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aMAZE is a workBench for the representation, management, annotation and analysis of information on networks of cellular processes: genetic regulation, biochemical pathways, signal transductions.
BIOBASE develop and distribute molecular biological databases and software tools encompassing all areas of gene regulation and signal transduction.
BioCyc is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism.
BIND: Biomolecular Interaction Network Database is an expanding database of biomolecular interaction, pathway and complex information. All information is stored in BIND database records that are freely available through a web interface that allows users to query, view, and submit records.
BRITE: Biomolecular Relations in Information Transmission and Expression is a database of binary relations for network computation and logical reasoning involving genes, proteins, and other biological molecules. It contains diverse sets of binary relations, including the generalized protein interactions that underlie the KEGG pathway diagrams, systematic experimental data on protein-protein interactions by yeast two-hybrid systems, expression similarity relations by microarray gene expression profiles, cross-reference links between database entries, and parent-child relations in the hierarchies of terminology (ontologies).
BRENDA is the main collection of enzyme functional data available to the scientific community. It is available free-of-charge for academic, non-profit users via the internet.
CSNDB: Cell Signaling Networks Database is a data- and knowledge- base for signaling pathways of human cells. It compiles the information on biological molecules, sequences, structures, functions, and biological reactions which transfer the cellular signals. Signaling pathways are compiled as binary relationships of biomolecules and represented by graphs drawn automatically.
DIP: Database of Interacting Proteins catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
GRID: General Repository for Interaction Datasets is a database of genetic and physical interactions.
KEGG: Kyoto Encyclopedia of Genes and Genomes is a bioinformatics resource for understanding higher order functional meanings and utilities of the cell or the organism from its genome information.
MEDLINE is NLM's database of indexed journal citations and abstracts now covering nearly 4,500 journals published in the United States and more than 70 other countries. Available for online searching since 1971, MEDLINE includes references to articles indexed from 1966 to the present. New citations are added weekly. All citations in MEDLINE are assigned MeSH® Terms and Publication Types from NLM's controlled vocabulary. MEDLINE citations and abstracts are available as the primary component of NLM's PubMed database, which is searchable via the Internet.
MetaCyc contains pathways from over 150 different organisms. MetaCyc describes metabolic pathways, reactions, enzymes, and substrate compounds. The MetaCyc data were gathered from a variety of literature and on-line sources, and contain citations to the source of each pathway.
MINT: Molecular Interactions Database is a relational database designed to store interactions between biological molecules. Beyond cataloguing the formation of binary complexes, MINT was conceived to store other type of functional interactions namely enzymatic modifications of one of the partners. Presently MINT focuses on experimentally verified protein-protein interactions with special emphasis on mammalian organisms. MINT consists of entries extracted from the scientific literature by curators.
PathDB is a research tool for scientists interested in analyzing their experimental or computational data in the context of biological pathways and networks.
Reactome is a curated database of biological processes in humans. It covers
biological pathways ranging from the basic processes of metabolism to high-level processes such as hormonal signalling. While Reactome is targeted at
human pathways, it also includes many individual biochemical reactions from non-human systems such as rat, mouse, fugu fish and zebra fish.
SPAD: Signaling Pathway Database is an integrated database for genetic information and signal transduction systems.
TRANSFAC is a database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles.
TRANSPATH comprises data about molecules participating in signal transduction and the reactions they undergo, thus spanning a complex network of interconnected signalling components. TRANSPATH focuses on signalling cascades that aim at transcription factors and thus alter the gene expression profile of a given cell.
Alliance for Cellular Signaling aims to understand as completely as possible the relationships between sets of inputs and outputs in signaling cells that vary both temporally and spatially.
Beilstein-Institut is a non-profit making foundation established under civil law and is located in Frankfurt am Main. The foundation pursues its purpose in paricular in chemistry and its related areas and disciplines, espeically information and communication.
BioKin is a scientific consulting and software development business with a range of software including DynaFit for the simulation and statistical analysis of complex kinetics and multiple simultaneous equilibria arising in chemistry, biochemistry, biology.
BioPathways Consortium aims to catalyze the emergence and development of computational pathways biology, by building up a strong and coherent scientific community, sharing knowledge, facilitating collaborations, and fostering the development of methods and tools of wide interest to the community.
BioPAX: Biological Pathways Exchange aims to develop a common exchange format for biological pathways data.
BioSPICE aim to create an open source framework and toolset for modeling dynamic cellular network functions and around this to develop a user community committed to using, extending and exploiting these tools to further our knowledge of biologic processes.
CellML is an open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based biological models.
DOEgenomes.org is the website of the genome programs of the US Department of Energy Office of Science, founder of the Human Genome Project and leader in systems biology research.
Gene Network Sciences accelerates the drug discovery process by creating dynamic computer models of living cells and next generation data-mining tools for pharmaceutical and biotechnology companies. GNS combines the power of mathematics, computation, experimental molecular biology, and bioinformatics to bring genomics data to its most valuable end -- making drug discovery predictive.
HUPO: Human Proteome Organisation aims to consolidate national and regional proteome organisations into a worldwide organisation (HUPO).
PSI: Proteomics Standards Initiative aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification.
Signaling Gateway is a comprehensive and up-to-the-minute resource for anyone interested in signal transduction. This Gateway represents a unique collaboration between academia and scientific publishing and is designed to facilitate navigation of the complex world of research into cellular signaling.
STKE: Signal Transduction Knowledge Environment aims to identiyy and develop a mix of tools and approaches (algorithms, schemas, programs, and human organizational structures) that are stable, scalable, inter-operable, and cost-effective for providing access to information on cell signaling.
Systems Biology is an emergent field that aims at system-level understanding of biological systems.
SBML: Systems Biology Markup Language is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and many other areas in systems biology.
BPS: Biochemical Pathway Simulator aims to model diverse biochemical networks and develop an associated computational system to facilitate the analysis of the behaviour of these networks. Biochemical pathways govern fundamental biological control networks; while individual pathways are understood, the combinatorial complexity of the biological control apparatus is too high to be fully understood through "wet" analysis alone.
COPASI: Complex Pathway Simulator is a new simulator for biochemical networks that follows the directions set by the popular Gepasi software. COPASI is expected to be released in beta version before the end of 2003. The software will be free for non-profit research purposes.
E-Cell is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation.
Genomic Object Net is an enviroment for simulating and representing biological systems. It is an integrated tool consisting of several kinds of software tools for describing biopathways, visualizing simulation results, evaluating a hypothesis, biopathways recreation from biopathway databases, and so on.
GEPASI: General Pathway Simulator is a software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any function of the model, perform metabolic control analysis and linear stability analysis. Gepasi simplifies the task of model building by assisting the user in translating the language of chemistry (reactions) to mathematics (matrices and differential equations) in a transparent way. This is combined with a set of sophisticated numerical algorithms that assure the results are obtained fast and accurate.
JigCell allows users to input models for intra-cellular regulatory networks using a spreadsheet paradigm for subsequent simulation and analysis.
JWS is an online cellular systems modelling facility complete with a database of models.
KineCyte is a full-functioned Macintosh application written for biologists for describing, simulating and analyzing both simple and complex cell biological systems.
METATOOL serves to derive conclusions about the pathway structure of metabolic networks from the stoichiometric reaction equations and information about reversibility and irreversibility of enzymes.
National Resource for Cell Analysis and Modeling is developing methods for modeling cell physiological processes in the context of the actual three dimensional structure of individual cells. Approaches in computational cell biology are coupled with high resolution light microscopy to facilitate the interplay between experimental manipulation and computational simulation of specific cellular processes. NRCAM has developed a general computational tool, the Virtual Cell for modeling cell biological processes. This new technology associates biochemical and electrophysiological data describing individual reactions with experimental microscopic image data describing their subcellular locations. A transparent mathematics framework develops numerical simulations, and results can be analyzed as images.
Quantifying Signal Transduction is an EC-funded project starting early in 2004 that deals with signalling through MAP kinase pathways, taking a systems biology approach.
Proteomic Pathway Project allows you to observe genes interacting in dynamic graphical models. Online maps depict molecular relationships from areas of active research. In an "open source" approach, this community-fed forum constantly integrates emerging proteomic information from the scientific community. It also catalogs and summarizes important resources providing information for over 120,000 genes from multiple species.
ScrumPY is an open-source Python package for biochemical modelling.
BioMiner is a new software system for analyzing and visualizing complex biochemical networks and processes.
Biopathways Graph Data Manager is a general purpose graph data management system which can be adapted (by means of suitable schema(s)) to support biopathways and protein interaction network databases for microbial organisms.
Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. As a key feature, Cytoscape provides an algorithm which filters through a network to identify the particular cellular signaling and regulatory pathways that control the changes in gene expression observed by microarray.
ExPASY Biochemical Pathways gives access to the digitized version of the Roche Applied Science Biochemical Pathways wall chart.
GeneWays is a system for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. The system focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as an open platform, allowing researchers to query, review and critique the integrated information.
NetBuilder is a graphical tool for building logical representations
of genetic regulatory networks.
PathExplore is a "K" based system that takes individual biochemical reactions and from them builds metabolic pathways. However, PathExplore is more than just a metabolic database it is designed to help users analyze gene expression (microarray), metabolomic and/or proteome data with respect to biochemical pathways and metabolism.
PathwayAssist is a powerful, user-friendly software package that allows you to build, visualize and explore biological association networks (BAN). A BAN is an interactive diagram that shows the biological interactions amongst different proteins, small molecules and cellular processes.
GO: Gene Ontology Consortium aims to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. GO provides three structured networks of defined terms to describe gene product attributes.
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