Welcome to FunGem
FunGem predicts TRY metrics — Titer, Rate, and Yield — for filamentous fungi in submerged fermentation, directly from your genome and bioreactor conditions. Upload a fungal genome, define your substrate and reactor parameters, and get an instant in-silico prediction to focus your wet lab effort. Any feedback is greatly appreciated.
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Upload Genome
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Define Media & Reactor
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GEM Reconstruction
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FBA Optimisation
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TRY Prediction
Configure Your Run
What GEMgen predicts
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Taxon detection — reads your FASTA header, queries the BV-BRC taxonomy API to confirm the organism is fungal, and selects the appropriate reconstruction template
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GEM reconstruction — uploads your genome to BV-BRC and triggers the ModelReconstruction app, which builds a genome-scale metabolic model (SBML) automatically
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Model retrieval — fetches the completed SBML model from BV-BRC, stores it in the database, and passes it to the FBA layer along with organism-specific biological constants
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Flux Balance Analysis — runs escher-FBA client-side on the reconstructed model, applying Michaelis-Menten kinetics, kLa O₂ constraints, C:N ratio, temperature & pH corrections, and maintenance energy
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TRY output — returns Titer (g/L), Rate (g/L/h), and Yield (g biomass / g substrate) calibrated to your exact bioreactor conditions and inoculum
Assumptions: submerged liquid fermentation; no oxygen limitation (fully aerated);
no solid-state or moisture-dependent processes. GEM reconstruction is performed by simplified locally coded scripts (BV-BRC
ModelReconstruction will be used in future iterations - on private servers). Predictions are model-based estimates —
experimental validation is always recommended.
Not sure where to start?
Try the pre-loaded example dataset: a proprietary filamentous fungi strain grown on corn steep liquor + glucose at 28 °C, 200 RPM. All TRY outputs are pre-computed so you can see exactly what to expect. Example ready