Bioinformatics. 2007 Feb 1;23(3):392-3. Epub 2006 Nov 30.

BioNetBuilder: automatic integration of biological networks.

Avila-Campillo I, Drew K, Lin J, Reiss DJ, Bonneau R.

Source

Department of Biology, New York University, New York, NY, USA. iliana_avila-campillo@merck.com

Abstract

BioNetBuilder is an open-source client-server Cytoscape plugin that offers a user-friendly interface to create biological networks integrated from several databases. Users can create networks for approximately 1500 organisms, including common model organisms and human. Currently supported databases include: DIP, BIND, Prolinks, KEGG, HPRD, The BioGrid and GO, among others. The BioNetBuilder plugin client is available as a Java Webstart, providing a platform-independent network interface to these public databases. Availability: http://err.bio.nyu.edu/cytoscape/bionetbuilder/

PMID:: 17138585; [PubMed - indexed for MEDLINE]

Free full text

MeSH Terms, Substances

MeSH Terms

Substances

Proteome

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Save items

Related citations in PubMed

NetMatch: a Cytoscape plugin for searching biological networks. [Bioinformatics. 2007]
NetMatch: a Cytoscape plugin for searching biological networks.
Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D. Bioinformatics. 2007 Apr 1; 23(7):910-2. Epub 2007 Feb 3.
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. [Bioinformatics. 2008]
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks.
Zinovyev A, Viara E, Calzone L, Barillot E. Bioinformatics. 2008 Mar 15; 24(6):876-7. Epub 2007 Nov 16.
The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins. [Bioinformatics. 2007]
The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins.
Salwinski L, Eisenberg D. Bioinformatics. 2007 Aug 15; 23(16):2193-5. Epub 2007 Jun 6.
Review Tools for visually exploring biological networks. [Bioinformatics. 2007]
Review Tools for visually exploring biological networks.
Suderman M, Hallett M. Bioinformatics. 2007 Oct 15; 23(20):2651-9. Epub 2007 Aug 25.
Review Towards zoomable multidimensional maps of the cell. [Nat Biotechnol. 2007]
Review Towards zoomable multidimensional maps of the cell.
Hu Z, Mellor J, Wu J, Kanehisa M, Stuart JM, DeLisi C. Nat Biotechnol. 2007 May; 25(5):547-54.

See reviews... See all...

Cited by 18 PubMed Central articles

Comparative microbial modules resource: generation and visualization of multi-species biclusters. [PLoS Comput Biol. 2011]
Comparative microbial modules resource: generation and visualization of multi-species biclusters.
Kacmarczyk T, Waltman P, Bate A, Eichenberger P, Bonneau R. PLoS Comput Biol. 2011 Dec; 7(12):e1002228. Epub 2011 Dec 1.
Construction of gene regulatory networks using biclustering and Bayesian networks. [Theor Biol Med Model. 2011]
Construction of gene regulatory networks using biclustering and Bayesian networks.
Alakwaa FM, Solouma NH, Kadah YM. Theor Biol Med Model. 2011 Oct 22; 8:39. Epub 2011 Oct 22.
The Proteome Folding Project: proteome-scale prediction of structure and function. [Genome Res. 2011]
The Proteome Folding Project: proteome-scale prediction of structure and function.
Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, et al. Genome Res. 2011 Nov; 21(11):1981-94. Epub 2011 Aug 8.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

BioNetBuilder: automatic integration of biological networks.
BioNetBuilder: automatic integration of biological networks.
Bioinformatics. 2007 Feb 1 ;23(3):392-3. Epub 2006 Nov 30 .

PubMed
Activation of SHP2 protein-tyrosine phosphatase increases HoxA10-induced repress...
Activation of SHP2 protein-tyrosine phosphatase increases HoxA10-induced repression of the genes encoding gp91(PHOX) and p67(PHOX).
J Biol Chem. 2007 Jan 26 ;282(4):2237-49. Epub 2006 Nov 30 .

PubMed
The effect of the phase of prestimulus alpha activity on the averaged visual evo...
The effect of the phase of prestimulus alpha activity on the averaged visual evoked response.
Electroencephalogr Clin Neurophysiol. 1991 Jul-Aug ;80(4):241-50.

PubMed
Moderate coffee intake may reduce the risk of oral, pharyngeal, and esophageal c...
Moderate coffee intake may reduce the risk of oral, pharyngeal, and esophageal cancer.
J Evid Based Dent Pract. 2005 Mar ;5(1):31-2.

PubMed
Sentinel-lymph-node biopsy as a staging procedure in breast cancer: update of a ...
Sentinel-lymph-node biopsy as a staging procedure in breast cancer: update of a randomised controlled study.
Lancet Oncol. 2006 Dec ;7(12):983-90.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: