Before you start

• You will end with: the sample files open in tabs, the enzyme ticks cleared, and a picture of what the Bench is.
• Time: about 5 minutes.
• Files: the synthetic sample files.
• Before this: nothing.

What every tutorial assumes. Nothing to install: PlasmidPop runs in the browser, and the files stay on your device. If digesting a plasmid or amplifying a gene with primers is new to you, do Digest and PCR basics next: it is the basics the other tutorials build on.

Opening the sample files

The tutorials come with synthetic sample files: invented sequences, no catalogue or database records. Download the ones a tutorial names. Either drag them onto the PlasmidPop window, or use File ▸ Open and select several at once. Each opens in a tab of its own; File ▸ Show files (the Files tab) lists them. Open only what an exercise names, in the order it names, and close the rest.

The Golden Gate panel puts every open tab in the tube, so close the tabs an exercise does not name.

What the Bench is

The Bench is a tab beside Files in the tab strip, where cloning is simulated. It has three columns: the shelf of parts on the left, the reaction in the middle (Ligation, Golden Gate and the others, picked at the top), and what it makes on the right once the parts go together, with a check digest. A product opens as a document of its own. The Bench page of the user guide is the reference.

Enzyme ticks

Hide all in the Enzymes tab clears the ticks. A file you open yourself opens with every enzyme that cuts once ticked, so clear them and tick only what the exercise says; the Filter box finds an enzyme by name. A product from a ligation, a restriction-cloning Simulate or a Golden Gate or Modular assembly opens with only the reaction's enzymes ticked (a mutant keeps its template's ticks); a Gibson, In-Fusion, Overlap PCR or Gateway product has none to seed and opens with the default ticks, every single cutter. The exercises say which.

Scratch documents

A tutorial changes nothing on disk: the app never writes to your files. Products and edits live in tabs until you close them or download them, so try things freely, and close a tab you do not want to keep.

A gene from NCBI

Each exercise is done once with a synthetic ORF and, where it makes sense, once with a real gene, human insulin (INS), that you fetch from NCBI inside the app. Only the accession you type goes to NCBI. A gene off NCBI has no cloning sites at its ends, so those exercises start by designing primers that add them.

If a number does not match

The numbers in the tutorials are for the bundled enzyme set (the default) and for the documents with their default host methylation (dam+ dcm+). None of the sites in these files lies in a dam or dcm context, so the numbers are the same with either; the ranking of the check digest's enzymes depends on the enzyme set in use, the band sizes of the named enzymes do not.

Back to the tutorials index.