BioCyc Tutorials on Youtube
Tutorials on Demand: Download Tutorial Videos
The BioCyc on Demand Tutorial series introduces basic and advanced features of the BioCyc website and the Pathway Tools software system via a combination of narration and practical demonstration. Tutorial videos can be downloaded directly from the links on this page.
Tutorial #1: Introduction to BioCyc
Make the most of BioCyc! The "Introduction to BioCyc" Tutorial introduces you to the BioCyc.org site and to the BioCyc collection of thousands of Pathway/Genome Databases.
"Introduction to BioCyc" is presented here in 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.
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. To download or view, click one of the links below.
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
in various respects, such as overlaying omics data, altering the relative
positions of pathways, and modifying connections among pathways.
This Tutorial will show you how to generate, customize and export
high-quality pathway-collage diagrams showing collections of user-specified pathways.
Tutorial #6: Creating a Pathway/Genome Database
This Tutorial walks you through the process of building a BioCyc-like Pathway/Genome Database (PGDB)
for an organism with a sequenced and annotated genome. Learn how to predict metabolic pathways and operons, how
to revise gene and protein annotations, build metabolic pathways, make protein complexes,
add metabolic reactions and compounds, and assign Gene Ontology (GO) terms to genes. Build a PGDB for your own lab
or for the whole scientific community. Segments:
Tutorial #7: Using the Structured Advanced Query Page
The Structured Advanced Query Page enables construction of complex queries to PGDBs, and queries across one or more databases in the BioCyc collection. In this Tutorial, 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
To download or view, click one of the links below.
Recordings from Live BioCyc Tutorials
We have been conducting tutorials and other special webinars on Zoom since 2021. We record many of these and make them available here.
- Introduction to BioCyc for new Students and PostDocs.
- Part 1, Presented by Peter Karp, November 3, 2021. YouTube or
- Part 2, Presented by Peter Midford, November 10, 2021. YouTube or
- Part 3, Presented by Suzanne Paley, November 17, 2021. YouTube or
- PGDB Editing Tutorial, presented by Ron Caspi.
- Helicobacter pylori Tutorial, presented by Ron Caspi, March 17, 2022.
- Introduction to Pathway Tools Tutorial, presented by Peter Karp, April 5, 2022.
- Pathway Tools Computational Inferences Tutorial, presented by Peter Karp, April 12, 2022.