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The first part of this bioinformatics workshop provides a tutorial for using the BioCyc pathway/genome web portal and Pathway Tools software developed by the Bioinformatics Research Group at SRI International.

BioCyc contains genomes and metabolic reconstructions for about 18,000 organisms (bacteria, yeast, mouse, fly and human) as well as tools for omics data analysis. Users can paint omics data onto pathway diagrams and zoomable metabolic network diagrams, conduct enrichment analysis and, using the Omics Dashboard, get an integrative visual view of the activation levels of different cellular systems. The Pathway Tools software enables scientists to create metabolic reconstructions and quantitative metabolic models for genomes sequenced in their labs or elsewhere.

In the second part of the workshop, Jeremy Zucker of the Pacific Northwest National Lab gives a talk about Pathway Tools-based metabolic reconstructions. It is titled “AI-assisted metabolic and regulatory investigations of the circadian clock in the filamentous fungus Neurospora crassa.”