Collects Pathway/Genome Databases from the Human Gut. GutCyc is a compendium of over 418 environmental pathway genome databases (ePGDBs) constructed from public shotgun metagenome datasets generated by the HMP5, the MetaHIT inflammatory bowel disease study, and the Blood Glucose Indexes (BGI) diabetes study. The platform provides consistent taxonomic and functional annotations, facilitates large-scale and reproducible comparisons between ePGDBs, and directly links into software and database resources for exploring and interpreting metabolic networks.
Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Koonkie Inc., Menlo Park, CA, USA; Biomedical Informatics, Stanford University School of Medicine, Stanford, CA, USA; Whole Biome, Inc., San Francisco, CA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Computer Science, University of British Columbia, Vancouver, BC, Canada; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA; Ecosystem Services, Commercialization and Entrepreneurship (ECOSCOPE), University of British Columbia, Vancouver, BC, Canada
GutCyc funding source(s)
Supported by Compute/Calcul Canada, Genome Canada, Genome British Columbia, Genome Alberta, the Natural Science and Engineering Research Council (NSERC) of Canada, Ecosystem Services, Commercialization Platforms and Entrepreneurship (ECOSCOPE) program, the Canadian Foundation for Innovation (CFI), and the Canadian Institute for Advanced Research (CIFAR) through grants, the Alexander Graham Bell Canada Graduate Scholarships-Doctoral Program (CGS D) administered by NSERC, the Tula Foundation funded Centre for Microbial Diversity and Evolution (CMDE) at UBC, a four year doctoral fellowship (4YF) administered through the UBC Faculty of Graduate and Postdoctoral Studies, the Stanford University School of Medicine Dean’s Funds, the NIH Biotechnology Training Grant at Stanford (grant number 5T32 GM008412 a King Abdullah University of Science and Technology (KAUST) research grant under the KAUST Stanford Academic Excellence Alliance program, NIH/NIGMS 5R01GM099534 and by the Thomas C. and Joan M. Merigan Endowment at Stanford University.