{"id":"https://openalex.org/W2106541878","doi":"https://doi.org/10.1109/bibe.2008.4696661","title":"A web based tool for integration of molecular pathway models","display_name":"A web based tool for integration of molecular pathway models","publication_year":2008,"publication_date":"2008-10-01","ids":{"openalex":"https://openalex.org/W2106541878","doi":"https://doi.org/10.1109/bibe.2008.4696661","mag":"2106541878"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2008.4696661","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2008.4696661","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 8th IEEE International Conference on BioInformatics and BioEngineering","raw_type":"proceedings-article"},"type":"conference-paper","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/A5053068096","display_name":"\u202c\u202c\u202c\u202c\u202c\u202cEva Sciacca","orcid":"https://orcid.org/0000-0002-5574-2787"},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Eva Sciacca","raw_affiliation_strings":["Department of Mathematics and Computer Science, Universita Catania, Catania, Italy","Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, Universita Catania, Catania, Italy","institution_ids":["https://openalex.org/I39063666"]},{"raw_affiliation_string":"Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019760518","display_name":"V. A. Shiva Ayyadurai","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"V. A. Shiva Ayyadurai","raw_affiliation_strings":["Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109870759","display_name":"C. Forbes Dewey","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C. Forbes Dewey","raw_affiliation_strings":["Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987999796867371,"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"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9979000091552734,"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":0.8165755271911621},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6596640348434448},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.574018657207489},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5519256591796875},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.5281938314437866},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5232055187225342},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.4811324179172516},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4728339612483978},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.4603959918022156},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.44607239961624146},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.3950927257537842},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3941918611526489},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.35259875655174255},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.19881990551948547},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.09774434566497803},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08689010143280029}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8165755271911621},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6596640348434448},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.574018657207489},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5519256591796875},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.5281938314437866},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5232055187225342},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.4811324179172516},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4728339612483978},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.4603959918022156},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.44607239961624146},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.3950927257537842},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3941918611526489},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.35259875655174255},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.19881990551948547},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.09774434566497803},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08689010143280029},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2008.4696661","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2008.4696661","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 8th IEEE International Conference on BioInformatics and BioEngineering","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6399999856948853,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W6905619","https://openalex.org/W1505561515","https://openalex.org/W1516732544","https://openalex.org/W1533710340","https://openalex.org/W1963861745","https://openalex.org/W2001620484","https://openalex.org/W2107062718","https://openalex.org/W2110345898","https://openalex.org/W2117344541","https://openalex.org/W2137063199","https://openalex.org/W2143784594","https://openalex.org/W2150908245","https://openalex.org/W2156877380","https://openalex.org/W2164459678","https://openalex.org/W2170122529","https://openalex.org/W2197056051","https://openalex.org/W2308480130","https://openalex.org/W3144826544","https://openalex.org/W4241509948","https://openalex.org/W6600295013","https://openalex.org/W6632167371"],"related_works":["https://openalex.org/W3180179400","https://openalex.org/W2118366689","https://openalex.org/W2154998455","https://openalex.org/W2116888309","https://openalex.org/W2477652530","https://openalex.org/W2039055059","https://openalex.org/W2381088774","https://openalex.org/W2281900275","https://openalex.org/W2183494409","https://openalex.org/W963721989"],"abstract_inverted_index":{"Developing":[0],"complex":[1,92],"models":[2,38,83,93,123,152],"of":[3,9,12,19,39,47,79,122,133,150],"cellular":[4,40],"function":[5],"requires":[6],"the":[7,45,95,114],"collaboration":[8,33],"multiple":[10],"teams":[11],"researchers":[13],"remotely":[14,85,111],"distributed":[15,151],"worldwide.":[16],"A":[17,131],"challenge":[18],"computational":[20,63,117],"systems":[21],"biology":[22],"is":[23],"to":[24,30,34,56,84,87,110,139,147],"find":[25],"easy":[26],"and":[27,61,90,105],"accessible":[28,104],"mechanisms":[29],"enable":[31],"such":[32],"construct":[35],"higher":[36],"level":[37],"function.":[41],"This":[42],"paper":[43],"presents":[44],"development":[46],"an":[48,58,148],"on-line":[49,99,155],"Web":[50,100,156],"portal":[51,101],"for":[52,65,77],"enabling":[53],"open":[54],"access":[55],"Cytosolve,":[57],"existing,":[59],"proven":[60],"scalable":[62],"architecture":[64],"integrating":[66],"quantitative":[67,80],"molecular":[68,81],"pathways.":[69],"The":[70,98],"developed":[71],"graphical":[72],"user":[73],"interface":[74],"allows":[75],"ease-of-use":[76],"developers":[78],"pathway":[82],"collaborate":[86,112],"build":[88],"larger":[89],"more":[91],"using":[94],"Cytosolve":[96,116],"infrastructure.":[97],"will":[102,107,136],"be":[103,137],"it":[106],"allow":[108],"users":[109],"with":[113],"existing":[115],"environment":[118],"that":[119],"supports":[120],"integration":[121],"in":[124],"a":[125,134],"parallel":[126],"manner":[127],"without":[128],"geographical":[129],"restrictions.":[130],"creator":[132],"model":[135,142],"able":[138],"integrate":[140],"their":[141,144],"from":[143],"local":[145],"location":[146],"ensemble":[149],"through":[153],"this":[154],"portal.":[157]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
