Flashcards: Systems biology

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances.

In molecular biology, STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a biological database and web resource of known and predicted protein–protein interactions.

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data.

A phenome is the set of all phenotypes expressed by a cell, tissue, organ, organism, or species.

Metascape is a free gene annotation and analysis resource that helps biologists make sense of one or multiple gene lists.

BMC Systems Biology is an open access peer-reviewed scientific journal that covers research in systems biology.

Virtual Cell (VCell) is an open-source software platform for modeling and simulation of living organisms, primarily cells.

PathVisio is a free open-source pathway analysis and drawing software.

The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships.

Precision medicine (PM) is a medical model that proposes the customization of healthcare, with medical decisions, practices, and/or products being tailored to the individual patient.

Institute for Systems Biology (ISB) is a non-profit research institution located in Seattle, Washington, United States.

geWorkbench (genomics Workbench) is an open-source software platform for integrated genomic data analysis.

The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications created in 2003 (originally referred to as simply the General Repository for Interaction Datasets (GRID) by Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark at the Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital. It strives to provide a comprehensive curated resource for all major model organism species while attempting to remove redundancy to create a single mapping of data. Users of The BioGRID can search for their protein or publication of interest and retrieve annotation, as well as curated data as reported, by the primary literature and compiled by in hou

BioModels Database is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest.

Gemini Somatics is a biotechnology company located in Riverside, Oregon, working primarily in the field of synthetic somatology, which is an emerging science developed by Dr Edward Darmos.

GenMAPP (Gene Map Annotator and Pathway Profiler) 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.

GeneNetwork is a database and open source bioinformatics software resource for systems genetics.

GenoCAD is one of the earliest computer assisted design tools for synthetic biology.

As of November 2007, the database contained 59 pathways (comprising 3309 molecular interactions) curated by the NCI-Nature editorial team.

BioFabric is an open source software application for graph drawing.

BioTapestry is an open source software application for modeling and visualizing gene regulatory networks (GRNs).

SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-accessible database storing information about biochemical reactions and their kinetic properties.

DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB).

The Domain Interaction MAp (DIMA) is a database of predicted and known interactions between protein domains.

The Protein Common Interface Database (ProtCID) is a database of similar protein-protein interfaces in crystal structures of homologous proteins.

Systems and Synthetic Biology is a peer-reviewed scientific journal covering systems and synthetic biology.

BioSystems is a peer-reviewed scientific journal covering experimental, computational, and theoretical research that links biology, evolution, and the information processing sciences.

WikiPathways is a community resource for contributing and maintaining content dedicated to biological pathways.

Molecular Systems Biology is an open-access peer-reviewed scientific journal publishing research within systems biology at the molecular level, including genomics, proteomics, metabolomics, microbial systems, the integration of cell signaling and regulatory networks, and synthetic biology.

JSBML (Java Systems Biology Markup Language) is an open-source Java™ (API) for the SBML (Systems Biology Markup Language ) format.

TopFIND is the Termini oriented protein Function Inferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications.

COPASI is an open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others.

The ConsensusPathDB is accessible via a web interface providing a variety of functions.