Previous value: -"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)."New value: +"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) or differential_expression (params gene as its count-table ID, symbol? as papers name it for the literature query, counts and samples as the tables themselves, and design/reference/test/reduced/contrast/name/fitType/sfType/lfcThreshold/altHypothesis/cooksFilter/cooksCutoff/minReplicatesForReplace as the tool takes them; direction greater for higher in the contrast's numerator, less for lower, or two-sided; one-sided needs the Wald test at lfcThreshold 0; needs no corpus) or gene_set_overrepresentation (params set as its GMT ID, genes, geneSets as GMT text, universe?, forceUniverse?, minGSSize?, maxGSSize?; direction greater; needs no corpus) or gene_set_enrichment (params set as its GMT ID, ranked as 'gene statistic' lines, geneSets as GMT text, minGSSize/maxGSSize/exponent/scoreType/eps/sampleSize/nPermSimple/seed; direction greater for toward the top of the list, less for the bottom, or two-sided; 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)."

Previous value: -"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."New value: +"seconds this call may spend running tests: whole tests run until the budget is spent and the rest are deferred, so a long program 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."

Previous value: -"the programme as text lines: registrations, runs, refusals, verdicts, literature queries"New value: +"the program as text lines: registrations, runs, refusals, verdicts, literature queries"

Previous value: -"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"New value: +"the whole program 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"