{"id":"https://openalex.org/W4241271456","doi":"https://doi.org/10.1109/cbms.2004.1311764","title":"Toward a systems biology software toolkit","display_name":"Toward a systems biology software toolkit","publication_year":2004,"publication_date":"2004-10-04","ids":{"openalex":"https://openalex.org/W4241271456","doi":"https://doi.org/10.1109/cbms.2004.1311764"},"language":"en","primary_location":{"id":"doi:10.1109/cbms.2004.1311764","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cbms.2004.1311764","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 17th IEEE Symposium on Computer-Based Medical Systems","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064370364","display_name":"D.J. Johann","orcid":null},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I1299022934","display_name":"United States Department of Health and Human Services","ror":"https://ror.org/033jnv181","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"D.J. Johann","raw_affiliation_strings":["National Institutes of Health DHHS, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Institutes of Health DHHS, Bethesda, MD, USA","institution_ids":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024249743","display_name":"M.D. McGuigan","orcid":null},"institutions":[{"id":"https://openalex.org/I200870766","display_name":"Brookhaven National Laboratory","ror":"https://ror.org/02ex6cf31","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I200870766","https://openalex.org/I39565521","https://openalex.org/I4210142672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M.D. McGuigan","raw_affiliation_strings":["Brockhaven National Laboratory, Upton, NY, USA"],"affiliations":[{"raw_affiliation_string":"Brockhaven National Laboratory, Upton, NY, USA","institution_ids":["https://openalex.org/I200870766"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053699070","display_name":"S. Tomov","orcid":null},"institutions":[{"id":"https://openalex.org/I200870766","display_name":"Brookhaven National Laboratory","ror":"https://ror.org/02ex6cf31","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I200870766","https://openalex.org/I39565521","https://openalex.org/I4210142672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Tomov","raw_affiliation_strings":["Brockhaven National Laboratory, Upton, NY, USA"],"affiliations":[{"raw_affiliation_string":"Brockhaven National Laboratory, Upton, NY, USA","institution_ids":["https://openalex.org/I200870766"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082985140","display_name":"E. Blum","orcid":null},"institutions":[{"id":"https://openalex.org/I200870766","display_name":"Brookhaven National Laboratory","ror":"https://ror.org/02ex6cf31","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I200870766","https://openalex.org/I39565521","https://openalex.org/I4210142672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"E. Blum","raw_affiliation_strings":["Brockhaven National Laboratory, Upton, NY, USA"],"affiliations":[{"raw_affiliation_string":"Brockhaven National Laboratory, Upton, NY, USA","institution_ids":["https://openalex.org/I200870766"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032031970","display_name":"G.R. Whiteley","orcid":null},"institutions":[{"id":"https://openalex.org/I1299022934","display_name":"United States Department of Health and Human Services","ror":"https://ror.org/033jnv181","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G.R. Whiteley","raw_affiliation_strings":["National Institutes of Health DHHS, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Institutes of Health DHHS, Bethesda, MD, USA","institution_ids":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046581361","display_name":"E.F. Petricoin","orcid":null},"institutions":[{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"E.F. Petricoin","raw_affiliation_strings":["Food and Drug Administration, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"Food and Drug Administration, Bethesda, MD, USA","institution_ids":["https://openalex.org/I1320320070"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059709062","display_name":"L.A. Liotta","orcid":null},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I1299022934","display_name":"United States Department of Health and Human Services","ror":"https://ror.org/033jnv181","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"L.A. Liotta","raw_affiliation_strings":["National Institutes of Health DHHS, Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Institutes of Health DHHS, Bethesda, MD, USA","institution_ids":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5064370364"],"corresponding_institution_ids":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"],"apc_list":null,"apc_paid":null,"fwci":0.3403,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.59129254,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"62","issue":null,"first_page":"500","last_page":"505"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9958000183105469,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9958000183105469,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9923999905586243,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9811999797821045,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.619606614112854},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5366029143333435},{"id":"https://openalex.org/keywords/medical-imaging","display_name":"Medical imaging","score":0.5192532539367676},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.497875452041626},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4770897328853607},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4670252799987793},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4553833305835724},{"id":"https://openalex.org/keywords/system-integration","display_name":"System integration","score":0.45480889081954956},{"id":"https://openalex.org/keywords/translational-bioinformatics","display_name":"Translational bioinformatics","score":0.41055941581726074},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32770001888275146},{"id":"https://openalex.org/keywords/medical-physics","display_name":"Medical physics","score":0.32328224182128906},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.2629314661026001},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2504734992980957},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1861245334148407},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1485118567943573}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.619606614112854},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5366029143333435},{"id":"https://openalex.org/C31601959","wikidata":"https://www.wikidata.org/wiki/Q931309","display_name":"Medical imaging","level":2,"score":0.5192532539367676},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.497875452041626},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4770897328853607},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4670252799987793},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4553833305835724},{"id":"https://openalex.org/C19527686","wikidata":"https://www.wikidata.org/wiki/Q1665453","display_name":"System integration","level":2,"score":0.45480889081954956},{"id":"https://openalex.org/C163293594","wikidata":"https://www.wikidata.org/wiki/Q7834541","display_name":"Translational bioinformatics","level":5,"score":0.41055941581726074},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32770001888275146},{"id":"https://openalex.org/C19527891","wikidata":"https://www.wikidata.org/wiki/Q1120908","display_name":"Medical physics","level":1,"score":0.32328224182128906},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2629314661026001},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2504734992980957},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1861245334148407},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1485118567943573},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cbms.2004.1311764","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cbms.2004.1311764","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 17th IEEE Symposium on Computer-Based Medical Systems","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.41999998688697815},{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.41999998688697815}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1905709030","https://openalex.org/W2004685742","https://openalex.org/W2043256631","https://openalex.org/W2052088499","https://openalex.org/W2066135299","https://openalex.org/W2119908867","https://openalex.org/W2130213158","https://openalex.org/W2134389439","https://openalex.org/W2159079963","https://openalex.org/W2172300860","https://openalex.org/W4232722314","https://openalex.org/W6679212166"],"related_works":["https://openalex.org/W4391852341","https://openalex.org/W2057769265","https://openalex.org/W2273308837","https://openalex.org/W2612203007","https://openalex.org/W2152199722","https://openalex.org/W2138715795","https://openalex.org/W2612152940","https://openalex.org/W2770548163","https://openalex.org/W2906138614","https://openalex.org/W2612219231"],"abstract_inverted_index":{"Insight":[0],"to":[1,22,41,61,124],"complex":[2,191],"problems":[3,24],"may":[4,121],"be":[5,122,208,217],"revealed":[6],"when":[7],"domain":[8],"data":[9,34],"sets":[10],"are":[11,79,161],"viewed":[12],"or":[13,147],"structured":[14],"in":[15,104,188,219],"new":[16,83,189],"and":[17,28,66,181,185,190],"innovative":[18],"ways.":[19],"Systems":[20],"approaches":[21],"biomedical":[23],"fundamentally":[25],"involve":[26],"forecasting,":[27],"a":[29,37,57,62,82,116,139,145,154,171],"deliberate":[30],"integration":[31,87],"of":[32,49,88,110,115,129,131,138,153,164],"diverse":[33],"sources.":[35],"Adding":[36],"clinical":[38,117],"proteomic":[39,148,212],"dimension":[40],"these":[42,73,165],"developing":[43],"efforts":[44],"affirms":[45],"the":[46,54,86,127,151,220,226],"ultimate":[47],"aims":[48],"enhanced":[50],"diagnostic":[51,77],"prediction,":[52],"maximizing":[53],"possibility":[55],"for":[56,173,210,228],"rational":[58],"therapy":[59],"individualized":[60],"patient's":[63],"pathologic":[64],"process,":[65],"thus,":[67],"improving":[68],"patient":[69],"outcomes.":[70],"Consistent":[71],"with":[72,91,144],"evolving":[74,195],"goals,":[75],"computer-aided":[76],"systems":[78,100,186],"rapidly":[80],"approaching":[81],"paradigm":[84],"involving":[85,225],"medical":[89,98,156],"imaging":[90,99,132,141],"high":[92],"throughput":[93],"molecular":[94],"medicine":[95],"tests.":[96],"As":[97],"become":[101],"more":[102,114],"sensitive":[103],"finding":[105],"anatomic":[106],"anomalies,":[107],"their":[108],"lack":[109,128],"specificity":[111,130],"becomes":[112],"much":[113],"dilemma.":[118],"Proteomic":[119],"tests":[120],"used":[123,218],"help":[125],"resolve":[126],"findings.":[133],"A":[134],"synergistic":[135],"test":[136],"composed":[137],"targeted":[140],"study":[142],"correlated":[143],"genomic":[146],"test(s),":[149],"offers":[150],"potential":[152],"tremendous":[155],"advancement.":[157],"Bioinformatic":[158],"software":[159,169],"toolkits":[160],"crucial":[162],"components":[163,198],"systems.":[166],"Open":[167],"source":[168,203],"provides":[170],"mechanism":[172],"leveraging":[174],"existing":[175,201],"toolkits,":[176],"sharing":[177],"expertise,":[178],"accelerating":[179],"development,":[180],"furthering":[182],"biomedical,":[183],"software,":[184],"sciences":[187],"multi-disciplinary":[192],"fields.":[193],"Our":[194],"toolkit":[196],"utilizes":[197],"from":[199],"several":[200],"open":[202],"projects.":[204],"It":[205],"will":[206,216],"initially":[207],"customized":[209],"serum":[211],"pattern":[213],"diagnostics,":[214],"which":[215],"upcoming":[221],"NCI/CCR":[222],"Clinical":[223],"Trial":[224],"monitoring":[227],"ovarian":[229],"cancer":[230],"recurrence.":[231]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
