Isolation Run Skill¶

Version 1.4.1 · Download the skill (isolation-run) · CC0 · Disclaimer

The companion to the Dregs Analysis Skill. That skill writes the isolation plan; this one runs it. An isolation lasts weeks, spans many short sessions and produces dozens of tubes, plates and photos. What goes wrong is rarely the science: labels drift, a sample's origin blurs, facts get corrected after the fact and the current state ends up scattered across files and chats. This skill keeps one small, current record of the run, so that any session can pick it up and the journey can be written up from evidence at the end. Everything here is experimental home practice: read the disclaimer first.

What it does¶

Side tracks are not recorded. A question that changes nothing on the bench stays in the chat.

Titles follow the wiki's rules (0.31.0). An organism page gets a descriptive title, <Genus> from <Producer> <Beer> for an isolate ("Brettanomyces from Cantillon Rosé de Gambrinus") or <Genus> [species] <Origin> [<Name>] for a pure commercial culture ("Brettanomyces claussenii WLP645"), and keeps its short label ("Boon Gueuze - Brett") for the sidebar and links. A journey is titled <Producer> <Beer> dregs: isolating the <targets>, as the Dregs Analysis Skill sets it.

The run record¶

Five files next to the plan, in work/isolation-plans/<bottle-slug>/ (or the session's outputs folder without the author's wiki):

The atlas flag. Each micrograph is marked candidate (sharp, one organism, or croppable to one: worth comparing in the Microscope atlas), no, or done once the atlas register holds it. At a milestone and at the close the candidates go to the Micrograph Atlas Skill, which crops, measures through the Dregs Analysis Skill and places them. Runs started before 1.4 gain the two columns at their next update.

Sample IDs and photo names¶

Every vessel gets an ID when it is made; write it on the vessel. The ID says what the vessel is and what it was made for. It never changes, and where it came from is kept in the register and the tree, not in the name. Upper case and hyphens only: handwriting and Windows file names both lose case.

• Sources are one word: DREGS, TOP (top layer of the rested dregs), STIR (stir flask), MOTHER, WAKE (a wake-up tube). A digit marks a repeat: TOP2.
• Everything else is TARGET-FORMn:
• Target: what the vessel is meant to isolate, agreed at the start: SAC, BRA and BRB for two Brett types, LAC, MIX for no single target yet. A plate that turns out to hold something else keeps its name; the next vessel gets the new target.
• Form: PL plate, TU tube, SA saline, SL slant, ST stab, FL flask, plus a letter when the medium is not the usual wort agar or wort: S sorbate, H hopped, L agar lid, C chalk, B beer. So LAC-PLS9 is a sorbate plate for the Lacto.
• Number: one series per target, whatever the form, in the order things are made: BRB-SA1, BRB-PL2, BRB-SA3 ... The number alone finds the vessel, so a smudged form code cannot send you to the wrong one.
• Test arms run side by side take a short tag instead of the number: LAC-TU-A33.

Name photos <ID>_<date>_<time>, for example BRB-PL7_2026-10-22_2030.jpg. A photo not tied to one sample takes a plain word instead (LABEL, BENCH). Photos named any other way still work: the skill asks once which sample they show. It never renames or moves your files.

The sample tree¶

The skill keeps a tree of every vessel: what it came from, when it was made, and where it stands. Abandoned branches stay in, with the reason they stopped, because they are part of the story. A branch you give up on is marked discarded with its reason, even if the plate is still on the bench. Where a vessel's parent is not known for sure (picks from one of two plates, say), the tree shows both, with a dotted line.

A Brett B line from the Fair Isle Tove run, as the outline shows it:

STIR · flask · 09-26 · g1 · ◇ fridge
└── MIX-PL2 · plate · 10-03 · g2 · ◇ fridge
    └── BRB-SA1 · saline · 10-10 · g3 · ◇ fridge
        └── BRB-PL2 · plate · 10-10 · g4 · ✗ mould after 15 picks; 10-17
            └── BRB-SA5 · saline · 10-17 · g5 · ◇ fridge
                └── BRB-SA6 · saline · 10-17 · g6 · ◇ fridge
                    └── BRB-PL7 · plate · 10-17 · g7 · ● active

g7 is the generation: seven steps from the bottle. The same tree as a diagram goes on the culture journey at every milestone, always the latest copy. The script that draws it also checks the register (no repeated numbers, no form that disagrees with the vessel, no missing parent) and gives the next free number for each target.

A session, start to finish¶

1. Open the chat with the pick-up prompt the last session printed (below).
2. The skill tells you where each target stands, what is due today and what is overdue, and which new photos it found.
3. Report what you did and saw, in your own words, with the IDs. Save photos with their IDs first.
4. It records, reads, checks the gates, gives new vessels their IDs and tells you what is next. Ask technical questions freely: they go to the Dregs Analysis Skill.
5. End with "hand over". You get the pick-up prompt for next time.

Pick up the isolation run for <beer> with the isolation-run skill.
Run folder: work/isolation-plans/<bottle-slug>/ (start from state.md).
Since the last session: <what I did and saw; photos saved as ID_date_time>.

How to install and use it¶

1. Download the zip, and the Dregs Analysis Skill if you don't have it: this skill relies on it for micrograph readings, technical questions and plan versions.
2. In Claude, install the skill by uploading the zip (Settings → Capabilities → Skills), or place the folder where your Claude set-up reads skills. Installed at account level, it is available in every project. The tree script (scripts/tree.py) needs Python 3, with no extra packages.
3. Start a run with "start an isolation run for from plan-vN" in the chat where the plan lives, or with the plan file attached. A run already under way can be started too: describe what has been done and point to the photos.
4. Keep using the same run folder. With the author's wiki connected the files sit beside the plan in work/; otherwise they go to the session's outputs, and you attach state.md and the last part of log.md when you pick up.

Changelog¶