Importing a set of Eugene design specification rules

After naming a part on the design canvas, it is possible to create Eugene design specification rules (Bilitchenko 2011A, Bilitchenko 2011B) for the part to ensure that only desired DNA designs are constructed. NOTE: mapping a sequence to the part, as long as the part has been named, is not a pre-requisite.

Any Eugene rules that do not solely relate to parts on the design canvas or do not use one of the six currently supported operators ("AFTER", "BEFORE", "THEN", "NEXTTO", or "MORETHAN") or their negated "NOT" variants, are ignored.

With one or more parts on the design canvas, it is possible to import a set of Eugene design specification rules by going to the "File" at the top menu, and clicking on "Import Eugene Rules". Doing so will pop-up a new dialog box for selecting a file to upload, allowing you to select which Eugene rules file you would like to import. After selecting the file, a new "Eugene Rules Import" dialog box will pop up.

Rules with name conflicts are displayed in red. A rule name conflict means that a previously defined rule has the same name as a new rule to be imported from the selected Eugene file, but the contents of the previously defined rule is not identical to the contents of the new rule. When this type of conflict happens, DeviceEditor automatically renames the new rule to be imported so as to resolve the name conflict.

New rules are displayed in green. Lines within an "Eugene rules file" could be ignored if they either i) don't contain valid Rule statements (e.g., comment lines beginning with "//"), ii) contain invalid operators or iii) contain invalid operands, namely parts that are not currently on the design canvas. Repeated rules, those identical among the previously defined rules and the new rules to be imported, are displayed in black. All parts associated with Eugene rules are identifiable on the design canvas by orange circle indicator lights at bottom right.

Note: See also how to manually create and delete Eugene design specification rules for a selected part. For more information about how j5 implements these Eugene design specification rules (and why they are useful) when designing DNA assemblies, refer to the "Eugene rules list file" page in the "j5 input files" section.