run_discovery_programme
Run a discovery programme end to end under pre-registration: every hypothesis names its test (discover_site_avoidance: a site, optionally a record, and its null; discover_codon_outliers: a gene and its genetic code; validate_gene_trait: a human gene, the trait's own gene or tissues, and GWAS Catalog categories; discover_flag_rates: a cryptic-element flag, optionally a record, against k-let shuffles; discover_tree_incongruence: a locus of a multi-locus alignment, by the ILD test; discover_gene_tree_discordance: a gene alignment against a species tree, by the SH test; discover_reference_stability: a candidate reference gene against its GTEx abundance peers; discover_annotation_contradictions: a UniProt signal peptide or transmembrane segment against the experimentally confirmed ones; discover_reference_concordance: a Cq table whose conditions should rank its reference genes alike) and direction, and all are registered in a hypothesis ledger before any test runs. Each registered test then runs once over the corpus, every answering result is attached as a κ-calibrated e-value (evidence from another test, a changed parameter or the same data twice is refused and reported), and e-BH decides over all hypotheses, those without evidence included. Returns the verdicts, the whole ledger as a file that imports into the Hypothesis Ledger, every run's input, the refusals, and the literature query each supported hypothesis needs before it may be called new. Pass a previous ledger with posterior beliefs to get the follow-up order by Bayesian surprise, which ranks what to test next and never changes a verdict. Also returns the whole programme as a sealed run file (every corpus input pinned by SHA-256, the last attempt at each hypothesis); pass it back as run to add hypotheses and retry the ones whose test failed, or to research_run_status and resume_research_run. Evidence that read one source (one table, or one sequence under two names) is averaged, not multiplied, and each verdict names the rule.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| run | No | a run file from an earlier call, to continue it: its seal and its pinned inputs are checked, hypotheses whose test failed or was deferred are retried, new ones are added, and nothing answered is run again. | |
| alpha | No | e-BH level the verdicts are decided at, across every hypothesis in the ledger. | |
| kappa | No | κ of the p-to-e calibrator e = κ·p^(κ−1); fixed for a ledger once it holds evidence. Advanced. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| ledger | No | a ledger file from an earlier run, to continue: its hypotheses keep their evidence and new ones are added beside them. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| organism | No | the organism the corpus is from, for the literature query each supported hypothesis needs. Advanced. | |
| sequences | No | the corpus every registered test runs over: library document or file names, or wired records. | |
| hypotheses | No | each {statement, test, params, direction, prior_belief?}. test: discover_site_avoidance (params site, record?, null_model, shuffle_k/shuffles/seed under the shuffle null; direction less, greater or two-sided) or discover_codon_outliers (params gene as its library name, genetic_code, alt_init?, min_codons?; direction two-sided) or validate_gene_trait (params gene as its HGNC symbol, expression_test coexpression with trait_genes or tissue with tissues, categories as GWAS Catalog parent categories, alpha?; direction greater; needs no corpus) or discover_flag_rates (params flag as one of sigma70-strongest, splice-donor, splice-acceptor, homopolymer, tandem-repeat, long-repeat, inverted-repeat, record?, shuffle_k/shuffles/seed; direction greater, meaning beyond chance in the flag's own tail) or discover_tree_incongruence (params locus as its alignment file's name, permutations/seed; direction greater; the corpus is one aligned FASTA per locus) or discover_gene_tree_discordance (params gene as its alignment file's name, species_tree in Newick, replicates/sh_form/gamma_categories/seed; direction greater, meaning the gene fits another tree better; the corpus is one aligned FASTA per gene) or discover_reference_stability (params gene as its HGNC symbol, tissues?, neighbours?, pseudocount?; direction greater for more variable than its abundance peers, less for steadier, or two-sided; needs no corpus) or discover_annotation_contradictions (params annotation as a UniProt accession, or accession:start-end where the protein has several, feature signal or transmembrane, predictor for signal, decoding for transmembrane; direction less, meaning it scores below the experimentally confirmed features; needs no corpus) or discover_reference_concordance (params cq_table as the long-format Target,Sample,Group,Cq table itself, permutations/seed; direction greater, meaning the conditions rank the genes more alike than independent orders; needs no corpus). prior_belief: the proposer's belief before any result, one sample or a list of them (true, false, definitely true, maybe true, uncertain, maybe false, definitely false, cannot comment). | |
| budget_seconds | No | seconds this call may spend running tests: whole tests run until the budget is spent and the rest are deferred, so a long programme returns before a client's timeout and resume_research_run continues it. A test is never cut short and at least one runs per call. Unset: every test runs in this call. In s. Advanced. | |
| posterior_beliefs | No | each {id, samples}: the proposer's belief in a hypothesis after reading its evidence. With prior beliefs these give the follow-up order by Bayesian surprise. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| run | Yes | the whole programme as a sealed jane.research-run file: the ledger, every corpus input pinned by SHA-256, the last attempt at each hypothesis. Pass it back to continue | |
| ledger | Yes | the whole ledger as a jane.discovery-ledger file, every hypothesis and its evidence with traces | |
| report | Yes | the programme as text lines: registrations, runs, refusals, verdicts, literature queries | |
| result | Yes | the full result | |
| followUp | Yes | hypotheses with prior and posterior beliefs, most surprising first: what to test next, never a verdict | |
| decisions | Yes | every hypothesis: verdict (supported, not-supported, no-evidence), product e-value and tests | |
| supportedCount | Yes | how many hypotheses e-BH supports |