BioTapestry protocols

View BioTapestry computational protocol

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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 in pipeline

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

[…] using david (). go terms were filtered using number of term items ≥10, fdr ≤0.05 and fold enrichment ≥4., 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 […]


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BioTapestry in publications

 (27)
PMCID: 5730191
PMID: 29206223
DOI: 10.1371/journal.pcbi.1005741

[…] similar to []) and reran the simulations (). given an interaction target, we looked for the attractors that positively influence the dna damage response phenotype., network figures were drawn with biotapestry (www.biotapestry.org). simulations of the boolean network were performed with the package boolnet [, ] in r (www.r-project.org)., this model contains two external signals (dna damage […]

PMCID: 5522468
PMID: 28733657
DOI: 10.1038/s41598-017-05472-0

[…] the network that pass through a particular node) or out-degree of each node in the network and the edges were weighted according to the im values. the gene regulatory network models were drawn using biotapestry–., , maryam anwar and monica tambalo contributed equally to this work., electronic supplementary material , supplementary information accompanies this paper […]

PMCID: 5399671
PMID: 28264836
DOI: 10.1242/dev.148494

[…] mean count 300 is empirical based on the observation that genes not expressed or very weakly expressed in the otic region had a count of less than 300., grn construction was performed manually using biotapestry. different regions of the network were defined according to the known biology of oep induction, segregation of otic and epibranchial domains and the signalling input from adjacent tissues […]

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

[…] 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 […]

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

[…] 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, […]


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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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