Desktop Application
Bring the power of BioCyc.org securely in-house, with the abilities to create and
edit PGDBs, perform metabolic modeling, and query/update using APIs.
BioCyc integrates genome data with a comprehensive body of additional data including metabolic reconstructions, regulatory networks, protein features, orthologs, gene essentiality, and atom mappings.
Browsers for genomes, metabolic networks, and regulatory networks. Transcriptomics and metabolomics data analysis, comparative analysis, and metabolic route search. Sequence search and alignment.
Cellular Overview image generated by Pathway Tools.
Pseudomonas aeruginosa on your iPhone and iPad
Have you ever wanted to quickly find out what is known about a gene, protein or pathway that was just mentioned in a talk or on a poster? Download the free BioCyc iPhone app to browse BioCyc on the go! Try the iPad version as well.
Cellular Dashboard image generated by Pathway Tools.
Pseudomonas aeruginosa Pathway/Genome Databases
This webside contains 117 Pseudomonas aeruginosa genomes (show list) and associated metabolic pathways. This site is part of the larger BioCyc collection of thousands of Pathway/Genome Databases for sequenced genomes. Click the "Change Current Database" bottom (above) explore the available databases.
This site includes extensive retrieval, visualization and analysis tools, including a genome browser and a Metabolic map diagram. There are tools for analysis of gene expression, metabolomics and ChIP-chip data. You can search and align sequences for Pseudomonas aeruginosa and other microbial genomes and perform comparative analysis. You can store groups of genes and pathways into a SmartTable, and then browse, analyze and share with other users.
Paul Babitzke Prof. of Biochemistry & Molecular Biology
"My lab uses these resources on a daily basis."
Patricia Kiley, Professor and Chair, Dep't. of Biomolecular Chemistry
"We rely on BioCyc's Gene Pages and Overview Diagrams almost daily."
Arkady Khodursky Assoc. Prof. Biochemistry
"We use BioCyc and MetaCyc extensively to investigate the metabolic and regulatory processes of organisms we study."
William Cannon, Team Lead Computational Biology
"BioCyc is the go-to resource of knowledge and tools for Ginkgo scientists."
"BioCyc is a tremendous resource for pathway analysis in metabolomics."
Art Edison, Dept of Genetics
"We make extensive use of the BioCyc full metabolic network diagram for omics data analysis."
Timothy J. Donohue, Director
"I have not found another database that has a better interface than BioCyc."
Gary B. Huffnagle, Professor Microbiology and Immunology
Learning Library
Tutorial Videos
Tutorial #1: Introduction to BioCyc
These six sequential
segments, giving you a guided tour of the BioCyc collection in concise
bites. To download or view, just click on one of the links
following each segment's name.
The following Tutorial will guide you through SmartTables, which enable you
to create, upload, share, and analyze sets of genes, metabolites, pathways, and sequence sites.
The Tutorial is broken up into parts, ranging from basic operations to more advanced uses such
as gene expression analysis and metabolomics. To download or view, click one of the links below.
This tutorial introduces users to many of the advanced tools available on the BioCyc.org website for navigating cellular networks, analyzing large-scale datasets, and comparing organisms.
This tutorial will show you how to use BioCyc's tools for omics data analysis, including the cellular omics viewer, the omics dashboard, and other tools.
Pathway collages are multi-pathway diagrams that you can customize
by, for example, overlaying omics data, altering the relative
positions of pathways, and modifying connections among pathways.
Learn how to generate, customize and export
high-quality pathway-collage diagrams showing collections of user-specified pathways.
Learn the entire process of building a BioCyc-like Pathway/Genome Database (PGDB)
for an organism with a sequenced and annotated
genome. Build a PGDB for your own lab or for the whole scientific community.
Tutorial #7: Using the Structured Advanced Query Page
An introduction to the Structured Advanced Query Page, which allows
complex queries and queries across one or more databases in the
BioCyc collection. You'll learn about:The basic steps of setting up an advanced query;
Four examples of increasingly complex queries, including how to query across multiple databases;
Where to learn more about the structure of BioCyc databases.
