How Ingence thinks#

Ingence is built on a few ideas. Knowing them helps you read what it shows you, and decide how far to trust it.

Four inputs, one result#

Every conclusion Ingence reaches can be rebuilt from four things.

The Index: What was observed. For every file and folder: where it sits, its name, size and dates, and what a dive read from inside it. Each reading of a folder is kept as a run, beside the earlier ones. A finished run is never edited.
The Dictionary: What words mean in this body of files. It ties a spelling such as bf or western to a meaning such as brightfield or immunoblot, and ties dates and units to theirs. Part of it ships with Ingence. Part of it is yours, because what a word means in your laboratory is a question only your laboratory can answer.
The Rulebook: The rules that turn observations into readings. Each rule is written in plain words, has a name and a version, and says what would make its conclusions wrong. Read them with ingence rule show.
The Record: Your decisions. Every answer you give is added to a log under your name. It never overwrites an earlier one.

Give Ingence the same four inputs and it reaches the same conclusions. That is what “reproducible” means here. It is also why a conclusion can always be traced: it carries the rule that made it, the version of that rule and the evidence it used.

Observations and readings#

An observation is something the filesystem states: this file is a certain size, was changed on a certain date and sits in this folder. A reading (the engine’s word is an interpretation) is what the observations might mean: this file is raw data from an imaging experiment.

Ingence keeps the two in separate places, and a fact and an inference cannot be written into the same field. So you can always tell which is which, and changing a rule can never rewrite a fact.

A reading Ingence publishes is called a claim. A rule publishes a claim only where it names what would defeat it: a reason, written down in advance, that it might be wrong. Adding more evidence can raise a claim’s standing or add such a reason. It never quietly weakens a claim.

Three kinds of “not known”#

Ingence does not have to conclude. Saying nothing is a valid answer, and there are three different ways to say it.

Unknown: Ingence looked and nothing it has settles the question. A word that no Dictionary entry covers is unknown. The remedy is knowledge: teach it the word.
Unexamined: Ingence has not looked. A file that a dive’s time budget did not reach is unexamined. The remedy is time: dive again with a fresh budget.
Conflicting: Ingence looked and found answers that disagree. A spelling with two meanings that tie is conflicting. Rather than pick one, Ingence reports both and asks you. The remedy is a choice.

They stay apart because they ask for different things from you. A single “null” would hide which. A rule that cannot decide records that it abstained and why.

Proposals, and Re-run#

Some questions a rule cannot settle alone. So it proposes: two files where one may have been made from the other, experiments that belong together, a word it cannot read, or a set of laboratory words (a pack) to load. Ingence does not act on a proposal until you say yes, on the Dashboard’s Questions page.

A proposal is a particular kind of conclusion, and not every grouping is one. Some rules publish groups and claims on their own, each naming its rule, so you can always see why. And one case is automatic: where the folder you read holds three or more files in a format that declares its pack (today, Nikon’s ND2 files for the microscopy pack), the pack is loaded without a yes. You can refuse it.

Your answer goes straight into the Record. It does not change what you see yet. Every change waits for Re-run: an answer, a word’s meaning, a pack, a setting. A count on the Re-run button says how many are waiting. Re-run reads the affected names again and runs the rules again. While it works, the pages keep showing the last finished run. Nothing runs by itself.

The same two steps by hand are ingence index --rebind -p PROJECT, which reads the stored names again without touching your folder, and then ingence infer -p PROJECT.

The eight ways two things relate#

Everything Ingence says about how things connect is built from eight relations. There is no catch-all “related to”. If it cannot say how two things relate, it abstains.

Relation	In plain words
contains	This folder holds that file or folder. After a census, this is complete.
embeds	This file holds that part inside it, such as a member of a zip archive. Never known to be complete.
derives	This was made from that. It never runs in a circle. Only the direct step is asserted; the chain of steps is the file’s provenance.
identical	These are the same byte for byte. The only relation that lets you treat one as the other.
equivalent	These are the same in one stated respect, such as the same kind of experiment. Every grouping is built from it.
succeeds	This comes after that in an ordered series, such as versions one, two and three. It is not the same as being made from.
references	This mentions or points at that. The only relation that may form a circle.
concerns	These are about the same subject. It works both ways but never chains: if A concerns B and B concerns C, nothing follows about A and C.

What Ingence does not do#

Ingence does not interpret your science, and it makes no claim that what it finds is scientifically valid. It says how your files appear to relate. What that means for your work is yours to judge. It also never needs a language model, and uses none: see Privacy and your data.