ABACUS

ABACUS is an Algorithm based on a BivAriate CUmulative Statistic to identify single nucleotide polymorphisms (SNPs) significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions

AbsIDconvert

AbsIDconvert is an absolute approach for converting genetic identifiers at different granularities

ADaCGH

ADaCGH is a parallelized web-based application and R package for the analysis of aCGH data

AgBase

AgBase is a functional genomics resource for agriculture

Algal Functional Annotation Tool

Algal Functional Annotation Tool is a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data

AltAnalyze

AltAnalyze is a platform for analyzing and visualizing exon expression data

AMMO_Prot

AMMO-Prot is an amine system project 3D-model finder

Annotate-it

Annotate-it is a Swiss-knife approach to annotation, analys is and interpretation of single nucleotide variation in human disease

Arabidopsis Reactome

Arabidopsis Reactome is a curated knowledgebase of plant biological pathways that contains many plant pathways curated by the John Innes Centre team, plus plant pathways imported from AraCyc and KEGG

ARACNe

ARACne is an Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

Asterias

Asterias includes applications for the analysis of genomic and proteomic data that cover from data normalization to development of prediction models for survival data

atBioNet

atBioNet is an integrated network analysis tool for genomics and biomarker discovery

Atlas of Genetics and Cytogenetics in Oncology and Haematology

The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal and database in free access on internet devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases

AutismKB

An evidence-based knowledgebase of autism genetics

Babelomics

Babelomics is a complete suite of web tools for the analysis, integration and interpretation of different types of genomic data

Baysian Pathway Analysis

A computational method to identify significant pathways from microarray data with samples from test and control classes

BcCluster

BcCluster is a Bladder Cancer Database at the Molecular Level

BCML

The biological Connection Markup Language is a SBGN-compliant format for visualization, filtering and analysis of biological pathways

BIANA

Biological interactions and network analysis (BIANCA) is a software framework for compiling biological interactions and analyzing networks

BindingDB

A public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules

BiNoM

Biological Network Manager is a Cytoscape plug-in, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX)

Bio3graph

Automated extraction of biological relations from the literature, resulting in a set of (component1, reaction, component2) triplets and composing a graph structure which can be visualised, compared to the manually constructed topology and examined by the experts

BioBin

BioBin is a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge

BioDB

BioDB is an ontology-enhanced information system for heterogeneous biological information

BioDWH

BioDWH is a Data Warehouse Kit for Life Science Data Integration

Biofilter

Biofilter is a knowledge-integration system for the multi-locus analysis of genome-wide association studies

biofilter 2.0

A single interface for accessing multiple publicly available human genetic data sources that have been compiled in the supporting database of Library of Knowledge Integration (LOKI)

BioGPS

BioGPS is a free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function

BioGRID

The Biological General Repository for Interaction Datasets (BioGRID) database was developed to house and distribute collections of protein and genetic interactions from major model organism species

BioHealthBase BRC

BioHealthBase Bioinformatics Resource Center (BRC) is a public bioinformatics database and analysis resource for the study of specific biodefense and public health pathogens-Influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin

BioJS

BioJS is an open source standard for biological visualisation

BiologicalNetworks

Data integration and network based research environment with tools for inference and analysis of gene regulatory modules

BioMart

BioMart enables scientists to perform advanced querying of biological data sources through a single web interface

BioMoby

BioMOBY is an Open Source research project which aims to generate an architecture for the discovery and distribution of biological data through web services

BioModels

BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests

BioMyn

BioMyn is an integrated human gene and protein knowledgebase

BioPAX

Biological Pathway Exchange (BioPAX) is a RDF/OWL-based standard for the exchange of biological pathways

BioPAX Cytoscape PlugIn

BioPAX Cytoscape PlugIn enables Cytoscape users to load and visually render BioPAX files from the web or a local file system; distributed with Reactome sample files

BioPP

BioPP is a tool for web-publication of biological networks

BioProfiling.de

BioProfiling de provides a common interface for a collection of recently developed analytical tools for genomics, proteomics and metabolimics data

BioSemantic

BioSemantic is a framework that was designed to speed integration of relational biological databases

Biovista

Systematic drug repositioning capability offers decision makers a reliable tool for pipeline optimization, asset protection and life cycle management

BioWisdom SRS

BioWisdom Sequence Retrival System (SRS) is a proven and scalable data integration platform delivering genomic data to thousands of users

BirdsEyeView

Visualizing experimental transcriptomic data using different views that users can switch among and compare

BirdsEyeView

BirdsEyeView (BEV) is a graphical overviews of experimental data

BisoGenet

BisoGenet is a Cytsocape app for gene network building, visualization and analysis

BNP

Bayesian Network Prior (BNP) depicts the relation between various evidence types that contribute to the event gene interaction and is used to calculate the probability of a candidate graph (G) in the structure learning process

BowTieBuilder

BowTieBuilder is aModeling signal transduction pathways

C2Cards - Human

Consensus and Conflict Cards (C2Cards) provides concise overviews of what pathway databases do or do not agree on

caBIG

cancer Biomedical Informatics Grid¬ caBIG¬ is an information network enabling all constituencies in the cancer community _ researchers, physicians, and patients _ to share data and knowledge

CAERUS

CAERUS predicts CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data

CancerResource

CancerResource is a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge

CANGES

CANGES provides a means to rapidly identify networks for any set of genes and generate novel hypotheses

canSAR

canSAR is an integrated cancer public translational research and drug discovery resource

CardioNet

A human metabolic network suited for the study of cardiomyocyte metabolism

CardioNet

CardioNet is a human metabolic network suited for the study of cardiomyocyte metabolism

CardioVINEdb

CardioVINEdb is a data warehouse approach for integration of life science data in cardiovascular diseases

CCDB

Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle

CEGP

Cancer Gene Encyclopedia will allow scientists to identify new cancer targets

Cell Cycle Ontology

The Cell Cycle Ontology is an application ontology for the representation and integrated analysis of the cell cycle process

Cell Illustrator

Cell Illustrator is an environment for simulating and representing biological systems

CellBase

CellBase is a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources

CellCircuits

CellCircuits is a database of protein network models

CellDesigner

CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks

CellFrame

CellFrame is a data structure for abstraction of cell biology experiments and construction of perturbation networks

Characterization Tool

The Characterization Tool is a novel knowledge-based database and web application that allows the storage and analysis of various kinds of data associated with cell, cell line and tissue characterization across different species

ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds

Chem2Bio2RDF

Chem2Bio2RDF is a semantic framework for linking and data mining chemogenomic and systems chemical biology data

ChemProt

ChemPort is a disease chemical biology database, which is based on a compilation of multiple chemical_protein annotation resources, as well as disease-associated protein_ protein interactions

ChiBE

Chisio BioPAX Editor (ChiBE) is a free editing and visualization tool for pathway models represented by the BioPAX format

Chipster

Chipster is a user-friendly analysis software for microarray and other high-throughput data

CIDeR

CIDeR is aMultifactorial interaction networks in human diseases

CIDMS

Cardiac Integrated Database Management System (CIDMS) integrates the heterogeneous -omic data (available from multitude of sources and in various formats such as publication and associated supplementary files, databases and web pages) that are generated at different biological levels

Cluepedia

CluePedia provides insights into pathways by integrating experimental and in silico information

CMS

A Web-Based System for Visualization and Analysis of Genome-Wide Methylation Data of Human Cancers

COFECO

COFECO is a web-based tool for a composite annotation of protein complexes

ConsensusPathDB

ConsensusPathDB is a database system for the integration of human functional interactions

COPASI

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics

cPath

cPath is an open source pathway database and software suite designed for systems biology research

CPNM

Context-specific Protein Network Miner derives context-specific PPI networks in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system

CSAX

Characterizing Systematic Anomalies in eXpression Data (CSAX) aids in both identifying anomalies and explaining the underlying biology in expression datasets

CTD

The Comparative Toxicogenomics Database (CTD) is a curated database that promotes understanding about the effects of environmental chemicals on human health

CTSA Pharmaceutical Assests Portal

The Pharmaceutical Assets Portal aims to facilitate industry-academic collaborations for discovery of new indications for compounds no longer being developed by pharmaceutical companies, through eliminating barriers to access such compounds

CyTargetLinker

A Cytoscape App to Integrate Regulatory Interactions in Network Analysis

Cytoscape

Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks

DAPD

DAPD is a knowledgebase for Diabetes Associated Proteins

DAPPER

DAPPER is a data-mining resource for protein-protein interactions

DAPPLE

Disease Association Protein-Protein Link Evaluator (DAPPLE) looks for significant physical connectivity among proteins encoded for by genes in loci associated to disease according to protein-protein interactions reported in the literature

DAVID

Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes

DawnRank

DawnRank is a discover tool for personalized driver genes in cancer

dbOGAP

dbOGAP is a Database of O-GlcNAcylated Proteins and Sites

DC-ATLAS

DC-ATLAS is a systems biology resource to dissect receptor specific signal transduction in dendritic cells

DDEC

Dragon Database of genes implicated in Esophageal Cancer (DDEC) is an integrated knowledge database aimed at representing a gateway to esophageal cancer related data

DDESC

DDESC is Dragon database for exploration of sodium channels in humans,

DDPC

Dragon Database of Genes associated with Prostate Cancer (DDPC) is an integrated knowledge database aimed at representing a gateway to prostate cancer related data

DECODE

DECODE is an integrated differential co-expression and differential expression analysis of gene expression data

DeDaL

DeDaL is a Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts

DEEP

DEEP is a tool for differential expression effector prediction

DESHCV

Dragon Exploratory System on Hepatitis C Virus (DESHCV) is a biomedical text-mining and relationship exploring knowledgebase is the first reported comprehensive Hepatitis C Virus (HCV)

DESSCD

Dragon Exploration System for Sickle Cell Disease permits the exploration of text-mined and data-mined information about SCD

DESTAF

Dragon Exploration System for Toxicants and Fertility (DESTAF) is a specialized, public resource specifically aimed at researchers investigating reproductive toxicity

DICS

The DICS database is a dynamic web repository of computationally predicted functional modules from the human protein-protein interaction network

Dintor

Dintor is a data integration framework that provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets

Discovery-2

An interactive resource for the rational selection and comparison of putative drug target proteins in malaria Phelelani T

DisGeneNet

DisGeNET is a discovery platform integrating information on gene-disease associations (GDAs) from several public data sources and the literature

DNAtraffic

DNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life

DR-GAS

DR-GAS is a database of functional genetic variants and their phosphorylation states in human DNA repair systems

DriverDB:

DriverDB is an exome sequencing database for cancer driver gene identification

DriverNet

DriverNet is auncovering the impact of somatic driver mutations on transcriptional networks in cancer

DroID

Drosophila Interactions Database is a comprehensive resource for annotated gene and protein interactions

DrugViz

DrugViz is a Cytoscape plugin that is designed to visualize and analyze small molecules within the framework of the interactome

DRYGIN

Data Repository of Yeast Genetic Interactions (DRYGIN) is a web database system that provides a central platform for yeast genetic network analysis and visualization

ECMDB

ECMDB is The E coli Metabolome Database

EDdb

Eddb is a web resource for eating disorder and its application to identify an extended adipocytokine signaling pathway related to eating disorder

EndoNet

EndoNet is an information resource about the intercellular signaling network

ENFIN

ENFIN is a network to enhance integrative systems biology

Enrichment map

Enrichment map is a network-based method for gene-set enrichment visualization and interpretation

Enrichr

Enrichr is an Interactive and collaborative HTML5 gene list enrichment analysis tool

Enzyme Portal

Mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature

Eu.Gene Analyzer

Eu Gene Analyzer is a tool for integrating gene expression data with pathway databases

Expander

EXPression ANalyzer and DisplayER) is an integrated software platform for the analysis of gene expression data, which is freely available for academic use

ExPASy Proteomics Server

Expert Protein Analysis System (ExPASy) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE

FACT

FACT is a framework for the functional interpretation of high-throughput experiments

FLIGHT

FLIGHT an online resource compiling data from over 100 Drosophila in vivo and in vitro RNAi screens

FluMap

Comprehensive pathway map that can serve as a graphically presented knowledgebase and as a platform to analyze functional interactions between IAV and host factors

FluxMap

A VANTED add-on for the visual exploration of flux distributions in biological networks

FlyMine

FlyMine is an integrated database for Drosophila and Anopheles genomics

FlyReactome

FlyReactome is a curated knowledgebase of Drosophila melanogaster pathways

fuga

Functional Genomics Assistant is an extensible and portable MATLAB toolbox for the inference of biological relationships, graph topology analysis, random network simulation, network clustering, and functional enrichment statistics

FunGenES

The FunGenES database is a genomics resource for mouse embryonic stem cell differentiation

g:Profiler

g:Profiler is a web-based toolset for functional profiling of gene lists from large-scale experiments

G2SBC

Genes-to-Systems Breast Cancer (G2SBC) Database is a bioinformatics resource that collects and integrates data about genes, transcripts and proteins which have been reported in literature to be altered in breast cancer cells

Gaggle

Gaggle is a framework for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data

Gallus Genome GBrowse

Gallus Genome GBrowse provides online access to genomic and other information about the chicken

GallusReactome

GallusReactome is a curated knowledgebase of chicken pathways

GANPA

A novel gene-weighed pathway analysis approach, as implemented in an R package called ñGene Associaqtion Network-based Pathway Analysis"

GAP

Gene functional Association Predictor is an integrative method for predicting and characterizing gene functional associations

GATE

Grid Analysis of Time-series Expression (GATE) is an integrated computational software platform for the analys is and visualization of high-dimensional bio-molecular time-series

GBMBase

GBMBase focuses on data used in Glioblastoma multiforme (GBM) research

GCMAP

GCMAP is a user-friendly connectivity mapping with R

GEDI

Genetic Diseases Gene Discovery (GEDI) provides integrated bioinformatics platforms that will support systems analysis of Human multigene disorders

Gene Ontology

The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases

Gene3D

Gene3D is a domain-based resource for comparative genomics, functional annotation and protein network analysis

GeneAnswers

Using the Bioconductor GeneAnswers Package to Interpret Gene Lists

GeneBrowser 2

GeneBrowser 2 is an application to explore and identify common biological traits in a set of genes

GeneCards

Extracts and integrates gene-related data, including genomic, transcriptomic, proteomic, genetic, clinical, and functional information

GeneMANIA

Helps you predict the function of your favourite genes and gene sets

GeneSigDB

GeneSigDB is a manually curated database and resource for analysis of gene expression signatures

GeneSpring

GeneSpring GX provides powerful, accessible statistical tools for fast visualization and analysis of expression and genomic structural variation data

GeneSrF

GeneSrF is a web-based tool for gene selection and classification using random forest

GeneTrail 2

GeneTrail 2 is a web-interface providing access to different tools for the statistical analysis of molecular signatures

GenMAPP

Gene Map Annotator and Pathway Profiler (GenMAPP) is a free, open-source bioinformatics software tool designed to visualize and analyze genomic data in the context of pathways (metabolic, signaling), connecting gene-level datasets to biological processes and disease

GenomeSpace

A cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface

GenWay Biotech, Inc.

GenWay Biotech, Inc is a protein, antibody and ELISA solutions provider

gespeR

gespeR is a statistical model for deconvoluting off-target-confounded RNA interference screens

GEYSIR

Genomic Explorer Y Survey of Immune Response (GEYSIR) is a web application designed to correlate case-control association data with genetic and physical maps of the human genome, including key human genes associated with host immune response

GingerSNP

GingerSNP tools help you explore standard human SNP arrays by interaction, pathway, and function

GLAMM

GLAMM is a Genome-Linked Application for Metabolic Maps

GOAL

GOAL is a software tool for assessing biological significance of genes groups

GOMiner

GoMiner» is a tool for biological interpretation of 'omic' data _ including data from gene expression microarrays

GPEC

GPEC is a Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection

graphite

A Bioconductor package to convert pathway topology to gene network

GraphWeb

GraphWeb is a public web server for graph-based analysis of biological networks

GSEA

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states

GuavaH

GuavaH is a compendium of host genomic data in HIV biology and disease

HAPMAP

The International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals

HCVpro

HCVpro is a Hepatitis C virus protein interaction database

HDAPD

HDAPD is a web tool for searching the disease-associated protein structures

HEFalMp

HEFalMp (Human Experimental/FunctionAL MaPper) is a tool that allows interactive exploration of functional maps (or functional relationship networks) predicted from integration of many genome-scale experimental results

HepatoNet1

HepatoNet1 is a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

HGNC

The HGNC database in 2008 is a resource for the human genome

hiPathDB

hiPathDB is a human-integrated pathway database with facile visualization

hLGDB

hLGDB is a database of human lysosomal genes and their regulation

HMDB

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body

HMPAS

Human Membrane Protein Analysis System provides comprehensive information about human membrane proteins including specific features of certain membrane protein groups

HMPAS

HMPAS is a Human Membrane Protein Analysis System

HMTD

Human Membrane Transporter Database

HOCCLUS2

bicluster miRNAs and target messenger RNAs (mRNAs) on the basis of their experimentally-verified and/or predicted interactions

HomoMINT

HomoMINT is an inferred human network based on orthology mapping of protein interactions discovered in model organisms

HPD

Human Pathway Database (HPD) is an integrated human pathway database providing comprehensive and combined view connecting human proteins, genes, RNAs, enzymes, signaling, metabolic reactions and gene regulatory events

HPIDB

HPIDB is a unified resource for host-pathogen interactions

Hubba

Hubba is ahub objects analyzer--a framework of interactome hubs identification for network biology

HuPho

HuPho is a human phosphatase portal

IBDsite

A disease-oriented platform, which collects data related to biomolecular mechanisms involved in the Inflammatory Bowel Disease onset

IDClight

IDClight converts single IDs through an URL

Idconverter

Idconvertor map IDs to other known public DBs

ImmPort

Immunology Database and Analysis Portal (ImmPort), is a one stop shop to access reference and experiment data for immunologists

Influenza Research Database

Influenza Research Database is a resource for the influenza virus research community that will facilitate an understanding of the influenza virus and how it interacts with the host organism

InnateDB

InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans and mice to microbial infection

INOH

Integrating Network Objects with Hierarchies (INOH) is a pathway database of model organisms including human, mouse, rat and others

INRICH

NRICH is an Interval-based Enrichment Analysis Tool for Genome Wide Association Studies

IntAct

IntAct is an open source resource for molecular interaction data

IntegromeDB

IntegromeDB is an integrated system and biological search engine

Interactome3D

A resource for the structural annotation and modeling of protein-protein interactions

Intermine

An open source data warehouse built specifically for the integration and analysis of complex biological data

IPAD

Integrated Pathway Analysis Database for Systematic Enrichment Analysis for defining inter-association between pathway, disease, drug and organ specificity

iPAS

iPAS is series of integrative steps, which extend existing pathway analysis techniques It consists of four parts is a data processing, gene-level statistics, individualized pathway aberrance score (iPAS) and a significance test

IPAVS

IPAVS is an Integrated Pathway Resources, Analysis and Visualization System

ISAAC

InterSpecies Analysing Application using Containers is a web based tool, which analyses sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis

KaBOB

KaBOB is an ontology-based semantic integration of biomedical databases

KDBI

Update of KDBI is a Kinetic data of bio-molecular interaction database

KeyPathwayMiner

KeyPathwayMiner is a condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape

KOBAS 2.0

KOBAS is an update of KOBAS (KEGG Orthology Based Annotation System) Its purpose is to identify statistically enriched related pathways and diseases for a set of genes or proteins, using pathway and disease knowledge from multiple commonly used databases

LDGIdb

LDGIdb is a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs

Linked Life Data

Linked Life Data is a semantic integration platform for the biomedical domain

LipidHome

A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics

Lists2Networks

Lists2Networks provides integrated analysis of gene/protein lists

LiverAtlas

LiverAtlas is a unique integrated knowledge database for systems-level research of liver and hepatic disease

LOKI

Library of Knowledge Integration (LOKI), which contains diverse prior knowledge from multiple collections of biological data

MAGeCK

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens

Manteia

Manteia is a predictive data mining system for vertebrate genes and its applications to human genetic diseases

mAPKL

mAPKL is aR/Bioconductor package for detecting gene exemplars and revealing their characteristics

MassVis

MassVis is a Visual analysis of protein complexes using mass spectrometry

MeSH

MeSH ORA framework is aR/Bioconductor packages to support MeSH over-representation analysis

Meta-All

Meta-All is a system for managing metabolic pathway information

MetaboLights

The MetaboLights repository is a Curation challenges in metabolomics

MetaCrop

MetaCrop 20 is a managing and exploring information about crop plant metabolism

METACYC

MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways

MetaMapp

Mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity

METANNOGEN

METANNOGEN is a flexible tool to manage information for the design of metabolic networks

MetaReg

MetaReg is a platform for modeling, analysis and visualization of biological systems using large-scale experimental data

metaTIGER

metaTIGER is a collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes

MetNet Online

MetNet Online is a novel integrated resource for plant systems biology

MetNetAPI

MetNetAPI is a flexible method to access and manipulate biological network data from MetNet

MetRxn

MetRxn is a knowledgebase of metabolites and reactions spanning metabolic models and databases

MGV

MGV is a generic graph viewer for comparative omics data

MiMI

Michigan Molecular Interactions (MiMI) provides access to the knowledge and data merged and integrated from numerous protein interactions databases

MIMO

MIMO is an efficient tool for molecular interaction maps overlap

Mimoza

Mimoza is a web-based semantic zooming and navigation in metabolic networks

MINT

MINT is a public repository for molecular interaction data

mirDIP

microRNA Data Integration Portal (mirDIP) integrates twelve microRNA prediction datasets from six microRNA prediction databases, allowing users to customize their microRNA target searches

MIRIAM

MIRIAM is an effort to standardise the Minimal Information Required In the Annotation of Models, so that different groups can collaborate on annotating and curating computational models in biology

miRror-Suite

miRror-Suite platform provides a concise, plausible explanation for the regulation of miRNAs in such complex settings

miRSystem

miRSystem is an Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets

MK4MDD

MK4MDD is a Multi-Level Knowledge Base and Analysis Platform for Major Depressive Disorder

MMMDB

MMMDB is a Mouse Multiple Tissue Metabolome Database

modMine

modMine is a flexible access to modENCODE data

MODOMICS

MODOMICS is a database of RNA modification pathways - 2013 update

MoKCa

The MoKCa (Mutations of Kinases in Cancer) database has been developed to structurally and functionally annotate, and where possible predict, the phenotypic consequences of mutations in protein kinases implicated in cancer

MoonDB

MoonDB is a database containing information on all the candidates identified in the analys is and a set of manually curated human moonlighting proteins

MOPED

Model Organism Protein Expression Database enables discoveries through consistently processed proteomics data

MSigDB

The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software

MuSiC

MuSiC is an Identifying mutational significance in cancer genomes

MyBiosource

MyBiosource is a provider of antibody, protein, peptide and ELISA reagents

NaviCell

NaviCell is a web-based environment for navigation, curation and maintenance of large molecular interaction maps

NAViGaTOR

A powerful graphing application for the 2D and 3D visualization of biological networks

NCBI BioSystems

The NCBI Biosystems database centralizes and cross-links existing biological systems databases

NCBI Gene

Entrez Gene is a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer

NCBO Bioportal

BioPortal is a Web-based application for accessing and sharing biomedical ontologies

NCIS

NCIS is a Network-assisted Co-clustering for the Identification of cancer Subtypes

ncRNA

ncRNA is a portal site for bioinformatics tools and databases specialized for functional RNAs

NeMo

NeMo is a Network Module identification in Cytoscape

NetBox

NetBox is a Java-based software tool for performing network analysis on human interaction networks

NetHiKe

A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network

NetPath

NetPath is a public resource of curated signal transduction pathways

NetSlim

NetSlim is a High-confidence curated signaling maps

NetWalker

NetWalker is a contextual network analysis tool for functional genomics

Network

Network Screening is a New Method to Identify Active Networks from an Ensemble of Known Networks

Network2Canvas

Network2Canvas is a Network Visualization on a Canvas with Enrichment Analysis

NetWORKIN

NetWORKIN is a method for predicting in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins

NetworkLego

NetworkLego is a general computational framework for detecting cellular networks that are activated in a particular cell state or in response to a perturbation and for determining core cellular networks that are activated in response to multiple perturbations

NetworkPrioritizer

A versatile tool for network-based prioritization of candidate disease genes or other molecules

NeuroDNet

An open source platform for constructing and analyzing neurodegenerative disease networks

neXtProt

neXtProt is a human-centric discovery platform offering its users a seamless integration of and navigation through proteins-related data

NGP

Networked Gene Prioritizer integrates gene expression and protein-protein interaction network to prioritize cancer-associated genes

OncoRep

OncoRep is an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing

Onto-Tools

Onto-Tools is a New additions and improvements in 2006

OntoSlug

OntoSlug is a dynamic visual front-end program for ontologies

OPHID

Integrated known, experimental and predicted PPIs for five model organisms and human in the I2D database

ORCID

ORCID provides a persistent digital identifier that distinguishes you from every other researcher

OREMPdb

Ontology Reasoning Engine for Molecular Pathways is a semantic dictionary of computational pathway models

p53 Knowledgebase

The p53 Knowledgebase is an integrated information resource for p53 research

PAGED

PAGED is a pathway and gene-set enrichment database to enable molecular phenotype discoveries

PAGER

PAGER is a new database framework to perform integrative ñgene-set, network, and pathway analysisî (GNPA)

PaLS

PaLS is a tool that filters, from a list or a set of lists of gene/clone/protein identifiers, those that meet certain criteria related to their references to articles in PubMed, Gene Ontology terms and KEGG and Reactome pathways

Pancreatic Expression database

The Pancreatic Expression database is the main repository for pancreatic-derived -omics data

Pandora

Pandora is a novel integrated approach that uses network topology to predict biological pathways

PARADIGM-SHIFT

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

Path2Models

Path2Models is a Large-scale generation of computational models from biochemical pathway maps

PathAgent

PathAgent is a Multi-agent System for Updated Pathway Information Integration

PathCase-SB

PathCase-SB is integrating data sources and providing tools for systems biology research

PathJam

PathJam is a public tool which provides an intuitive and user-friendly framework for biological pathway analysis of human gene lists

PATHLOGIC-S

A Scalable Boolean Framework for Modelling Cellular Signalling

PathNER

Pathway Named Entity Recognition is a tool for systematic identification of biological pathway mentions in the literature

Pathprinting

Pathprinting is an integrative approach to understand the functional basis of disease

PathRings

PathRings is a web-based tool for exploration of ortholog and expression data in biological pathways

PathScan

PathScan is Tool for Discerning Mutational Significance in Groups of Putative Cancer Genes

PathVar

PathVar is analysis of gene and protein expression variance in cellular pathways using microarray data

Pathview

Pathview is an R/Bioconductor package for pathway-based data integration and visualization

PathVisioRPC

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment

Pathway Projector

Pathway projector is a Web-based zoomable pathway browser using KEGG Atlas and Google Maps API

Pathway Commons

Pathway Commons provides researchers with convenient access to a comprehensive collection of pathways from multiple organisms

Pathway Interaction Database

Pathway Interaction Database (PID) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes

Pathway Knowledge Base

Pathway Knowledge Base is a public repository for searching biological pathways

Pathway-GPS

Pathway-GPS and SIGORA identifies relevant pathways based on the over-representation of their gene-pair signatures

PathwayCaseMAW

PathwayCaseMAW is an online system for metabolic network analysis

PathwayLinker

A system of integrating protein-protein interaction and signaling pathway data from several sources with statistical significance tests and clear visualization

PATIKAmad

PATIKAmad puts microarray data into pathway context

PATIKAweb

Pathway Analysis Tool for Integration and Knowledge Acquisition

PaxTools

An open-source, Java library that contains facilities and algorithms for common but difficult to implement tasks such as reading, writing, searching, merging, comparing and transforming pathway information

Payao

Payao is a community platform for SBML pathway model curation

PBSK browser

PBSK browser allows users to navigate biological pathways of PSI-MI, BioPAX, SBML and KGML formats

PDB

An Information Portal to Biological Macromolecular Structures

PDBe

The Protein Data Bank in Europe (PDBe) is bringing structure to biology

PDDB

Prion Disease Database (PDDB) focuses on data used in Prion Disease (PD) research This site provides tools which allow scientists to analyze, store, and share this PD data with other scientists

PEANuT

Pathway enrichment analysis tool provides an up-front method to identify underlying biological principles by calculating enriched pathways in focus networks

PENTACON

The Personalized NSAID Therapeutics Consortium (PENTACON) is a group of scientists with a wide range of expertise from multiple institutions whose collective aim is to develop a paradigm for the personalization of drug treatment

PharmGKB

Integrated data resource about how variation in human genetics leads to variation in response to drugs

PhosphoELM

PhosphoELM is a database of phosphorylation sites - Update 2008

PIG

Pathogen Interaction Gateway is a database of host-pathogen PPI (HP-PPI) data from a number of public resources

PIR

Protein Information Resource (PIR) is an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies

PlantReactome

A freely accessible plant pathway database which hosts plant metabolic and regulatory pathways

PLAZA

A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

PolyDoms

PolyDoms is a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease

Pomelo II

Pomelo II is an open-source, web-based, freely available tool for the analysis of gene (and protein) expression and tissue array data

PosMed

Positional MEDLINE (PosMed) prioritizes candidate genes for positional cloning

PpiTrim

PpiTrim is for constructing non-redundant and up-to-date interactomes

Predicted Arabidopsis Interactome Resource

A database of potential plant interactions, detailed annotations and more specific per interaction confidence measurement

PRGdb

PRGdb is a community-based database model for the analysis of R-genes in plants

PRIDE

The Proteomics Identifications database at EBI is a mass spectrometry-derived proteomics data repository

Prioritizer

A prioritization method for positional candidate genes, by assuming that the majority of causative genes are functionally closely related

PRO

Protein Ontology (PRO) is a formal representation of protein objects, providing both descriptions of these objects and the relationships between them

PROGgeneV2

PROGgeneV2 is a Pan Cancer Prognostics Database

ProKinO

ProKinO is a framework for protein kinase ontology

Proteomic

Proteomic atlas of the human olfactory bulb

PSI-MI

The HUPO Proteomics Standards Initiative Molecular Interaction (PSI-MI) workgroup defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification

PSIQUIC

PSIQUIC a web service to access the PSI-MI interaction data

pSTIING

pSTIING is a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer

PUPPI

PUPPI is a pathway analysis method using protein-protein interaction network for case-control data

PyBioS

PyBioS is a system for the modeling and simulation of cellular processes

Quartz-Seq

Quartz-Seq is a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

RDF2Graph

RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource

RDFScape

RDFScape is a plugin that has been developed to to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape

Reactome.db

A set of annotation maps for reactome assembled using data from Reactome

ReactomePA

ReactomePA is a R package for Reactome Pathway Analysis

ReConn

ReConn is a Java plugin that connects Cytoscape to the Reactome database

RefNetBuilder

RefNetBuilder is a platform for construction of integrated reference gene regulatory networks from expressed sequence tags

Regulatory Genomics

A Database of Annotated Promoters of Genes Associated with Common Respiratory and Related Diseases

ReMatch

ReMatch is a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis

REPAIRtoire

REPAIRtoire is a database of DNA repair pathways

RGD

Rat Genome Database (RGD) is a collection of genetic and genomic information on the rat

Rhea

Rhea is a manually curated resource of biochemical reactions

RhesusBase

RhesusBase is a knowledgebase for the monkey research community

RMOD

A Tool for Regulatory Motif Detection in Signaling Network

RNApathwaysDB

RNApathwaysDB is a database of RNA maturation and decay pathways

ROCK

ROCK is a breast cancer functional genomics resource

Rspider

R spider is a web-based tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions in human biology accumulated in the REACTOME and KEGG databases

RxnFinder

RxnFinder is a Biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity

SABIO-RK

System for the Analysis of Biochemical Pathways - Reaction Kinetics is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured

SAGA

SAGA is a subgraph matching tool for biological graphs

SASD

Synthetic Alternative Splicing Database for identifying novel isoform from proteomics

SASD

SASD is the Synthetic Alternative Splicing Database for identifying novel isoform from proteomics

SB-KOM

SB-KOM provides integration of pathway information using BioPax

SBGN

Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in maps of biological processes

SBKD

The Structural Biology Knowledgebase is a portal to protein structures, sequences, functions, and methods

SBML

The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biological processes

SBML-Bridge

SBML-Bridge is an XML Pathway Converting Tool

SciMiner

SciMiner is a dictionary- and rule-based biomedical literature mining and functional enrichment analysis tool

SIDEKICK

SIDEKICK is a genomic data driven analys is and decision-making framework

SigCS

An integrated genetic information resource for human cerebral stroke

SignaLink

SignaLink allows system-level analyses using the network of the major intracellular signaling pathways

Signalogs

Signalogs is an Orthology-based identification of novel signaling pathway components in three metazoans

SignS

SignS is a web tool for gene selection and signature finding in problems where the dependent variable is patient survival or, more generally, a right-censored variable

SimBiology 3.1

SimBiology¬ provides graphical and programmatic tools for computational systems biology and pharmacokinetics

SIPPER

SIPPER is a flexible method to integrate heterogeneous data into a metabolic network

SMART

SMART displays domains in the context of genomes and networks

SMPDB

The Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 350 small-molecule pathways found in humans

SNPranker

SNPranker is a gene-centric data mining tool for diseases associated SNP prioritization in GWAS

SOURCE

SOURCE is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports

SPARQLGraph

SPARQLGraph is a web-based platform for graphically querying biological Semantic Web databases

SPIKE

Signaling Pathway Integrated Knowledge Engine is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA microarray and other functional genomics data on interaction maps

SPIRE

SPIRE is a Systematic protein investigative research environment

StarBase

StarBase will decode miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data

STITCH

STITCH is an interaction network database for small molecules and proteins

STRING

STRING is global view on proteins and their functional interactions in 630 organisms

SuperTarget

SuperTarget is an on drug-target interactions resource

SyBiL

Systems Biology Linker is designed for visualizing pathway data files in BioPAX format, such as imported from Reactome and converting BioPAX file into SBML file

SZGR

SZGR is a comprehensive schizophrenia gene resource

T1DBase

T1DBase focuses on two research areas in type 1 diabetes (T1D) and the genetics of T1D susceptibility and beta cell biology

T2D-Db

T2D-Db is a database of all molecular factors reported to be involved in the pathogenesis of Type 2 diabetes in human, mouse and rat

T2D@ZJU

T2D@ZJU is a knowledgebase integrating heterogeneous connections associated with type 2 diabetes mellitus

T2DM-GeneMiner

T2DM-GeneMiner is a web resource for analysing genes in relation to type 2 diabetes mellitus

Taverna

Taverna Workbench is an open source tool for designing and executing workflows created by the myGrid project

TcoF-DB

TcoF-DB is provide a comprehensive starting point for investigations into transcriptional regulation that include PPIs between Transcription Factors, Transcription Co-factors and other proteins

TEAK

TEAK is a Topology Enrichment Analysis frameworK for detecting activated biological subpathways

The Cell Collective

The Cell Collective is an open and collaborative approach to systems biology

The Cell Cycle Ontology

The Cell Cycle Ontology is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process

TIM

TIM (Tools to Input Models) is a tool which integrates biological objects and information about biological process modelling

Toppgene

Toppgene Suite is an one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network

TranscriptomeBrowser

TranscriptomeBrowser is introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

TransDomain

TransDomain is a transitive domain-based method in protein-protein interaction prediction

TRANSPATH

TRANSPATH is an information resource for storing and visualizing signaling pathways and their pathological aberrations

tYNA platform

The tYNA platform for comparative interactomics is a web tool for managing, comparing and mining multiple networks

UCD 2D-PAGE Database

UCD 2D-PAGE Datavase is a Two-dimensional polyacrylamide gel electrophoresis database

UCSC Genome Browser

UCSC Genome Browser is an up-to-date source for genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations

UCSD-Nature Signaling Gateway

The UCSD-Nature Signaling Gateway is a comprehensive and up-to-the-minute resource for anyone interested in signal transduction

UniHI

The Unified Human Interactome database provides researchers with a comprehensive platform to query and access human protein-protein interaction (PPI) data

UniProtKB

The UniProt Knowledgebase is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation

VANTED

Visualization and Analysis of Networks containing Experimental Data makes it possible to load and edit graphs, which may represent biological pathways or functional hierarchies

varSelRF

varSelRF is a R package for gene selection and classification using random forest

VeryGene

VeryGene serves as a tissue-specific genes knowledgebase and a discovery tool to generate testable hypotheses for basic and clinical research

viPEr

Virtual pathway explorer is a cytoscape app, which integrates _omics data with interactome data

VirHostNet

VirHostNet (Virus-Host Network) is a knowledgebase system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annotation (molecular functions, cellular pathways, protein domains)

visANT

visANT is an integrative visual analysis tool for biologucal networjs and pathways

VisHiC

VisHiC is a public web server for clustering and interpreting gene expression data

Voronto

Voronto is a Mapper for expression data to ontologies

WAVe

WAVe is a web analysis of the variome

Web Apollo

Web Apollo is a web-based genomic annotation editing platform

WhichGenes

WhichGenes is a web-based interactive gene set building tool offering a very simple interface to extract always-updated gene lists from multiple databases and unstructured biological data sources

Wiki-Pi

A Web-Server of Annotated Human Protein-Protein Interactions to Aid in Discovery of Protein Function

WikiCell

WikiCell is a unified resource platform for human transcriptomics research

WikiPathways

WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community

WIM

WIM (Web Interfac for Modelling) is a tool which integrates biological objects and information about biological process modelling

WormBase

WormBase is a central data repository for nematode biology

YMDB

YMDB is a yeast metabolome database

yOWL

yOWL represent knowledge found in the Saccharomyces Genomes Database using OWL (Web Ontology Language).