BioCyc Updates

New subscription services from BioCyc.org

Mon, 15 Mar 2010 08:19:42 PDT

You can now keep track of events and updates from BioCyc.org and Pathway Tools via RSS and iCal feeds in addition to our email announcement list.

Upcoming Pathway Tools Tutorial and Workshop

Mon, 15 Mar 2010 08:19:42 PDT

Pathway Tools Tutorial Date: May 17th - 20th, 2010 Location: SRI International, Menlo Park, CA Pathway Tools Workshop Date: June 14th - 18th, 2010 Location: SRI International, Menlo Park, CA

Pathway Tools Tutorial: Spots Available

Thu, 29 Apr 2010 11:25:42 PDT

Pathway Tools Tutorial Date: May 17th - 20th, 2010 Location: SRI International, Menlo Park, CA The tutorial will consist of a four day introduction to Pathway Tools that will introduce users to the Pathway/Genome Navigator, Editors, and PathoLogic, and will include creation of a new Pathway/Genome Database (PGDB). Please register soon as only a few spots remain. A few spots remain for this May's Pathway Tools Tutorial. Register today!

Pathway Tools Workshop: Registration Now Open

Wed, 16 Jun 2010 11:25:42 PDT

Pathway Tools Workshop Date: June 14th - 18th, 2010 Location: SRI International, Menlo Park, CA The Pathway Tools Workshop will cover several topics: o Scientific talks by Pathway Tools users and SRI staff o Tutorials on advanced aspects of Pathway Tools, such as its schema and how to query PGDBs programatically o Working sessions to upgrade user PGDBs based on new Pathway Tools functionality o 'Hackathons' where users and Pathway Tools staff develop add-on software modules to Pathway Tools, such as using the Lisp, Perl and Java APIs.

BioCyc.org 14.1 Website Release

Wed, 16 Jun 2010 11:25:42 PDT

BioCyc.org 14.1 includes 673 databases.

EcoCyc [release notes] EcoCyc updates include two new signal-transduction pathways and three new catabolic pathways.
MetaCyc [release notes] In this release of MetaCyc we added 67 new pathways and significantly revised 37 pathways, for a total of 104 new and updated pathways. In microbial metabolism we added numerous pathways describing the biosynthesis or degradation of a large variety of compounds. One of the main topics in microbial metabolism during this release was peptidoglycan biosynthesis. We now cover more details of this important process, such as amidation of L-glutamate residues in the pentapeptide component, formation of cross-bridges, and trans-peptidation. We added new variants that describe peptidoglycan biosynthesis in important pathogens among the staphylococci, mycobacteria and enterococci, as well as new pathways that explain the nature of resistance to antibiotics that interfere with peptidoglycan synthesis such as vancomycin and teicoplanin. New plant pathways cover the metabolism of plant defense compounds, signaling compounds, polyamines, fatty acids and sphingolipids. Of note are six monoterpene biosynthesis pathways whose products are used in cosmetic fragrances and as food additives. Last, but not least, are a few animal pathways, including the degradation of hemoglobin by the malaria parasite Plasmodium, the biosynthesis of diphthamide, and the biosynthesis of certain melanin pigments.
HumanCyc [release notes] curation continues in conjunction with the Pharmacometabolomics Research Network (PMRN). This is a multi-year collaboration to develop tools and provide resources for the metabolomics community; to this end we have focused on curation of information from the scientific literature concerning chemical compoundsand enzymes of interest to the PMRN and the larger field of metabolomics. For this release, we have curated metabolic pathways for vitamins, ingested nutrients and energy regulation.
BsubCyc [release notes] now includes data on transcriptional regulation that was imported from DBTBS. Orthologs for B.subtilis genes have been included in this release, enabling use of all comparative analysis tools.

Pathway Tools Workshop 2010 Registration Now Open

Thu, 8 Jul 2010 11:25:42 PDT

Pathway Tools Workshop 2010 Registration Now Open Registration is now open for the Pathway Tools Workshop on October 25th - 29th, 2010 in Menlo Park, CA. Please visit our registration website for details on speakers, fees, travel, and hotels: http://bioinformatics.ai.sri.com/ptools10/ Registration fees go up on September 1st. Looking forward to seeing you at an upcoming Pathway Tools event. Best regards, ~Tomer Altman (650)859-2692 Pathway Tools Workshop Coordinator --- Pathway Tools Workshop October 25th-29th, 2010 Hosted by the Bioinformatics Research Group http://brg.ai.sri.com/ at SRI International http://www.sri.com http://bioinformatics.ai.sri.com/ptools10/