Pick a tool. Everything runs locally — no server, no waiting queue.
Genome-scale metabolic models for every strain, solved live in your browser with a WebAssembly LP solver. Choose an analysis below.
All results and plots are downloadable. Verified against COBRApy & scipy.
Explore & Compare
Pick a strain model and a growth medium, then solve FBA or pFBA. Switch to Compare A vs B to contrast two models, two media, or the effect of a knockout. Media from Ardalani et al. (PLOS Pathogens, ppat.1013775).
Flux Variability Analysis
Compute the minimum and maximum possible flux of each exchange reaction while biomass stays at a chosen fraction of its optimum — revealing which secretions are obligatory vs optional.
Dynamic FBA (batch culture)
Simulate a batch fermentation over time: substrate uptake follows Michaelis–Menten kinetics, biomass and metabolite concentrations integrate step by step (static-optimization dFBA). Watch growth, substrate depletion and product accumulation.
Multi-model analytics
Run FBA across many strains on one medium, then explore the flux landscape: growth by phylogroup, interactive flux scatter, a PCA of exchange-flux profiles, and a heatmap. Click any point to inspect that strain.
Group comparison
Define two groups of strains by metadata — phylogroup, MLST, pathotype, isolation source, host… — then run FBA across each and test which metabolic capabilities differ. Growth is compared with a Mann–Whitney U test; per-exchange flux differences are shown as a volcano plot with Benjamini–Hochberg FDR.
Production Envelope
The trade-off between biomass and a target product: for each production level, the maximum (and minimum) growth the network allows. The frontier is the bioengineer's design space.
Phenotype Phase Plane
Maximum growth rate across a grid of two uptake capacities — the classic Edwards–Palsson phenotype landscape. The surface reveals distinct metabolic regimes and their boundaries.
Essentiality Screen
Knock out each reaction one at a time and measure the growth impact — mapping the essential, redundant and dispensable reactions of a strain on a given medium.
Nutrient Essentiality
Remove each medium component one at a time and re-run FBA — mapping which nutrients this strain must take up (its auxotrophies) and which are dispensable on the chosen medium. Edit the medium above to test any formulation.
Robustness Scan
Vary the uptake capacity of a single nutrient from starvation to excess and trace the maximum growth rate at each level — a one-dimensional slice of the phenotype landscape. It reveals whether a nutrient is limiting, where growth saturates, and the critical supply below which the strain cannot grow. Edit the medium above to set the background formulation.
Gene Essentiality
Delete every gene, one at a time, through its GPR rule. That is not the same as deleting a reaction: an isozyme (a or b) survives losing one gene, a complex (a and b) does not. Matches COBRApy single_gene_deletion exactly.
Synthetic Lethality
Double deletions. A pair is synthetically lethal when neither knockout hurts on its own but the two together kill the cell: the redundancy that single-gene screens miss. Pairwise over the candidates below, so keep the set small.
Strain Design (FSEOF)
Flux Scanning with Enforced Objective Flux (Choi et al. 2010). Force secretion of a product upward in steps while the cell still maximises growth, and watch which internal reactions have to carry more flux. Those are your over-expression targets.
Flux Sampling
ACHR hit-and-run through the flux solution space, the family COBRApy’s OptGP belongs to. FBA gives you one optimum out of many; sampling shows the distribution a reaction can take while the cell still grows. Approximate: a few hundred warm-up points explore the space, they do not prove uniformity.
Model QC
What is wrong with this reconstruction. Blocked reactions can carry no flux at all on this medium, so they are dead code. Mass and charge imbalance is checked from the stoichiometry and formulas, the way MEMOTE does it, with no solving. Dead-end metabolites are only ever produced or only ever consumed.