{
"@context": "/terms/",
"@id": "/model-sets/IGVFDS3627LKSF/",
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],
"accession": "IGVFDS3627LKSF",
"aliases": [
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"bill-majoros:bluestarr-k562-model"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7883WOIS](/in-vitro-systems/IGVFSM7883WOIS/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM7883WOIS/"
},
{
"category": "missing publication",
"detail": "Model set [IGVFDS3627LKSF](/model-sets/IGVFDS3627LKSF/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/model-sets/IGVFDS3627LKSF/"
}
],
"WARNING": [
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS3627LKSF](/model-sets/IGVFDS3627LKSF/) links to file(s) [IGVFFI6828UIAH](/model-files/IGVFFI6828UIAH/), [IGVFFI5128IAHI](/model-files/IGVFFI5128IAHI/) that have no `derived_from`. Files in prediction sets and model sets are expected to be derived from other files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_sets_derived_from",
"path": "/model-sets/IGVFDS3627LKSF/"
}
]
},
"award": {
"@id": "/awards/HG011967/",
"component": "predictive modeling",
"contact_pi": {
"@id": "/users/42adfdcc-7ff1-4c2a-b9af-d424c71c6e5a/",
"title": "Andrew Allen"
},
"title": "Design, prediction, and prioritization of systematic perturbations of the human genome"
},
"control_for": [],
"creation_timestamp": "2024-03-20T21:21:02.409325+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"description": "BlueSTARR is a neural network trained on STARR-seq data that takes genomic sequence as input and predicts STARR-seq activity as output. This version of BlueSTARR was trained on a STARR-seq experiment done in K562 cells, and takes a 300 bp sequence as input. Variant predictions are made by running the model twice (once for the reference allele and once for the alternate allele) and computing the predicted log2 fold change in STARR-seq activity for the change from reference to alternate.",
"documents": [
"/documents/616c46f5-7f2e-4d31-af0a-d91f8084bcc4/"
],
"externally_hosted": false,
"file_set_type": "neural network",
"files": [
{
"@id": "/model-files/IGVFFI6828UIAH/",
"accession": "IGVFFI6828UIAH",
"aliases": [
"andrew-allen:bluestarr-k562-wg3M-model-file-hdf5"
],
"content_type": "edge weights",
"creation_timestamp": "2024-06-18T21:21:58.706629+00:00",
"file_format": "hdf5",
"file_size": 63138304,
"href": "/model-files/IGVFFI6828UIAH/@@download/IGVFFI6828UIAH.h5",
"md5sum": "cfff70964f7e145a66cedc179f228dc2",
"s3_uri": "s3://igvf-files/2024/06/18/94cbff9e-5cfd-4118-ac4e-827ac80b0c7e/IGVFFI6828UIAH.h5",
"status": "archived",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/predictive_modeling/wg3M.h5",
"upload_status": "validated"
},
{
"@id": "/model-files/IGVFFI5128IAHI/",
"accession": "IGVFFI5128IAHI",
"aliases": [
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],
"content_type": "graph structure",
"creation_timestamp": "2024-06-18T21:22:11.038142+00:00",
"file_format": "json",
"file_size": 9333,
"href": "/model-files/IGVFFI5128IAHI/@@download/IGVFFI5128IAHI.json",
"md5sum": "17b958e003897666131ca5b30f02e3f0",
"s3_uri": "s3://igvf-files/2024/06/18/d3ca1f61-2d14-4ca2-a181-17b07f1a9f4b/IGVFFI5128IAHI.json",
"status": "archived",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/predictive_modeling/wg3M.json",
"upload_status": "validated"
}
],
"input_for": [
"/prediction-sets/IGVFDS0257SDNV/"
],
"lab": {
"@id": "/labs/bill-majoros/",
"title": "Bill Majoros, Duke"
},
"model_name": "BlueSTARR-K562",
"model_version": "v0.1.0",
"notes": "This model set previously specified e2746e08-b610-4d78-8c2b-56da42bf22d5, but this property has been removed and replaced by software_versions calculated through analysis_step_version on the model file.",
"prediction_objects": [
"regulatory elements"
],
"release_timestamp": "2025-01-08T18:46:33.441003+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7883WOIS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7883WOIS",
"aliases": [
"andrew-allen:bluestarr-k562-in-vitro-system"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "released",
"summary": "virtual Homo sapiens (female) K562 cell line",
"taxa": "Homo sapiens"
}
],
"schema_version": "5",
"software_versions": [
{
"@id": "/software-versions/bluestarr-v0.1.0/",
"download_id": "95b5033342fbbd7a5ffb532038946481ffafb6db",
"source_url": "https://github.com/bmajoros/BlueSTARR",
"status": "released",
"summary": "BlueSTARR v0.1.0"
}
],
"status": "archived",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-06-18T21:21:58.706629+00:00",
"submitter_comment": "This model set is superseded by IGVFDS0103FMQG, which is from a newer version of BlueSTARR.",
"summary": "BlueSTARR-K562 v0.1.0 neural network predicting regulatory elements",
"uuid": "1f877b14-5f82-445c-9727-9133828009a1"
}