BiologicalNetworks

Driving Projects (click to see all)

Research Modules

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Contribute a module or a plugin

BiologicalNetworks research environment enables integrative analysis of:

Interaction networks, metabolic and signaling pathways together with transcriptomic, metabolomic and proteomic data
Gene regulatory modules (modular networks)
Genomic sequences including gene regulatory regions (e.g. binding sites, promoter regions) and respective transcription factors
Comparative genomics, analysis of clusters of homologous/orthologous genes and phylogenies
3D protein structures and ligand binding, small molecules and drugs
Multiple ontologies including GeneOntology, Cell and Tissue types, Diseases, Anatomy and taxonomies

The database currently integrates over 100 curated and publicly contributed data sources for several thousands of eukaryotic, prokaryotic and viral organisms.

BiologicalNetworks system has been used by thousands of researchers world-wide, including over 20 collaborative Driving Projects.

Distribution

Windows

MacOSX

Linux/Ubuntu/Redhat

Need Help? | Feature request? | Report a bug

You can also download example data (microarrays, networks, sequences, structures, GO) (size:16MB).

Please see general Tutorial of BiologicalNetworks as well as step-by-step tutorial (.docx file) for the Gene Regulatory Modules tool.

News & Events

01/24/2012

A new Gene Regulatory Modules tool is availabe through the 'Transcription Regulatory Network Wizard'. See the step-by-step tutorial (.docx).

10/05/2011

A new version of BioogicalNetworks back-end database IntegromeDB (www.integromedb.org) is available.

09/27/2011

API to BiologicalNetworks and IntegromeDB database was added to our web site.

08/22/2011

A collection of Canonical Pathways is available in BiologicalNetworks.

07/15/2011

BiologicalNetworks presents its regulatory modules discovery platform at the ISMB 2011.

03/15/2011

BiologicalNetworks presented the Sequencing Data Storage and Management platform at the Next-Generation Sequencing Congress and Expo in San Diego.

01/18/2011

User Forum is available on our web site.

11/06/2010

New Video Demos and Use Cases are available on our main page.

08/02/2010

New version of the Tutorial is available.

See all news

Publications

"Mining and integration of pathway diagrams from imaging data", Bioinformatics, 2012; doi: 10.1093/bioinformatics/bts01.

"IntegromeDB: an integrated system and biological search engine", BMC Genomics, 2012.

"BiologicalNetworks - tools enabling the integration of multiscale data for the host-pathogen studies.", BMC Systems Biology, 2011.

"Integrative approach at building and analyzing gene regulatory networks", ISMB 2011.

"BiologicalNetworks 2.0 - an integrative view of genome biology data.", BMC Bioinformatics, 2010.

"Semantic Integration of Data on Transcriptional Regulation.", Bioinformatics, 2010.

"BiologicalNetworks: enabling systems-level studies of host-pathogen interactions", ECCB 2010.

"IntegromeDB: semantic integration of Transcriptional Regulation Data", RECOMB 2010.

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

"PathSys: integrating molecular interaction graphs for systems biology", BMC Bioinformatics, 2006.

See all publications

		Regulation of OCT4 in mammalian ES cells The OCT4 transcription factor regulatory modular network in mammalian embryonic stem (ES) cells, using microarrays and OCT4 binding data obtained in mouse ES cells (Sharov et al. 2008), as well as data from public Expression and Sequence databases is presented. Run Oct4 study				Gene Regulatory Modular Network of asthma A gene regulatory modular view of Asthma that integrates multiple levels of molecular, functional, sequence and experimental information is presented. Comparison of modules derived using BiologicalNetworks with respective module of Noverstern et al. is shown. Run Asthma study

		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.				NF-kB regulatory and signaling networks NF-kB regulatory network, playing role in immune system, cell survival and proliferation, carcinogenesis and cancer pathogenesis, with microarray and regulatory data collected from over 100 databases. Run NF-kB study

		Chemical Systems Biology of pharm off-targets A comprehensive analysis of off-target pathways build on the putative off-targets of CETP (cholesteryl ester transfer protein) inhibitors across the human structural genome identified from the off-target pipeline SMAP. Run CETP off-targets study				Host-pathogen interaction Systems studies of Influenza viruses identified host molecular pathways that are induced or repressed during infection. The results highlight pathways responses specific for a given pathogen infection. Run Host-Pathogen study

		Whole Genome Metabolic Reconstruction A high-quality genome-scale reconstructions of E. coli and Human metabolism built using quality-controlled reconstruction pipeline of Palsson's Lab in UCSD. Run Reconstruction Maps				Autism Spectrum Disorders GWAS of ~400 ASD patients was analyzed for genes and transcription factors working on each stage of brain development. It was shown that the genetic controls of brain development are significantly different from such controls in other organs development.

		Brain and consciousness development Analysis of brain development determinants, specific for the cortex neurons development was performed to find genetic mechanisms regulating consciousness appearance at specific times of brain development. Run brain development study				Senescence and apoptosis Discovering global alterations in autophagy pathways resulting in senescence and constructing gene regulatory modular network for senescence and progression to apoptosis in human melanoma cells

		Gene regulation in Yeast Whole genome gene expression analysis of yeast meiosis data integrated with p-p, p-DNA interaction maps and protein-kinase-transcription factor influence networks. Fourier and SVD analysis of harmonic waves and statistical enrichment of regulatory modules employed in the yeast meiosis are presented. Run gene regulation in yeast study.				Human hypertension Whole genome co-expression and multi factorial ANOVA analysis, together with an evolutionarily conserved promoter model with shared transcription factors generated a functional molecular network of chromogranins, catecholamins and transcription factors important for human Hypertension. Run human Hypertension study.

		Giardia lamblia differentiation Giardia lamblia cytological and regulatory remodeling based on Proteomic, Transcriptomic and Orthology analysis reveals spatiotemporally and functionally coherent modular signaling network of basal body proteins during differentiation. Run Giardia differentiation study.				Microbial studies Metabolic pathways analysis, integrated with 3D protein structure modeling of Thermatoga Maritima. More... Run Microbial study

						*To open Driving Projects BiologicalNetworks has to be installed on your computer.

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

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

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

3D protein structures
3D protein structures analysis environment.

Contact \|\|UCSD\|\|SDSC
	This project is currently supported by NIH R01 GM084881 grant to UCSD