https://w3id.org/np/RARgGQwFLhGMGKdfuR0yR-oKbxsGLvo91mTmb9YwriU3o/Head https://w3id.org/np/RARgGQwFLhGMGKdfuR0yR-oKbxsGLvo91mTmb9YwriU3o http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RARgGQwFLhGMGKdfuR0yR-oKbxsGLvo91mTmb9YwriU3o/assertion https://w3id.org/np/RARgGQwFLhGMGKdfuR0yR-oKbxsGLvo91mTmb9YwriU3o http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RARgGQwFLhGMGKdfuR0yR-oKbxsGLvo91mTmb9YwriU3o/provenance https://w3id.org/np/RARgGQwFLhGMGKdfuR0yR-oKbxsGLvo91mTmb9YwriU3o http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RARgGQwFLhGMGKdfuR0yR-oKbxsGLvo91mTmb9YwriU3o/pubinfo https://w3id.org/np/RARgGQwFLhGMGKdfuR0yR-oKbxsGLvo91mTmb9YwriU3o http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RARgGQwFLhGMGKdfuR0yR-oKbxsGLvo91mTmb9YwriU3o/assertion https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test http://purl.org/dc/terms/description analysis.py recomputes the UCS-memory screen defined for levin-2022-grn-learning-11, importing that screen and not its result file. A pair counts when a clamp changes the response by a factor of two and at least half of that change is still present after the clamp is released. No parameter or reaction is edited. One such pair supports the existential claim. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/Assessment https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 724 UCS memories formed with SBML parameters left unchanged (n = 31, deterministic given libroadrunner, the SBML files, and the tolerances recorded per model). Interpretation: The claim says memories, for example associative memory, can be formed by stimulation through dynamics alone, without changing structure or parameters. UCS memory is the simplest memory the same paper defines that way: one stimulus, then a lasting response, with the equations untouched. Associative memory is the example in parentheses, not a second requirement of this test. A success does not show that cells learn. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of levin-2022-grn-learning-08: supports, confidence 0.7 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2022-grn-learning-08/result.json https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/admissibleDatasets The 35 curated BioModels identifiers in Table S1 of Biswas, Clawson and Levin, doi:10.3390/ijms24010285, as public SBML. Parameters, reactions and initial conditions stay at the file's values. Clamps change only the stimulus concentration during a pulse. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/dataKind computational https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Every integrable Table S1 model, and at least 10 of them, fails to produce any such pair. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/evidenceAgainst No memory trajectory for this claim is generated before this registration. The Table S1 identifier list was fixed earlier, from the supplement, for the habituation test. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The memories found are UCS memories, a stimulus followed by a lasting response. The run did not train a neutral stimulus into a conditioned stimulus. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The result says these ODEs can keep a response after a clamp. It does not say that cells or patients learn. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The same screen, run separately for the retention claim, counted the same 724 memories in the same 29 models. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The screen does not train a neutral stimulus into a conditioned stimulus. A failure of this UCS test would not by itself say that associative conditioning is impossible, but a success is enough for the existential wording, because UCS memory is in the class the sentence asserts. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/expectedObservation At least one directed stimulus–response pair, in an unedited BioModels ODE, regulates the response by a factor of two during a clamp and still holds at least half of that excursion after the clamp is released. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered. Refutes if at least 10 models integrate and none of them has a UCS memory. If fewer than 10 models integrate and none shows a UCS memory, the verdict is inconclusive (underpowered if at least one model integrated, otherwise data-unavailable). There is no mixed outcome: the claim is existential. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.7 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/hypothesis If a pathway ODE can form a memory from stimulation alone, then at least one Table S1 model has a UCS memory: a stimulus changes a response by the factor of 2 used in the paper, the change is still at least half present after the stimulus is removed, and the SBML parameters and reactions were not modified. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/inferenceMethod Same UCS-memory screen as levin-2022-grn-learning-11: 50 time-unit baseline, clamp at 100 times the baseline max or the baseline min over 100, factor-of-two regulation against both the baseline and the next free window, then half-excursion retention over the next 50 time units. One success supports. Zero successes with at least 10 integrable models refutes. Confidence is 0.70 on supports, 0.55 on refutes, and 0.60 on inconclusive. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered (supports). Supports if the screen finds at least one UCS memory, as defined in the test contract, in any model that integrates. The claim is existential ('can be formed'), so one pair is enough, including when fewer than 10 models integrate. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/levin-2022-grn-learning-08 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-08--claim-test https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-1 http://purl.org/dc/terms/description Source of the 35 BioModels identifiers. Result figures were not used. The zip is over 1 MB and is not committed. https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-1 http://purl.org/dc/terms/license CC BY (article) https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: Supplementary PDF of Biswas, Clawson and Levin 2022, Table S1 (35 BioModels identifiers) https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://mdpi-res.com/d_attachment/ijms/ijms-24-00285/article_deploy/ijms-24-00285-s001.zip?version=1672829351 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://www.mdpi.com/article/10.3390/ijms24010285/s1 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:292a7f33bcb3a9589614507114de8c1a7a5f5d8bc11e382d546c3d08da381e39 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-2 http://purl.org/dc/terms/description ODE models integrated by analysis.py with parameters left at the SBML values. Cached under cache/sbml/ and not committed. https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-2 http://purl.org/dc/terms/license CC0 1.0 where the SBML says so (25 of 35 files). Ten files do not state a license in the XML: BIOMD0000000017, BIOMD0000000021, BIOMD0000000026, BIOMD0000000029, BIOMD0000000031, BIOMD0000000035, BIOMD0000000038, BIOMD0000000050, BIOMD0000000069, BIOMD0000000539. https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-2 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-2 http://www.w3.org/2000/01/rdf-schema#label Dataset: Curated SBML for the 35 BioModels identifiers in Table S1 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-2 http://www.w3.org/ns/prov#atLocation https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000001?filename=BIOMD0000000001_url.xml https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-08--claim-test--dataset-2 http://www.w3.org/ns/prov#atLocation 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