Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014

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Introduction to BioCyc
5500 Databases
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Web Services

Other Pathway/Genome Databases

Curated Pathway/Genome Databases for many organisms have been created by a variety of institutions and are available from the following Web sites.

In addition to accessing them through the Web, many of these PGDBs can be downloaded to your local copy of Pathway Tools through the PGDB registry described later in this page.

Database Scope Organization
ApiCyc Cryptosporidium hominis TU502
Cyrptosporidium parvum IOWA
Plasmodium berghei ANKA
Plasmodium chadaudi AS
Plasomodium falsiparum 3D7
Plasmodium vivax Sal-1
Plasomodium yoelii 17XNL
Toxoplasma gondii ME49
EuPathDB (Eukaryotic Pathogens Database Resources) , USA
AcypiCyc Acyrthosiphon pisum Universite de Lyon Universite de Lyon
AraCyc Arabidopsis thaliana S. Rhee, Department of Plant Biology, Carnegie Institution, USA
ArthropodaCyc PGDBs for 11 organisms ArthropodaCyc group, France
AsperCyc PGDBs for 8 organisms CADRE team, University of Manchester
BeoCyc 33 BioEnergy organisms BioEnergy Science Center
CalbiCyc Candida albicans Department of Genetics, Stanford U., USA
ChlamyCyc Chlamydomonas reinhardtii GoFORSYS, Germany
DictyCyc Dictyostelium discoideum dictyBase, Northwestern U., USA
FungiCyc PGDBs for 23 organisms Broad Institute, USA
GeneDB PGDBs for 3 organisms Sanger Institute
Gramene Arabidopsis lyrata
Arabidopsis thaliana
Brachypodium distachyon
Chlamydomonas reinhardtii
Cyanidioschyzon merolae
Glycine max
Oryza barthii
Oryza brachyantha
Oryza glaberrima
Oryza minutabb
Oryza minutacc
Oryza nivara
Oryza officinalis
Oryza punctata
Oryza rufipogon
Oryza rufipogon3s
Oryza sativa Nipponbare
(Japonica rice) Oryza indica 93-11 (Indica rice)
Physcomitrella patens
Populus trichocarpa
Selaginella moellendorffii
Sorghum bicolor BTX623
Vitis vinifera
Zea mays
EnsemblGenomes and Gramene , CSHL
LeishCyc Leishmania major Friedlin Bio21 Institute, University of Melbourne, Australia
MedicCyc Medicago truncatula Samuel Roberts Noble Foundation, USA
MicroScope PGDBs for 695 Organisms C. Medigue, Genoscope, France
MpCyc Moniliophthora perniciosa Laboratorio de Genomica e Expressao, Brazil
MouseCyc Mus musculus C. Bult, Jackson Laboratory, USA
Metabolic Network of P. chrysosporium and P. arnosa Phanerochaetea  chrysosporium
Phanerochaetea  carnosa
University of Toronto
PlantCyc Arabidopsis thaliana col
Manihot esculenta esculenta
Zea mays mays
Vitis vinifera
Populus trichocarpa
Glycine max
Plant Metabolic Network, Carnegie Institution, USA
PseudoCyc Pseudomonas aeruginosa F. Brinkman, Pseudomonas Genome Project, Simon Fraser U., Canada
RetliDB Rhizobium etli Center for Genomic Sciences, Mexico
RiceCyc Oryza sativa
Sorghum bicolor
Gramene curators, Cornell U. and CSHL
ScoCyc Streptomyces coelicolor A3(2) V. Armendarez, G. Chandra, M. Bibb, John Innes Centre, UK
ShewCyc 18 Shewanella genomes Margrethe H Serres, Marine Biological Laboratory
SolCyc Solanum lycopersicum
Solanum tuberosum
Solanum melongena
Petunia hybrida
Capsicum anuum
Coffee caniphora
Sol Genomics Network, USA
SoyCyc Glycine max Integrated Genetics and Molecular Biology for Soybean Researchers
TBestDB Taxonomically Broad EST Database TBestDB Group, Canada
TBCyc Mycobacterium tuberculosis H37Rv TB Database, Stanford U.
Yeast Biochemical Pathways Saccharomyces cerevisiae SGD Curators, Stanford U., USA

Contact us if you'd like your PGDB added to this list.

Registry of Downloadable Pathway/Genome Databases

The PGDB Registry allows users who have installed Pathway Tools locally to easily download PGDBs created by others, or share PGDBs that they have created. Advantages of this approach are that it makes the full power of Pathway Tools available for other PGDBs, and it allows comparative analysis of multiple PGDBs within the same instance of Pathway Tools. [access registry]

Create Your Own Pathway/Genome Database

Interested in creating a pathway/genome DB for your genome? [learn more]