: 4765714
PMID: 26962438
DOI: 10.12688/f1000research.7381.1

[…] hierarchical relationship between the transcription factors, signals, and the genes encoding them in each cell type over time. The regulatory interactions were assembled into a network model by using BioTapestry as a platform for visualizing network topologies , . Many of the interactions were validated by using cis-regulatory analysis to determine direct binding of the transcription factor to spe […]

library_books

NetworkPainter: dynamic intracellular pathway animation in Cytobank

2015
BMC Bioinformatics
PMCID: 4491883
PMID: 26003204
DOI: 10.1186/s12859-015-0602-4

[…] tiColoredNodes [], SpotXplore [], and VistaClara [], and VANTED [] place small sub-plots next to each observed node and edge to indicate its observed temporal dynamics. Third, several tools including BioTapestry [], DynNetwork [http://code.google.com/p/dynnetwork], and the Pathway Tools Cellular Overview [] animate network diagrams by coloring or boldening each observed node and edge at each time […]

library_books

HES5 silencing is an early and recurrent change in prostate tumourigenesis

2015
Endocr Relat Cancer
PMCID: 4335379
PMID: 25560400
DOI: 10.1530/ERC-14-0454

[…] 771). All GEO data were retrieved using the GEOquery package in the R statistical software and summary plots were generated using the same software (, ). Transcriptional networks were drawn using the BioTapestry application () constructing models using ChIP-seq binding profiles, expression correlations and published transcriptional links. […]

Citations

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BioTapestry institution(s)
Institute for Systems Biology, Seattle, WA, USA
BioTapestry funding source(s)
Supported by the National Institute of General Medical Sciences under Award Number R01GM061005, and by the Eunice Kennedy Shriver National Institute Of Child Health & Human Development of the National Institutes of Health under Award Number R01HD073113.

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