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HIVE-CensuScope_Test_Computation_BCO_015623.json
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HIVE-CensuScope_Test_Computation_BCO_015623.json
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{
"object_id": "https://portal.aws.biochemistry.gwu.edu/bco/BCO_015623",
"spec_version": "https://w3id.org/ieee/ieee-2791-schema/",
"etag": "86377b132f05ecfba148a94cddcd041e02024a5ee17a2c8425f44820876d76f9",
"description_domain": {
"keywords": [
"microbiome",
"gut",
"composition",
"FilteredNT"
],
"platform": [
"HIVE"
],
"pipeline_steps": [
{
"step_number": 1,
"input_list": [],
"output_list": [
{
"uri": "https://hive.aws.biochemistry.gwu.edu/dna.cgi?cmd=objFile&ids=3242&filename=alignment.hiveal"
},
{
"uri": "https://hive.aws.biochemistry.gwu.edu/dna.cgi?cmd=objFile&ids=3242&filename=dna-alignx_screenShannon.csv"
},
{
"uri": "https://hive.aws.biochemistry.gwu.edu/dna.cgi?cmd=objFile&ids=3242&filename=dna-alignx_screenResult.csv"
},
{
"uri": "https://hive.aws.biochemistry.gwu.edu/dna.cgi?cmd=objFile&ids=3242&filename=dna-alignx_acclist.csv"
}
],
"name": "Screen Short Read Against Genome",
"description": "Random pick sequences to run alignment with specific genome"
}
]
},
"error_domain": {
"empirical_error": {
"text": "3.7% Bacteroides fragilis"
},
"algorithmic_error": {
"text": "NA"
}
},
"execution_domain": {
"external_data_endpoints": [
{
"url": "https://hive.aws.biochemistry.gwu.edu/dna.cgi?cmd=login",
"name": "HIVE"
}
],
"environment_variables": [
{
"key": "HOSTTYPE",
"value": "x86_64-linux"
}
],
"script_driver": "HIVE",
"software_prerequisites": [
{
"name": "Censuscope",
"version": "babajanian.1",
"uri": {
"uri": "http://hive.aws.biochemistry.gwu.edu/dna.cgi?cmd=dna-alignx_screen&cmdMode=-",
"access_time": "2017-01-24T09:40:17-0500",
"sha1_checksum": "d60f506cddac09e9e816531e7905ca1ca6641e3c"
}
}
],
"script": [
{
"uri": {
"uri": "http://hive.aws.biochemistry.gwu.edu/dna.cgi?cmd=dna-alignx_screen&cmdMode="
}
}
]
},
"io_domain": {
"input_subdomain": [],
"output_subdomain": []
},
"parametric_domain": [
{
"step": "1",
"value": "svc-dna-screening",
"param": "_type"
},
{
"step": "1",
"value": "mgm4461125.3.050.upload.fna",
"param": "name"
},
{
"step": "1",
"value": "1",
"param": "CensusIterations"
},
{
"step": "1",
"value": "5",
"param": "CensuslimitIterations"
},
{
"step": "1",
"value": "4000",
"param": "chunk_size"
},
{
"step": "1",
"value": "0.0005",
"param": "cutOffvalue"
},
{
"step": "1",
"value": "true",
"param": "filterNs"
},
{
"step": "1",
"value": "0",
"param": "random_seed"
},
{
"step": "1",
"value": "2500",
"param": "Sample"
},
{
"step": "1",
"value": "0",
"param": "slice"
},
{
"step": "1",
"value": "species",
"param": "taxDepth"
},
{
"step": "1",
"value": "svc-align-blast",
"param": "alignSelector"
},
{
"step": "1",
"value": "0",
"param": "automanual"
},
{
"step": "1",
"value": "{\"26\":2218}",
"param": "query"
},
{
"step": "1",
"value": "2242",
"param": "subject"
},
{
"step": "1",
"value": "0",
"param": "resultInQueryDir"
},
{
"step": "1",
"value": "false",
"param": "selfStopping"
},
{
"step": "1",
"value": "true",
"param": "storeAlignments"
},
{
"step": "1",
"value": "{\"blastWordSize\":28,\"blastMegablast\":true,\"blastevalue\":0.000001}",
"param": "blastparams"
},
{
"step": "1",
"value": "{\"textBasedColumn\":0,\"textBasedFileSeparator\":1}",
"param": "censusScope_otherInput"
}
],
"provenance_domain": {
"embargo": {},
"name": "CensuScope Test Computation",
"license": "https://spdx.org/licenses/CC-BY-4.0.html",
"review": [
{
"date": "2020-01-31T00:00:00-0400",
"reviewer": {
"affiliation": "George Washington University",
"contribution": [
"contributedBy"
],
"name": "Charles Hadley King",
"email": "[email protected]"
},
"status": "unreviewed"
}
],
"version": "1.0.0",
"contributors": [
{
"affiliation": "",
"contribution": [
"createdBy"
],
"name": "FILL",
"email": "[email protected]"
},
{
"affiliation": "Creator",
"contribution": [
"createdBy"
],
"email": "[email protected]",
"name": "Demo User",
"orcid": ""
}
],
"created": "2020-12-24T03:42:50.182Z",
"modified": "2020-12-24T03:42:50.182Z"
},
"usability_domin": [
"This curated test pipeline evaluates the performance of CensuScope, a tool designed and optimized for the quick detection of the components of a given NGS metagenomic data set, providing users with a species-level composition of a given sample. CensuScope was used to map a human gut microbiome sample (sourced from MG-RAST) against FilteredNT to view the sample’s taxonomic composition"
]
}