Image courtesy of John Burns (Cyanolab) and Cyanosite.
Cellular Dashboard image generated by Pathway Tools.
Image courtesy of Jeff Johansen (John Carrol University) and Cyanosite
Cellular Overview image generated by Pathway Tools.
This image is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.
Image courtesy of Pacific Northwest National Laboratory.
This image is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.
Multiple Sequence Alignment results generated by Pathway Tools using MUSCLE.
PatMatch query and results by Pathway Tools.
Metabolic Modeling with MetaFlux
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One-stop destination to explore, analyze and visualize cyanobacteria genomes and metabolic pathways
CyanoCyc unique data content:
- Hundreds of cyanobacteria genomes; six curated from the cyanobacterial literature:
- Nostoc (Anabaena) sp. PCC 7120 *NEWLY CURATED*
- Synechocystis sp. PCC 6803 substr. Kazusa
(See our paper here ) - Synechococcus elongatus PCC 7942
- Synechococcus sp. WH8102
- Prochlorococcus marinus SS120 and MED4
- Curated information about protein function, transporters and pathways curated by biochemists and cyanobacteriologists with evidence from cyanobacteria literature
- New and old taxonomic nomenclature and accession #s provided - easy to find your favorite cyanobacteria and/or genes
Read more about these tools and other information about CyanoCyc and cyanobacteria on the CyanoCyc Intro page.
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Learning Library
Tutorial Videos
Tutorial #1: Introduction to BioCyc
Tutorial #2: Introduction to SmartTables
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.
Tutorial #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network
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.
Tutorial #4: Omics Data Analysis
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.
Tutorial #5: Pathway Collages
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.
Tutorial #6: Creating a Pathway/Genome Database
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.
- Part 1A: Introduction to Database Building and Pathologic (14:04)
- Part 1B: Building a Database: Detailed Pathologic Example (23:53)
- Part 2A: General Editing Strategies (8:00)
- Part 2B: Creating and Editing Reactions and Compounds (17:32)
- Part 2C: Updating Proteins, Citations, GO Terms, and Enzymatic Reactions (26:10)
- Part 2D: Making and Editing Pathways (9:42)
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.