{"id":"https://openalex.org/W2801610974","doi":"https://doi.org/10.1109/iscas.2018.8350960","title":"A Faster DiSH: Hardware Implementation of a Discrete Cell Signaling Network Simulator","display_name":"A Faster DiSH: Hardware Implementation of a Discrete Cell Signaling Network Simulator","publication_year":2018,"publication_date":"2018-05-01","ids":{"openalex":"https://openalex.org/W2801610974","doi":"https://doi.org/10.1109/iscas.2018.8350960","mag":"2801610974"},"language":"en","primary_location":{"id":"doi:10.1109/iscas.2018.8350960","is_oa":true,"landing_page_url":"https://doi.org/10.1109/iscas.2018.8350960","pdf_url":"https://ieeexplore.ieee.org/ielx7/8334884/8350884/08350960.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Symposium on Circuits and Systems (ISCAS)","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/8334884/8350884/08350960.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048801314","display_name":"Kevin Gilboy","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kevin Gilboy","raw_affiliation_strings":["Pittsburgh, University of Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Pittsburgh, University of Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024140128","display_name":"Khaled Sayed","orcid":"https://orcid.org/0000-0002-1252-3170"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Khaled Sayed","raw_affiliation_strings":["Pittsburgh, University of Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Pittsburgh, University of Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065800906","display_name":"Niteesh Sundaram","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Niteesh Sundaram","raw_affiliation_strings":["Pittsburgh, University of Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Pittsburgh, University of Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074846549","display_name":"Kara Bocan","orcid":"https://orcid.org/0000-0002-5780-5016"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kara Bocan","raw_affiliation_strings":["Pittsburgh, University of Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Pittsburgh, University of Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017141796","display_name":"Nata\u0161a Mi\u0161kov-\u017divanov","orcid":"https://orcid.org/0000-0003-1110-3403"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Natasa Miskov-Zivanov","raw_affiliation_strings":["Pittsburgh, University of Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Pittsburgh, University of Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5048801314"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03550423,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9994999766349792,"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":0.9994999766349792,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9955000281333923,"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/T10885","display_name":"Gene expression and cancer classification","score":0.982699990272522,"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":0.7257562279701233},{"id":"https://openalex.org/keywords/stochastic-simulation","display_name":"Stochastic simulation","score":0.652984082698822},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.6500020027160645},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.641704797744751},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6143275499343872},{"id":"https://openalex.org/keywords/random-number-generation","display_name":"Random number generation","score":0.5268501043319702},{"id":"https://openalex.org/keywords/scope","display_name":"Scope (computer science)","score":0.4978756904602051},{"id":"https://openalex.org/keywords/software-implementation","display_name":"Software implementation","score":0.4567107558250427},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.30649563670158386},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.11747497320175171},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08705416321754456},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.07822215557098389}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7257562279701233},{"id":"https://openalex.org/C25915931","wikidata":"https://www.wikidata.org/wiki/Q4180825","display_name":"Stochastic simulation","level":2,"score":0.652984082698822},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.6500020027160645},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.641704797744751},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6143275499343872},{"id":"https://openalex.org/C201866948","wikidata":"https://www.wikidata.org/wiki/Q228206","display_name":"Random number generation","level":2,"score":0.5268501043319702},{"id":"https://openalex.org/C2778012447","wikidata":"https://www.wikidata.org/wiki/Q1034415","display_name":"Scope (computer science)","level":2,"score":0.4978756904602051},{"id":"https://openalex.org/C2983609787","wikidata":"https://www.wikidata.org/wiki/Q10534782","display_name":"Software implementation","level":3,"score":0.4567107558250427},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.30649563670158386},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.11747497320175171},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08705416321754456},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.07822215557098389},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"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}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/iscas.2018.8350960","is_oa":true,"landing_page_url":"https://doi.org/10.1109/iscas.2018.8350960","pdf_url":"https://ieeexplore.ieee.org/ielx7/8334884/8350884/08350960.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Symposium on Circuits and Systems (ISCAS)","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:1811.07861","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1811.07861","pdf_url":"https://arxiv.org/pdf/1811.07861","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"mag:2801610974","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1811.07861","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1811.07861","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1811.07861","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"}],"best_oa_location":{"id":"doi:10.1109/iscas.2018.8350960","is_oa":true,"landing_page_url":"https://doi.org/10.1109/iscas.2018.8350960","pdf_url":"https://ieeexplore.ieee.org/ielx7/8334884/8350884/08350960.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Symposium on Circuits and Systems (ISCAS)","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2801610974.pdf","grobid_xml":"https://content.openalex.org/works/W2801610974.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1963855808","https://openalex.org/W2069125012","https://openalex.org/W2103723044","https://openalex.org/W2119530812","https://openalex.org/W2121525198","https://openalex.org/W2158185864","https://openalex.org/W2580670229","https://openalex.org/W2612129877","https://openalex.org/W2963528844"],"related_works":["https://openalex.org/W2963990577","https://openalex.org/W2979851654","https://openalex.org/W3034752518","https://openalex.org/W2775625857","https://openalex.org/W2087724934","https://openalex.org/W2124073900","https://openalex.org/W2909875703","https://openalex.org/W3002136461","https://openalex.org/W2947418285","https://openalex.org/W2904007204","https://openalex.org/W1981549778","https://openalex.org/W3136178412","https://openalex.org/W2886166961","https://openalex.org/W75005028","https://openalex.org/W2078180168","https://openalex.org/W2918577631","https://openalex.org/W2104827316","https://openalex.org/W2107850139","https://openalex.org/W331807190","https://openalex.org/W3159007080"],"abstract_inverted_index":{"Development":[0],"of":[1,12,89],"fast":[2],"methods":[3],"to":[4,62,102],"conduct":[5],"in":[6,21,54],"silico":[7],"experiments":[8],"using":[9],"computational":[10],"models":[11],"cellular":[13,26,90],"signaling":[14],"is":[15],"a":[16],"promising":[17],"approach":[18],"toward":[19],"advances":[20],"personalized":[22],"medicine.":[23],"However,":[24],"software-based":[25],"network":[27],"simulation":[28,40,50,74,99],"has":[29],"run-times":[30],"plagued":[31],"by":[32],"wasted":[33],"CPU":[34],"cycles":[35],"and":[36,56,85],"unnecessary":[37],"processes.":[38],"Hardware-based":[39],"affords":[41],"substantial":[42],"speedup,":[43],"but":[44],"prior":[45],"attempts":[46],"at":[47],"hardware-based":[48,73],"biological":[49],"have":[51,57],"been":[52],"limited":[53],"scope":[55],"suffered":[58],"from":[59],"inaccuracies":[60],"due":[61],"poor":[63],"random":[64,78],"number":[65],"generation.":[66],"In":[67],"this":[68],"work,":[69],"we":[70],"propose":[71],"several":[72],"schemes":[75],"utilizing":[76],"novel":[77],"update":[79],"index":[80],"generation":[81],"techniques":[82],"for":[83],"step-based":[84],"round-based":[86],"stochastic":[87],"simulations":[88],"networks.":[91],"Our":[92],"results":[93],"show":[94],"improved":[95],"runtimes":[96],"while":[97],"maintaining":[98],"accuracy":[100],"compared":[101],"software":[103],"implementations.":[104]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
