{"id":"https://openalex.org/W2342124515","doi":"https://doi.org/10.7916/d8p26z34","title":"An Open Pipeline for Generating Executable Neural Circuits from Fruit Fly Brain Data","display_name":"An Open Pipeline for Generating Executable Neural Circuits from Fruit Fly Brain Data","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2342124515","doi":"https://doi.org/10.7916/d8p26z34","mag":"2342124515"},"language":"en","primary_location":{"id":"pmh:oai:academiccommons.columbia.edu:10.7916/D8P26Z34","is_oa":false,"landing_page_url":"https://doi.org/10.7916/D8P26Z34","pdf_url":null,"source":{"id":"https://openalex.org/S4306402601","display_name":"Columbia Academic Commons (Columbia University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I78577930","host_organization_name":"Columbia University","host_organization_lineage":["https://openalex.org/I78577930"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Theses"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.7916/d8p26z34","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010972890","display_name":"Lev E. Givon","orcid":"https://orcid.org/0000-0002-2736-730X"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Givon, Lev E.","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5010972890"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0218709,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10423","display_name":"Neurobiology and Insect Physiology Research","score":0.8873000144958496,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10423","display_name":"Neurobiology and Insect Physiology Research","score":0.8873000144958496,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10320","display_name":"Neural Networks and Applications","score":0.8823000192642212,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7347337007522583},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.6305052042007446},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5472542643547058},{"id":"https://openalex.org/keywords/on-the-fly","display_name":"On the fly","score":0.49993062019348145},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3310151994228363},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.23191291093826294}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7347337007522583},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.6305052042007446},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5472542643547058},{"id":"https://openalex.org/C2781020372","wikidata":"https://www.wikidata.org/wiki/Q533093","display_name":"On the fly","level":2,"score":0.49993062019348145},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3310151994228363},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.23191291093826294}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:academiccommons.columbia.edu:10.7916/D8P26Z34","is_oa":false,"landing_page_url":"https://doi.org/10.7916/D8P26Z34","pdf_url":null,"source":{"id":"https://openalex.org/S4306402601","display_name":"Columbia Academic Commons (Columbia University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I78577930","host_organization_name":"Columbia University","host_organization_lineage":["https://openalex.org/I78577930"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Theses"},{"id":"mag:2342124515","is_oa":false,"landing_page_url":"https://academiccommons.columbia.edu/download/fedora_content/download/ac:197714/content/Givon_columbia_0054D_13269.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null},{"id":"doi:10.7916/d8p26z34","is_oa":true,"landing_page_url":"https://doi.org/10.7916/d8p26z34","pdf_url":null,"source":{"id":"https://openalex.org/S4306402601","display_name":"Columbia Academic Commons (Columbia University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I78577930","host_organization_name":"Columbia University","host_organization_lineage":["https://openalex.org/I78577930"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.7916/d8p26z34","is_oa":true,"landing_page_url":"https://doi.org/10.7916/d8p26z34","pdf_url":null,"source":{"id":"https://openalex.org/S4306402601","display_name":"Columbia Academic Commons (Columbia University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I78577930","host_organization_name":"Columbia University","host_organization_lineage":["https://openalex.org/I78577930"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2982561195","https://openalex.org/W3041379478","https://openalex.org/W1616542569","https://openalex.org/W3093958165","https://openalex.org/W2421555156","https://openalex.org/W3037842197","https://openalex.org/W2588597108","https://openalex.org/W2001035196","https://openalex.org/W1016882582","https://openalex.org/W2465883083","https://openalex.org/W1534764825","https://openalex.org/W1510014385","https://openalex.org/W2102793705","https://openalex.org/W1828169060","https://openalex.org/W2020462650","https://openalex.org/W2037086593","https://openalex.org/W2944996566","https://openalex.org/W2086313531","https://openalex.org/W2793826975"],"abstract_inverted_index":{"Despite":[0],"considerable":[1],"progress":[2],"in":[3,15,172,258,399,456],"mapping":[4],"the":[5,10,18,21,26,40,56,61,66,78,84,96,120,133,173,216,231,264,276,285,299,316,323,331,339,376,397,422,425,430,438,442,460,468,496],"fly\u2019s":[6,497],"connectome":[7,105],"and":[8,25,83,147,234,262,330,372,375,408,418,449,489],"elucidating":[9],"patterns":[11],"of":[12,20,29,44,60,73,80,90,99,116,119,132,139,156,164,168,210,218,230,255,266,279,302,315,319,325,335,341,368,394,410,424,437,441,459,491],"information":[13,57],"flow":[14],"its":[16,32,202],"brain,":[17],"complexity":[19],"fly":[22,46,62,104,122,159,232,287,444],"brain\u2019s":[23],"structure":[24,374],"still-incomplete":[27],"state":[28],"knowledge":[30],"regarding":[31,284,452],"neural":[33,308,412,498],"circuitry":[34],"pose":[35],"significant":[36],"challenges":[37],"beyond":[38],"satisfying":[39],"computational":[41,476],"resource":[42,295],"requirements":[43,204],"current":[45],"brain":[47,74,91,123,127,160,174,260,288,290,445],"models":[48,75,92,118,161,167,198,229,310],"that":[49,93,129,179,194,199,360,494],"must":[50],"be":[51,181],"addressed":[52],"to":[53,68,86,205,225,305,414,432,474,478],"successfully":[54],"reverse":[55],"processing":[58,240],"capabilities":[59],"brain.":[63],"These":[64],"include":[65],"need":[67,85],"explicitly":[69],"facilitate":[70],"collaborative":[71,154],"development":[72],"by":[76,162,222,270,428],"combining":[77],"efforts":[79],"multiple":[81,184,252,487],"researchers,":[82],"enable":[87],"programmatic":[88],"generation":[89],"effectively":[94],"utilize":[95],"burgeoning":[97],"amount":[98,278],"increasingly":[100],"detailed":[101],"publicly":[102],"available":[103],"data.":[106,348],"This":[107,136],"thesis":[108],"presents":[109],"an":[110,434],"open":[111],"pipeline":[112,137,427,469],"for":[113,153,296,365,390,416],"modular":[114],"construction":[115,155,407],"executable":[117,157,307,343,411,435],"fruit":[121,286,443],"from":[124,346,446,486],"incomplete":[125],"biological":[126,282,347,370,479],"data":[128,283,304,321,363,371,395,451],"addresses":[130],"both":[131,369,392,447],"above":[134],"requirements.":[135],"consists":[138],"two":[140],"major":[141],"open-source":[142],"components":[143],"respectively":[144],"called":[145,358],"Neurokernel":[146,149,189,415],"NeuroArch.":[148],"is":[150,311],"a":[151,176,191,237,259,271,292,355,362,381,387,400],"framework":[152],"connectome-based":[158],"integration":[163],"independently":[165,227],"developed":[166,228],"different":[169,320,457],"functional":[170,196,256,272],"units":[171,257],"into":[175,236],"single":[177,238,382],"emulation":[178,490],"can":[180,249],"executed":[182],"upon":[183],"Graphics":[185],"Processing":[186],"Units":[187],"(GPUs).":[188],"enforces":[190],"programming":[192,220],"model":[193,221,297,364,373,436,472],"enables":[195,406],"unit":[197,273],"comply":[200],"with":[201,386],"interface":[203,389],"communicate":[206],"during":[207],"execution":[208,417],"regardless":[209],"their":[211],"internal":[212],"design.":[213],"We":[214,242,420,464],"demonstrate":[215,421],"power":[217],"this":[219,303,404],"using":[223,429],"it":[224],"integrate":[226],"retina":[233],"lamina":[235],"vision":[239],"system.":[241],"also":[243,465],"show":[244,466],"how":[245,467],"Neurokernel\u2019s":[246],"communication":[247,267],"performance":[248],"scale":[250],"over":[251,263],"GPUs,":[253],"number":[254,265],"emulation,":[261],"ports":[268],"exposed":[269],"model.":[274],"Although":[275],"increasing":[277],"experimentally":[280],"obtained":[281],"affords":[289],"modelers":[291],"potentially":[293],"valuable":[294],"development,":[298],"actual":[300],"use":[301],"construct":[306],"circuit":[309,344,471],"currently":[312],"challenging":[313],"because":[314],"disparate":[317],"nature":[318],"sources,":[322],"range":[324],"storage":[326],"formats":[327,337],"they":[328],"use,":[329],"limited":[332],"query":[333],"features":[334],"those":[336],"complicates":[338],"process":[340],"inferring":[342],"designs":[345],"To":[349],"overcome":[350],"these":[351],"limitations,":[352],"we":[353],"created":[354],"software":[356],"package":[357],"NeuroArch":[359],"defines":[361],"concurrent":[366,484],"representation":[367,405],"relationships":[377],"between":[378],"them":[379],"within":[380,396],"graph":[383],"database.":[384],"Coupled":[385],"powerful":[388],"querying":[391],"types":[393],"database":[398],"uniform":[401],"high-level":[402],"manner,":[403],"dispatching":[409],"circuits":[413],"evaluation.":[419],"utility":[423],"NeuroArch/Neurokernel":[426],"packages":[431],"generate":[433],"central":[439,461],"complex":[440,462],"published":[448],"hypothetical":[450],"overlapping":[453],"neuron":[454],"arborizations":[455],"regions":[458],"neuropils.":[463],"empowers":[470],"designers":[473],"devise":[475],"analogues":[477],"experiments":[480],"such":[481],"as":[482],"parallel":[483],"recording":[485],"neurons":[488],"genetic":[492],"mutations":[493],"alter":[495],"circuitry.":[499]},"counts_by_year":[],"updated_date":"2025-11-06T06:51:31.235846","created_date":"2025-10-10T00:00:00"}
