Hi Niko,

Most synbio researchers I know think cloning is miserable, and not just because of failed reactions. A researcher might decide to use Golden Gate because that’s what they were trained on, fail to notice an internal BsaI site destroying the construct at every ligation cycle, and lose six weeks. Or they might ligate two restriction sites together without realizing the combination introduces an ATG upstream of the start codon, creating an out-of-frame translation initiation site that silently kills expression (true story, not mine thankfully). Months of debugging a construct that looks perfect on every gel. Across two labs and a diagnostics company running molecular assays at scale, I’ve seen DNA assembly method-choice errors cost research groups cumulative years of work-hours.

I want to build IceCreamClone, an interactive tool that makes cloning strategy selection fun instead of dreadful. You define your inputs (fragments, primers, plasmids on hand) and desired output (the construct you want). IceCreamClone ranks assembly strategies across restriction digest, Gibson, Golden Gate, PCR-based editing, and Sidewinder on cost, turnaround, steps, and failure risk. Automated QC runs on every candidate: internal restriction sites, scar problems, overlap secondary structure, and silent killers like that ATG.

It also teaches as it goes. Interactive simulations show how Gibson overlaps anneal, how Golden Gate cycling works, where restriction sites cut. Trainees learn cloning logic while making real design decisions. In labs with constant turnover, the bottleneck is usually new grad students spending three weeks on a strategy an experienced postdoc would have rejected in five minutes. Compressing that learning curve is how you speed up biology at scale.

IceCreamClone will ship with standard enzyme sets (e.g. MoClo standards) as defaults and a checkbox interface to add and subtract your lab’s inventory. If the top strategy requires something you don’t have, it suggests and teaches the best alternative. No existing tool has this integrated capability: NEB’s ligase fidelity viewer optimizes Golden Gate overhangs but won’t question whether Golden Gate is the right method; SnapGene simulates digests but doesn’t compare across techniques; j5 automates assembly design across multiple methods but doesn’t recommend which one fits your specific construct and inventory.