{"id":"https://openalex.org/W2981116567","doi":"https://doi.org/10.1186/s12859-019-3094-9","title":"PlantSimLab - a modeling and simulation web tool for plant biologists","display_name":"PlantSimLab - a modeling and simulation web tool for plant biologists","publication_year":2019,"publication_date":"2019-10-21","ids":{"openalex":"https://openalex.org/W2981116567","doi":"https://doi.org/10.1186/s12859-019-3094-9","mag":"2981116567","pmid":"https://pubmed.ncbi.nlm.nih.gov/31638901"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3094-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3094-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3094-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3094-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001966215","display_name":"Sook Shin Ha","orcid":null},"institutions":[{"id":"https://openalex.org/I185641255","display_name":"Virginia Military Institute","ror":"https://ror.org/01ngnm118","country_code":"US","type":"education","lineage":["https://openalex.org/I185641255"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Ha","raw_affiliation_strings":["Department of Computer and Information Sciences, Virginia Military Institute, Lexington, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences, Virginia Military Institute, Lexington, VA, USA","institution_ids":["https://openalex.org/I185641255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113858037","display_name":"E. Dimitrova","orcid":null},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"E. Dimitrova","raw_affiliation_strings":["School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081050112","display_name":"Stefan Hoops","orcid":"https://orcid.org/0000-0001-8503-8371"},"institutions":[{"id":"https://openalex.org/I4210151352","display_name":"Biocom","ror":"https://ror.org/03ymdxs56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151352"]},{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Hoops","raw_affiliation_strings":["Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I4210151352","https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012784808","display_name":"Doaa Altarawy","orcid":"https://orcid.org/0000-0002-7795-4422"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Altarawy","raw_affiliation_strings":["Virginia Tech, Blacksburg, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002949707","display_name":"Mitra Ansariola","orcid":"https://orcid.org/0000-0003-0092-1435"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Ansariola","raw_affiliation_strings":["Celgene, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Celgene, San Francisco, CA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076075336","display_name":"D. Deb","orcid":null},"institutions":[{"id":"https://openalex.org/I125924841","display_name":"Mercy University","ror":"https://ror.org/02s99ck98","country_code":"US","type":"education","lineage":["https://openalex.org/I125924841"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Deb","raw_affiliation_strings":["Department of Natural Sciences, Mercy College, Dobbs Ferry, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Natural Sciences, Mercy College, Dobbs Ferry, NY, USA","institution_ids":["https://openalex.org/I125924841"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033301769","display_name":"Jane Glazebrook","orcid":"https://orcid.org/0000-0001-5167-736X"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Glazebrook","raw_affiliation_strings":["College of Biological Sciences, University of Minnesota, St. Paul, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Biological Sciences, University of Minnesota, St. Paul, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049634308","display_name":"Rachel Hillmer","orcid":"https://orcid.org/0000-0003-0632-5597"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"R. Hillmer","raw_affiliation_strings":["Mendel Biological Solutions, San Franciso, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mendel Biological Solutions, San Franciso, CA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000237021","display_name":"Hady Shahin","orcid":"https://orcid.org/0000-0003-3894-6849"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"H. Shahin","raw_affiliation_strings":["Virginia Tech, Blacksburg, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063170424","display_name":"Fumiaki Katagiri","orcid":"https://orcid.org/0000-0001-6893-3788"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"F. Katagiri","raw_affiliation_strings":["College of Biological Sciences, University of Minnesota, St. Paul, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Biological Sciences, University of Minnesota, St. Paul, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089084257","display_name":"John M. McDowell","orcid":"https://orcid.org/0000-0002-9070-4874"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. McDowell","raw_affiliation_strings":["Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030831065","display_name":"Molly Megraw","orcid":"https://orcid.org/0000-0001-6793-6151"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Megraw","raw_affiliation_strings":["Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060418877","display_name":"Jo\u00e3o Carlos Set\u00fabal","orcid":"https://orcid.org/0000-0001-9174-2816"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]},{"id":"https://openalex.org/I4405260184","display_name":"The Jackson Laboratory for Genomic Medicine","ror":"https://ror.org/03cew3973","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Setubal","raw_affiliation_strings":["Biochemistry Department, University of Sao Paolo, Sao Paolo, Brazil","The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biochemistry Department, University of Sao Paolo, Sao Paolo, Brazil","institution_ids":[]},{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA","institution_ids":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011074546","display_name":"Brett M. Tyler","orcid":"https://orcid.org/0000-0003-1549-2987"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]},{"id":"https://openalex.org/I4210151352","display_name":"Biocom","ror":"https://ror.org/03ymdxs56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151352"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. M. Tyler","raw_affiliation_strings":["Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849","https://openalex.org/I4210151352"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091010756","display_name":"Reinhard Laubenbacher","orcid":"https://orcid.org/0000-0002-9143-9451"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]},{"id":"https://openalex.org/I162281398","display_name":"University of Hartford","ror":"https://ror.org/034gcgd08","country_code":"US","type":"education","lineage":["https://openalex.org/I162281398"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"R. Laubenbacher","raw_affiliation_strings":["Center for Quantitative Medicine, School of Medicine, University of Connecticut, Hartford, USA. laubenbacher@uchc.edu","Center for Quantitative Medicine, School of Medicine, University of Connecticut, Hartford, USA"],"raw_orcid":"https://orcid.org/0000-0002-9143-9451","affiliations":[{"raw_affiliation_string":"Center for Quantitative Medicine, School of Medicine, University of Connecticut, Hartford, USA. laubenbacher@uchc.edu","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Center for Quantitative Medicine, School of Medicine, University of Connecticut, Hartford, USA","institution_ids":["https://openalex.org/I140172145","https://openalex.org/I162281398"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5091010756"],"corresponding_institution_ids":["https://openalex.org/I140172145","https://openalex.org/I162281398","https://openalex.org/I4210098931"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.3034,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.55274405,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"20","issue":"1","first_page":"508","last_page":"508"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.5314000248908997,"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":0.5314000248908997,"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/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.08810000121593475,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.045499999076128006,"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":0.7635908722877502},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5605958700180054},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.5237645506858826},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5191580653190613},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5017659664154053},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4979116916656494},{"id":"https://openalex.org/keywords/mathematical-model","display_name":"Mathematical model","score":0.4857195019721985},{"id":"https://openalex.org/keywords/mathematical-software","display_name":"Mathematical software","score":0.4418056607246399},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.4341311752796173},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.4234650135040283},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.39569276571273804},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.37228724360466003},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.36439865827560425},{"id":"https://openalex.org/keywords/management-science","display_name":"Management science","score":0.3625563085079193},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.17013439536094666},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12088948488235474},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10316964983940125}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7635908722877502},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5605958700180054},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5237645506858826},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5191580653190613},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5017659664154053},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4979116916656494},{"id":"https://openalex.org/C76969082","wikidata":"https://www.wikidata.org/wiki/Q486902","display_name":"Mathematical model","level":2,"score":0.4857195019721985},{"id":"https://openalex.org/C2778400913","wikidata":"https://www.wikidata.org/wiki/Q1639024","display_name":"Mathematical software","level":3,"score":0.4418056607246399},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.4341311752796173},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.4234650135040283},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.39569276571273804},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.37228724360466003},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.36439865827560425},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.3625563085079193},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.17013439536094666},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12088948488235474},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10316964983940125},{"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/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-019-3094-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3094-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3094-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31638901","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31638901","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:d6fc276d62274949a991b0ff932f403a","is_oa":true,"landing_page_url":"https://doaj.org/article/d6fc276d62274949a991b0ff932f403a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-11 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5765376","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6805577","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:mouseion.jax.org:stfb2019-1223","is_oa":true,"landing_page_url":"https://mouseion.jax.org/stfb2019/230","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Research 2019","raw_type":"text"},{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/95176","is_oa":true,"landing_page_url":"http://hdl.handle.net/10919/95176","pdf_url":null,"source":{"id":"https://openalex.org/S4306400248","display_name":"VTechWorks (Virginia Tech)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I859038795","host_organization_name":"Virginia Tech","host_organization_lineage":["https://openalex.org/I859038795"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article - Refereed"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-3094-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3094-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3094-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Responsible consumption and production","score":0.46000000834465027,"id":"https://metadata.un.org/sdg/12"}],"awards":[{"id":"https://openalex.org/G3964338018","display_name":"Collaborative Research:   ABI Innovation:  PlantSimLab: A Simulation Laboratory for Plant Biology","funder_award_id":"1146819","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2981116567.pdf","grobid_xml":"https://content.openalex.org/works/W2981116567.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W58125149","https://openalex.org/W2000982470","https://openalex.org/W2088259098","https://openalex.org/W2103454055","https://openalex.org/W2141368462","https://openalex.org/W2158685692","https://openalex.org/W2166599532","https://openalex.org/W2187917465","https://openalex.org/W2509721407","https://openalex.org/W2529551304","https://openalex.org/W2544038273","https://openalex.org/W2606865284","https://openalex.org/W2625353905","https://openalex.org/W2643655279","https://openalex.org/W2752251463","https://openalex.org/W2754307390","https://openalex.org/W2791845486","https://openalex.org/W2794403750","https://openalex.org/W2949136837","https://openalex.org/W2963981820"],"related_works":["https://openalex.org/W4386563820","https://openalex.org/W631732704","https://openalex.org/W2155261113","https://openalex.org/W2349272733","https://openalex.org/W2064988479","https://openalex.org/W1748979965","https://openalex.org/W3199870583","https://openalex.org/W2380087464","https://openalex.org/W4254550161","https://openalex.org/W1497779830"],"abstract_inverted_index":{"BACKGROUND:":[0],"At":[1],"the":[2,27,37,54,131,181],"molecular":[3,118],"level,":[4],"nonlinear":[5],"networks":[6],"of":[7,29,36,117,212],"heterogeneous":[8],"molecules":[9],"control":[10],"many":[11,48],"biological":[12,140,168,182],"processes,":[13],"so":[14],"that":[15,47,90,202],"systems":[16],"biology":[17,31],"provides":[18],"a":[19,44,85,104,123,137,162,173,198,217],"valuable":[20],"approach":[21],"in":[22,122,130],"this":[23,42],"field,":[24],"building":[25],"on":[26],"integration":[28,43],"experimental":[30],"with":[32,197],"mathematical":[33,55,62,115,155,206,229],"modeling.":[34],"One":[35],"biggest":[38],"challenges":[39],"to":[40,58,66,93,108,112,126,146,187,216],"making":[41],"reality":[45],"is":[46,84,128,144,172,222],"life":[49],"scientists":[50],"do":[51],"not":[52,204,226],"possess":[53],"expertise":[56],"needed":[57],"build":[59],"and":[60,95,133,170,190,224],"manipulate":[61],"models":[63,116,214],"well":[64],"enough":[65],"use":[67,94,134,191],"them":[68,121,135],"as":[69,136,220],"tools":[70,89,179],"for":[71,87,97,139,165,175],"hypothesis":[72,141],"generation.":[73,142],"Available":[74],"modeling":[75,81,159,207],"software":[76,88],"packages":[77],"often":[78],"assume":[79],"some":[80],"expertise.":[82,208,230],"There":[83],"need":[86,174],"are":[91,161],"easy":[92],"intuitive":[96,192],"experimentalists.":[98],"RESULTS:":[99],"This":[100],"paper":[101],"introduces":[102],"PlantSimLab,":[103],"web-based":[105],"application":[106],"developed":[107],"allow":[109],"plant":[110],"biologists":[111],"construct":[113],"dynamic":[114,194],"networks,":[119],"interrogate":[120],"manner":[124],"similar":[125],"what":[127],"done":[129],"laboratory,":[132],"tool":[138,164],"It":[143,209],"designed":[145],"be":[147],"used":[148],"by":[149],"experimentalists,":[150],"without":[151],"direct":[152],"assistance":[153],"from":[154],"modelers.":[156],"CONCLUSIONS:":[157],"Mathematical":[158],"techniques":[160],"useful":[163],"analyzing":[166],"complex":[167,213],"systems,":[169],"there":[171],"accessible,":[176],"efficient":[177],"analysis":[178,211],"within":[180],"community.":[183],"PlantSimLab":[184],"enables":[185],"users":[186],"build,":[188],"validate,":[189],"qualitative":[193],"computer":[195],"models,":[196],"graphical":[199],"user":[200],"interface":[201],"does":[203,225],"require":[205,227],"makes":[210],"accessible":[215],"larger":[218],"community,":[219],"it":[221],"platform-independent":[223],"extensive":[228]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
