Dr Felix Meier

NeoFlex Synthetic Chromosome Designer turns a plain-language objective ("engineer yeast to utilise xylan") into a synthesis-ready synthetic neochromosome for Saccharomyces cerevisiae, designed end to end in silico and running live at neoflexgenome.com. Claude Opus parses the objective into a structured design specification. An eight-module pipeline then searches real protein and pathway databases (UniProt, KEGG, CAZy) for candidate genes and the transporters that move substrate across the membrane, runs the gene set through a genome-scale metabolic model (Yeast-GEM / FBA) to check growth and propose host knockouts, balances promoter and terminator strength against enzyme demand and rate limiting steps, tags each gene for its compartment (secretion, surface display, peroxisomal), lays out the chromosome parts, and fragments it into an order-able build plan behind a fail-closed go / no-go gate. The scaffold of the chromosome was synthesized and built before this submission, the software for designing the inserts represents the Hackathon submission. It generalizes: six objectives reach an order-able "go" from natural language alone, spanning carbon-source capabilities (xylan, cellulose, chitin) and metabolite production (L-lactate, 2,3-butanediol, isobutanol) among other things. It is grounded and stays honest, refusing what the science cannot validate. Chromosome-scale metabolic pathway design is otherwise manual, slow, and defeated by repeat-driven recombination. NeoFlex makes it a model-guided, provenance-tracked, auditable run that yields a build package a biofoundry could actually order. 1,000+ tests, 11 live data sources, built with Claude Code.