This is the official Mastodon account for BioCyc and Pathway Tools, including EcoCyc, MetaCyc and other related sites.
BioCyc is a collection of Pathway/Genome Databases for over 20,000 organisms, plus software tools for exploring them. BioCyc is an encyclopedic reference that contains curated data from 130,000 publications.
Pathway Tools is a comprehensive bioinformatics software package that spans enterprise genome data management, systems biology, and omics analysis.
| BioCyc | https://biocyc.org |
| EcoCyc | https://ecocyc.org |
| MetaCyc | https://metacyc.org |
| Pathway Tools | http://bioinformatics.ai.sri.com/ptools/ |
Our paper about CyanoCyc and the community curation review project of Synechocystis sp. PCC 6803 substrain Kazusa has just been published in Frontiers in Microbiology: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1340413/full
Read about how CyanoCyc started in order to address a real need by the research community and how to use some of the powerful bioinformatics tools available with the hundreds of cyanobacterial genome databases.
The Omics Dashboard is a software tool for interactive exploration and analysis of metabolomics, transcriptomics, proteomics, and multi-omics datasets. Organized as a hierarchy of cellular systems, the Dashboard at its highest level contains graphical panels for the full range of cellular systems, including biosynthesis, energy metabolism, and response to stimulus. Thus, the Dashboard top level surveys the state of the cell across a broad range of key systems in a single screen. Each Dashboard panel contains a series of X–Y plots depicting the aggregated omics data values relevant to different subsystems of that panel, e.g., subsystems within the biosynthesis panel include amino acid biosynthesis, carbohydrate biosynthesis and cofactor biosynthesis. Users can interactively drill down to focus in on successively lower-level subsystems of interest. In this article, we present for the first time the metabolomics analysis capabilities of the Omics Dashboard, along with significant new extensions to better accommodate metabolomics datasets, enable analysis and visualization of multi-omics datasets, and provide new data-filtering options.
Upcoming BioCyc Webinar:
The Comparative Genome Dashboard
May 18, 10am PDT
For more info and registration, see
https://sri.zoomgov.com/meeting/register/vJIsf-ytqTIuGYXu2mLvFN9RXt2D7fABt0E
#introduction
This is the official account for BioCyc and Pathway Tools. The account is currently being managed by @smpaley. I'll be posting announcements, answering any questions, and boosting relevant posts from members of our team and user community (will follow and engage with posts carrying hashtag #BioCyc).
