BiologicalNetworks

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BiologicalNetworks is a free Integrated Research Environment (IRE) for biologists.

It integrates molecular interaction networks, metabolic and signaling pathways with experimental data, genomic sequences, 3D structure information, ontologies and taxonomies. The database currently integrates over 100 curated and publicly contributed data sources for thousands of eukaryotic, prokaryotic and viral genomes. For full list see Database Catalog and Organism List.

BiologicalNetworks system allows querying over a large number of biological features related to transcriptional regulation, pathways and interaction maps, microarray and proteomic experiments, 3D structures and other types of data.

Distribution

Run BiologicaNetworks Windows application.

Also Mac OS X

Run BiologicalNetworks v. 1.9

Need Help?| Have a feature request?| Report a bug

You can also download additional data (microarray, GO, 3D structures etc.) for your analysis (Size: 5.3 MB).

See Tutorials section.

News

06/22/2009

New release.alpha.4 is available.
For the complete list of recent and coming releases please visit Roadmap.

05/01

BiologicalNetworks 2.0 alpha appeared!

New release provides many new features and enhancements and is based on the professional platform from Sun Microsystems.

See what's new in BiologicalNetworks 2.0

04/28

New web site appeared.

Publications

"BiologicalNetworks: visualization and analysis tool for systems biology", Nucleic Acids Research, Web Server Issue 2006.

"PathSys: integrating molecular interaction graphs for systems biology", BMC Bioinformatics.

Poster presentation at Chromatin Structure and Functions 2005.

Presentation and Demo at ISMB 2005.

Poster presentation at CSH Systems Biology Conference.

		Transcriptional regulation database Test out the new integrated database on transcriptional regulation which integrates over a 100 databases on transcription factors, binding sites, promoter structures and other regulatory elements of eukaryotes and prokaryotes. More...				Microbial studies Metabolic pathways analysis, integrated with 3D protein structure modeling of Thermatoga Maritima. Run Microbial study

		Gene regulation in Yeast Whole genome microarray gene expression analysis of yeast meiosis data integrated with protein-DNA, protein-protein interaction maps and protein-kinase-transcription factor influence networks. Fourier and SVD analysis of harmonic waves, statistical enrichment of regulatory modules, protein complexes and network motifs. Run gene regulation in yeast study.				Human hypertension studies Genome-wide co-expression and multi factorial ANOVA together with an evolutionarily conserved promoter model with shared transcription factors generated a functional molecular network of chromogranins, catecholamins and transcription factors that identified novel gene targets as well as transcription factors important for human Hypertension. Run human Hypertension study.

		Parasite studies Spatiotemporally and functionally coherent modular signaling network of basal body proteins during Giardia lamblia differentiation. Study of Giardia cytological and regulatory remodeling based on Proteomic, Transcriptomic, Orthology and Interaction networks analysis. Run Giardia differentiation study.				Host-pathogen interaction studies The systems level studies on influenza virus and Streptococcus pneumoniae identified host molecular pathways that appear to be induced or repressed during infection. The results highlight pathways exhibiting responses specific for a given pathogen infection. More...

						* BiologicalNetworks has to be installed on your computer before.

Pathways/Networks
Try out the new version of BiologicalNetworks pathways and networks analysis environment!

Microarray experiments
A tool for microarray gene expression, ChIP-Chip, protemics analysis: statistics, co-expression networks, perturbed and co-regulated pathways.

Sequences
The early prototype of Genomic Sequences analysis environment with Annotations of biomedical data from our integrated database.

3D protein structures
3D protein structures analysis environment.

Contact ||UCSD||SDSC||KGI

This project is currently supported by NIH R01 GM084881 and FIBR-0527023 grants
to UCSD and KGI

Past funding