Recent News

Come visit the PMN at PAG

There are many ways to connect with a PMN curator at the Plant and Animal Genome XIX Conference in San Diego, California. You can attend a computer demo featuring speakers from three groups who provide plant metabolic pathway databases, read our poster, or get one-on-one help at the Plant Genome DB Outreach Consortium booth 

  • Computer Demo:

Sunday, January 16, 3:50 PM

  • Poster: C891
  • Booth: 427

We look forward to seeing you there! 
 

New PMN BLAST datasets!

Are you looking for an enzyme in Arabidopsis or poplar that is similar to your favorite protein? Please check out the two new datasets that are available for BLAST analyses: 

  • AraCyc Enzymes
  • PoplarCyc Enzymes

Our original Reference Enzymes and PlantCyc Enzymes datasets are also still available for sequence similarity-based searching. 

New viewer for a global metabolic map

New viewer for a global metabolic map

  • Do you want to highlight a compound or reaction on a global metabolic map for a single species?
  • Would you like to overlay your transcript expression, proteomic, or metabolomic data onto a zoomable set of pathways?

Please come check out the new metabolic (cellular) overview using AraCyc or PoplarCyc. 

Read all about it . . . in the new PMN paper

  • Do you want a better understanding of how new PMN databases get predicted from genome sequences?
  • Would you like to read about potential ways to put the PMN to work in your research project?

Please come check out our recent article in Plant Physiology for this information and much more . . .

PlantMetabolomics.org and the PMN

The PMN is eager to work with scientists who want to do metabolic-pathway-based analyses.
PlantMetabolomics.org is a data repository for a series of metabolomic experiments performed in Arabidopis thaliana
You can read about efforts to incorporate their experimentally identified compounds into AraCyc in Bais et al 2010

New PMN releases! - PlantCyc 3.0, AraCyc 6.0, and PoplarCyc 1.0

The Plant Metabolic Network is pleased to announce new releases of the metabolic pathway databases AraCyc 6.0 and PlantCyc 3.0, plus the inaugural release of PoplarCyc 1.0

This PMN release includes many updates to AraCyc enzyme/reaction assignments based on a new PMN enzyme annotation pipeline, plus, 34 additional pathways have been added to AraCyc 6.0.

PoplarCyc 1.0 was created by applying the PMN enzyme annotation pipeline to the Populus trichocarpa 1.1 genome release sequences provided by JGI, and then using the Pathologic software from SRI International. The new computationally predicted database was then validated by PMN curators. 321 pathways and 3434 predicted poplar enzymes are now available in PoplarCyc 1.0. The data have also been incorporated into PlantCyc 3.0. In addition, 75 new pathways have been added to the new version of PlantCyc.

The PMN also now provides a BLAST tool and two customized enzyme sets for PMN users.

PMN Summer Road Shows!

Many researchers and students from around the world had a chance to see PMN presentations and posters at conferences and universities during the summer of 2009.

  • CIGRAS / UCR 

July 27-31 San Pedro, Costa Rica

  • American Society of Plant Biologists

July 18 - 22, Honolulu, HI

  • 20th International Conference on Arabidopsis Research

June 30 - July 4, Edinburgh, Scotland

Please see our presentations page for more details.

PlantCyc 2.0 and AraCyc 5.0 release!

These releases contain many new pathways, enzymes, reactions, and compounds!

A few highlights . . .

  • PlantCyc 2.0 has a whole new set of predicted enzymes from Medicago, tomato, and rice mapped onto the metabolic pathways and more . . .
  • AraCyc 5.0 has new compounds identified through the NSF 2010 Metabolomics Project and from the KNApSAcK database and more . . .
  • You can read about all the new data and features in the PlantCyc and AraCyc release notes.
  • New downloads of the database files are available for registered users. Please sign-up today if you would like to access these valuable resources.
  • We are grateful for help from our contributors in the scientific community.

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