DMTC Research Toolbox
Computational tools and resources for human and microbial metabolism, rare diseases and systems biology
Core Research Tools
Master-file Upload
Upload a reconstruction master file to extend a reconstruction (and optionally the WBM). Dry-run preview, then apply — with overview statistics and download of all added reactions.
Launch ToolPersephone
Tool to help users generate a configuration file for running the Persephone pipeline. Advanced metabolic modeling and simulation platform.
Launch ToolConstructor
Interactive metabolic network reconstruction platform for building and analyzing custom pathway models.
Open ToolPathway Reconstruction
Upload a PDF of a scientific paper to extract and reconstruct metabolic pathways using AI.
Open ToolMolecule Editor
Draw, upload, or browse VMH .mol files, view structures in 2D and 3D, and export to .mol or SMILES.
Launch ToolIMD & Rare Disease Tools
IMD Cases
Comprehensive literature and synthetic case studies for Inborn Metabolic Disorders research and education with analysis tools.
Browse CasesChatRD
Advanced phenotype and biomarker analysis for rare disease suggestion and diagnostic assistance.
Open ToolFastforest
Data analysis and reduction through random forests for metabolic and clinical data insights.
Open ToolQueryDB
Query the American Gut Project database for specific sample attributes and microbiome data.
Open ToolData Resources
Download Reconstructions
Access and download metabolic reconstructions for human and microbial organisms in standard formats.
Browse DownloadsSearch & Identifier Tools
Bulk ID Submission
Paste a list of identifiers to map and resolve them against VMH records in bulk.
Open ToolCross-domain explorers
Adverse event ↔ metabolism
A drug side effect → the drugs that cause it (FAERS) → the metabolic target genes they share → the subsystems and diseases behind them.
ExploreGene expression vs the WBM
GTEx tissue expression of a gene per organ, side-by-side with where the whole-body model carries its reactions.
ExploreMicrobiome × disease biomarkers
For an inherited metabolic disease, the gut microbes that metabolize its biomarker metabolite and can confound it.
ExploreFood ↔ metabolic pathways
A food's LanguaL classification, the metabolites it contributes, and the metabolic pathways they feed.
ExploreDrug interaction mechanism
The metabolizing enzymes and pharmacological targets two drugs share, from the VMH drug-metabolism reconstruction. A mechanism view — not an interaction checker.
ExploreAbout the Research Toolbox
The VMH Research Toolbox provides a comprehensive suite of computational tools for metabolic research and systems biology. These tools are designed to support researchers in understanding complex metabolic networks and their relationships.
Whether you're investigating metabolic pathways, analyzing patient data, or constructing novel metabolic models, our toolbox provides the computational power and user-friendly interfaces needed for cutting-edge research.
Genomics Integration
Connect genetic data with metabolic pathways
Advanced Analytics
Sophisticated analysis and modeling tools
Rich Databases
Comprehensive metabolic and clinical data