BioCyc database collection

BioCyc Database Collection

The BioCyc Database Collection is a comprehensive resource for bioinformatics and computational biology, focusing on the integration and analysis of genomic and metabolic information for thousands of organisms. Developed and maintained by the SRI International's Bioinformatics Research Group, BioCyc provides tools for navigating, visualizing, and analyzing the underlying data, and for facilitating systems biology research and education.

Overview

BioCyc encompasses a wide array of databases, each dedicated to a specific organism or a group of organisms. These databases are generated through an automated process that combines information from various sources, including genomic sequences, biochemical pathways, and gene functions. The most prominent databases within the BioCyc collection include the EcoCyc database, which focuses on Escherichia coli K-12, and the MetaCyc database, a comprehensive database of non-redundant, experimentally elucidated metabolic pathways from all domains of life.

Features

The BioCyc Database Collection offers a multitude of features designed to support the exploration and analysis of biological data:

• Pathway Tools Software: An integrated software environment that enables users to query, visualize, and analyze the databases.
• Pathway/Genome Navigator: Allows for interactive exploration of metabolic pathways, genome maps, and regulatory networks.
• Omics Viewer: Facilitates the visualization of omics data (e.g., transcriptomics, proteomics, metabolomics) in the context of metabolic pathways and genome maps.
• SmartTables: Enables users to create, share, and manipulate tables of data extracted from the databases.

Applications

The BioCyc Database Collection is utilized in a variety of research and educational settings:

• Systems Biology: Supports the modeling and simulation of biological systems to understand the complex interactions within cells and between organisms.
• Metabolic Engineering: Aids in the design of genetically modified organisms for the production of pharmaceuticals, biofuels, and other chemicals.
• Drug Discovery: Facilitates the identification of drug targets and the understanding of drug mechanisms.
• Education: Serves as a resource for teaching concepts in systems biology, metabolic pathways, and genomics.

Access

The BioCyc Database Collection is accessible online through subscription and free accounts, with different levels of access and functionality. Academic users and non-profit organizations can apply for free access, while commercial users require a subscription.

Future Directions

The BioCyc team continuously works on expanding the database collection, improving the software tools, and incorporating new types of data. Future developments aim to enhance the understanding of biological systems through the integration of more comprehensive and diverse datasets, including environmental and ecological data.

External Links

• BioCyc Database Collection Homepage

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BioCyc database collection gallery

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