{"id":"https://openalex.org/W4311023929","doi":"https://doi.org/10.1093/bioinformatics/btac787","title":"Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models","display_name":"Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models","publication_year":2022,"publication_date":"2022-12-10","ids":{"openalex":"https://openalex.org/W4311023929","doi":"https://doi.org/10.1093/bioinformatics/btac787","pmid":"https://pubmed.ncbi.nlm.nih.gov/36495209"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac787","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac787","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac787/48520890/btac787.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac787/48520890/btac787.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002950848","display_name":"Daniel Weilandt","orcid":"https://orcid.org/0000-0002-0556-8485"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Daniel R Weilandt","raw_affiliation_strings":["Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083134846","display_name":"Pierre Salvy","orcid":"https://orcid.org/0000-0002-3834-0356"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Pierre Salvy","raw_affiliation_strings":["Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003885943","display_name":"Mar\u00eda Masid","orcid":"https://orcid.org/0000-0001-6470-5083"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Maria Masid","raw_affiliation_strings":["Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076299421","display_name":"Georgios Fengos","orcid":"https://orcid.org/0000-0001-8110-8424"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Georgios Fengos","raw_affiliation_strings":["Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077771712","display_name":"Robin Denhardt-Erikson","orcid":"https://orcid.org/0000-0003-0964-8244"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Robin Denhardt-Erikson","raw_affiliation_strings":["Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039760526","display_name":"Zhaleh Hosseini","orcid":"https://orcid.org/0000-0003-4724-0637"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Zhaleh Hosseini","raw_affiliation_strings":["Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056011141","display_name":"Vassily Hatzimanikatis","orcid":"https://orcid.org/0000-0001-6432-4694"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Vassily Hatzimanikatis","raw_affiliation_strings":["Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-6432-4694","affiliations":[{"raw_affiliation_string":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5056011141"],"corresponding_institution_ids":["https://openalex.org/I5124864"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3237,"currency":"EUR","value_usd":3491},"fwci":1.5592,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.83245172,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.5971999764442444,"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":0.5971999764442444,"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":0.14309999346733093,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.11789999902248383,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/python","display_name":"Python (programming language)","score":0.9450275897979736},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.8655362129211426},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7380373477935791},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6437628865242004},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5316202044487},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4416027069091797},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3088551163673401},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.0787551999092102}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9450275897979736},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.8655362129211426},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7380373477935791},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6437628865242004},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5316202044487},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4416027069091797},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3088551163673401},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0787551999092102},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac787","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac787","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac787/48520890/btac787.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36495209","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36495209","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:infoscience.epfl.ch:299353","is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/193888","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"WoS","raw_type":"research article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9825757","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825757","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac787","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac787","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac787/48520890/btac787.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3496877176","display_name":"Modular cell factories for the production of 100 compounds from the shikimate pathway","funder_award_id":"814408","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3585592020","display_name":"Systematic Models for Biological Systems Engineering Training Network","funder_award_id":"675585","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6287278593","display_name":"Predictive and Accelerated Metabolic Engineering Network","funder_award_id":"722287","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7820999220","display_name":"NCCR Microbiomes: Microbial communities in health and environment","funder_award_id":"180575","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G8690525661","display_name":"Bioinformatics Services for Data-Driven Design of Cell Factories and Communities","funder_award_id":"686070","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4311023929.pdf","grobid_xml":"https://content.openalex.org/works/W4311023929.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1168318060","https://openalex.org/W1972863608","https://openalex.org/W1990812533","https://openalex.org/W2022238394","https://openalex.org/W2128852521","https://openalex.org/W2139038704","https://openalex.org/W2143784594","https://openalex.org/W2161227644","https://openalex.org/W2164898811","https://openalex.org/W2337275563","https://openalex.org/W2461742269","https://openalex.org/W2561960911","https://openalex.org/W2808435053","https://openalex.org/W2810239425","https://openalex.org/W2954040564","https://openalex.org/W3012829536","https://openalex.org/W3209964554"],"related_works":["https://openalex.org/W2068663075","https://openalex.org/W2978678743","https://openalex.org/W2797837731","https://openalex.org/W2150344375","https://openalex.org/W829257147","https://openalex.org/W3081389670","https://openalex.org/W4390832911","https://openalex.org/W2549786917","https://openalex.org/W2207495067","https://openalex.org/W1906486629"],"abstract_inverted_index":{"MOTIVATION:":[0],"Large-scale":[1],"kinetic":[2,54,73,84,107],"models":[3,24,39,55,85,108],"are":[4,151],"an":[5,71],"invaluable":[6],"tool":[7],"to":[8,34,48,105,124],"understand":[9],"the":[10,29,46,77],"dynamic":[11],"and":[12,20,36,51,57,80,95],"adaptive":[13],"responses":[14],"of":[15,22,31,82],"biological":[16,88],"systems.":[17],"The":[18,41,131],"development":[19],"application":[21],"these":[23],"have":[25],"been":[26],"limited":[27],"by":[28,69],"availability":[30],"computational":[32],"tools":[33],"build":[35],"analyze":[37,52],"large-scale":[38,53,83],"efficiently.":[40,58,113],"toolbox":[42,75,102],"presented":[43],"here":[44],"provides":[45],"means":[47],"implement,":[49],"parameterize":[50,106],"intuitively":[56],"RESULTS:":[59],"We":[60],"present":[61],"a":[62,110,136],"Python":[63,137],"package":[64,139],"(SKiMpy)":[65],"bridging":[66],"this":[67,101],"gap":[68],"implementing":[70],"efficient":[72],"modeling":[74],"for":[76,86],"semiautomatic":[78],"generation":[79],"analysis":[81],"various":[87],"domains":[89],"such":[90],"as":[91,135],"signaling,":[92],"gene":[93],"expression":[94],"metabolism.":[96],"Furthermore,":[97],"we":[98,115],"demonstrate":[99],"how":[100,117],"is":[103,133],"used":[104],"around":[109],"steady-state":[111],"reference":[112],"Finally,":[114],"show":[116],"SKiMpy":[118],"can":[119],"implement":[120],"multispecies":[121],"bioreactor":[122],"simulations":[123],"assess":[125],"biotechnological":[126],"processes.":[127],"AVAILABILITY":[128],"AND":[129],"IMPLEMENTATION:":[130],"software":[132],"available":[134,152],"3":[138],"on":[140],"GitHub:":[141],"https://github.com/EPFL-LCSB/SKiMpy,":[142],"along":[143],"with":[144],"adequate":[145],"documentation.":[146],"SUPPLEMENTARY":[147],"INFORMATION:":[148],"Supplementary":[149],"data":[150],"at":[153],"Bioinformatics":[154],"online.":[155]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}