Plasmid Version Ids: Parent Diff and the Live Stock

An implementation checklist for managing plasmid versions is an identity walk, not a software-selection page. The outcome is one approved map ID that a later person can distinguish from its parent. Inputs are the current sequence, the change that created it, and the physical stock that is allowed to travel. A file named vFinal_REAL is not a version. Plasmid metadata standards still own the field catalog. Map feature completeness still owns unnamed markers and origins. This page only assigns version IDs after those fields can be filled.

A New Filename Is Not a Version Until Parent and Diff Are Named

The search is how to manage plasmid versions. Treat a version as a triple: a stable ID, a parent ID, and a written diff. Public metadata guidance on this site already says not to overwrite a sequence while keeping the same version label. This page turns that rule into steps. It does not pick version-control software. After the IDs exist, ZettaGene can hold the versioned map. Official simulation is restriction, Gibson, and homologous alignment. Golden Gate is not a Zetta feature and is not a versioning method.

Steps: Assign and Retire Plasmid Versions

1. Give the current approved map a stable construct ID that does not include “final.” Checkpoint: two people independently type the same ID.
2. If this map was edited from an earlier construct, write the parent ID. A de novo backbone still needs a source sentence. Checkpoint: the parent resolves or the source is named.
3. Write the diff as sequence facts: bases added, deleted, or swapped, and the features those bases created or broke. “Improved the clone” is not a diff. Checkpoint: a reviewer can find the change on the map without opening chat.
4. Decide whether the change is a new version or only a metadata edit. A sequence change requires a new ID. A display-name change may not. Checkpoint: the rule is written before anyone saves.
5. Point the live physical stock at exactly one approved version. If two tubes exist, they need two stock IDs even when they claim the same map. Checkpoint: the tube label and the map ID match.
6. Retire the previous live version in the same step. Keep the old file. Mark it superseded. Do not delete it to “reduce clutter.” Checkpoint: a search for the old ID still returns a superseded record.
7. Record who approved the cutover and which experiment may use the new live stock. Checkpoint: the next cloning or transfection entry can cite the new ID.

Expected Result

The lab has one live stock, one approved map ID, a named parent, and a written diff. A later person can reconstruct why the new ID exists without guessing from a filename. Opening a new GenBank export is not verification. Neither is renaming the file.

Verification

Ask for the live ID, the parent, the diff, and the tube that is allowed to leave the box. If any of the four is missing, versioning did not happen. If the missing object is an unnamed ori or marker, open the feature checklist. If the missing object is a database accession field, open the database-entry checklist. This page does not replace those gates.

Common Failure Modes

The usual fail is two “current” maps in two folders. The second fail is a sequence overwrite that keeps the old ID so links do not break — they now point at the wrong molecule. The third fail is a tube that still says v3 while the shared map says v5. A metadata standard that lists “sequence version” as a field does not by itself create the parent or the diff. Prefer an ugly ID that stays put over a pretty name that moves. ZettaGene is the versioned map after the IDs are assigned. It is not a ranking of version-control products.

Frequently Asked Questions

Does a new filename create a plasmid version?

No. A version needs a stable ID, a parent, and a written diff. A new filename is only a path.

Can two live stocks share one plasmid version ID?

They can share a map ID only when they are the same approved sequence. Each tube still needs its own stock ID. Two different sequences cannot share one version ID.