Instructions for Ray

Every lab has conventions that never make it into the data: which genome build you align to, how you report fold changes, which wells on every plate are the controls. Without them Ray has to be told in each question, and forgets by the next thread.

Instructions for Ray is a field on Project Home where you write those conventions once. Every Ray conversation in that Project reads them.

Writing instructions

Open the Project, choose Edit next to the Project name, and fill in Instructions for Ray under the research question. Save.

Write them the way you would brief a new member of the lab. Short lines work best:

Genome build is mm10. Gene symbols, not Ensembl ids.
Report differential expression as log2 fold change with adjusted p.
On every plate, wells A1–A3 are untreated controls; B1–B3 are vehicle.
Timepoints are hours post-treatment unless a file name says otherwise.
Prefer notebooks over pipelines for anything exploratory.

Up to 6,000 characters. Anyone who can edit the Project can edit the instructions, and anyone who can see the Project can read them under Edit on Project Home.

How Ray uses them

Ray reads the instructions on the server at the start of each turn in the workspace chat bar, for whichever Project is active, and treats them as working conventions: how to name things, which units to use, how to present results, which choices to make without asking.

Note

An edit reaches Ray on your very next question. Ray reuses instructions it has already read for about a minute within one conversation, but a Project that had none is checked every time, so “ask Ray, write instructions, ask again” works straight away.

Warning

Instructions are conventions, not permissions. They cannot make Ray skip an approval it would otherwise ask for, share anything outside the Project, or invent data. Ray still asks before creating a share link, and still refuses to fabricate results, whatever the instructions say.

Tip

Ray in Slack does not read Project instructions yet, because a Slack thread is not tied to a Project when the question arrives. Say the convention in the message for now.