{"id":"https://openalex.org/W4410630208","doi":"https://doi.org/10.1093/bioinformatics/btaf174","title":"MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics","display_name":"MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4410630208","doi":"https://doi.org/10.1093/bioinformatics/btaf174","pmid":"https://pubmed.ncbi.nlm.nih.gov/40408146"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf174","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf174","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf174/63309645/btaf174.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf174/63309645/btaf174.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030689655","display_name":"Pedro Fontanarrosa","orcid":"https://orcid.org/0000-0002-0535-2684"},"institutions":[{"id":"https://openalex.org/I4210093127","display_name":"MRC Laboratory for Molecular Cell Biology","ror":"https://ror.org/00fv61j67","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I4210087105","https://openalex.org/I4210093127","https://openalex.org/I45129253","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Pedro Fontanarrosa","raw_affiliation_strings":["Research Department of Cell and Developmental Biology, University College London , London, WC1E 6BT,","Research Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-0535-2684","affiliations":[{"raw_affiliation_string":"Research Department of Cell and Developmental Biology, University College London , London, WC1E 6BT,","institution_ids":["https://openalex.org/I4210093127","https://openalex.org/I45129253"]},{"raw_affiliation_string":"Research Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, United Kingdom","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049382910","display_name":"Chania Clare","orcid":"https://orcid.org/0000-0002-5788-7453"},"institutions":[{"id":"https://openalex.org/I4210093127","display_name":"MRC Laboratory for Molecular Cell Biology","ror":"https://ror.org/00fv61j67","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I4210087105","https://openalex.org/I4210093127","https://openalex.org/I45129253","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Chania Clare","raw_affiliation_strings":["Research Department of Cell and Developmental Biology, University College London , London, WC1E 6BT,","Research Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-5788-7453","affiliations":[{"raw_affiliation_string":"Research Department of Cell and Developmental Biology, University College London , London, WC1E 6BT,","institution_ids":["https://openalex.org/I4210093127","https://openalex.org/I45129253"]},{"raw_affiliation_string":"Research Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, United Kingdom","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051465177","display_name":"Alex J. H. Fedorec","orcid":"https://orcid.org/0000-0003-0165-1705"},"institutions":[{"id":"https://openalex.org/I4210093127","display_name":"MRC Laboratory for Molecular Cell Biology","ror":"https://ror.org/00fv61j67","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I4210087105","https://openalex.org/I4210093127","https://openalex.org/I45129253","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alex J H Fedorec","raw_affiliation_strings":["Research Department of Cell and Developmental Biology, University College London , London, WC1E 6BT,","Research Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-0165-1705","affiliations":[{"raw_affiliation_string":"Research Department of Cell and Developmental Biology, University College London , London, WC1E 6BT,","institution_ids":["https://openalex.org/I4210093127","https://openalex.org/I45129253"]},{"raw_affiliation_string":"Research Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, United Kingdom","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031424617","display_name":"C. Barnes","orcid":"https://orcid.org/0000-0002-9459-1395"},"institutions":[{"id":"https://openalex.org/I4210093127","display_name":"MRC Laboratory for Molecular Cell Biology","ror":"https://ror.org/00fv61j67","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I4210087105","https://openalex.org/I4210093127","https://openalex.org/I45129253","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Chris P Barnes","raw_affiliation_strings":["Research Department of Cell and Developmental Biology, University College London , London, WC1E 6BT,","Research Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-9459-1395","affiliations":[{"raw_affiliation_string":"Research Department of Cell and Developmental Biology, University College London , London, WC1E 6BT,","institution_ids":["https://openalex.org/I4210093127","https://openalex.org/I45129253"]},{"raw_affiliation_string":"Research Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, United Kingdom","institution_ids":["https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1519,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.77410865,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"41","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.47540000081062317,"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/T10066","display_name":"Gut microbiota and health","score":0.47540000081062317,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.08550000190734863,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10900","display_name":"Listeria monocytogenes in Food Safety","score":0.03999999910593033,"subfield":{"id":"https://openalex.org/subfields/1305","display_name":"Biotechnology"},"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":0.8114829063415527},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.712184488773346},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5291464924812317},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.45754170417785645},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.44804441928863525},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.42467132210731506},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3941991627216339},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3773208558559418},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.35481831431388855},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.26762068271636963},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.19149640202522278},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1749686300754547}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8114829063415527},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.712184488773346},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5291464924812317},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.45754170417785645},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.44804441928863525},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.42467132210731506},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3941991627216339},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3773208558559418},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.35481831431388855},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.26762068271636963},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.19149640202522278},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1749686300754547}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056265","descriptor_name":"Microbial Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056265","descriptor_name":"Microbial Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056265","descriptor_name":"Microbial Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056265","descriptor_name":"Microbial Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf174","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf174","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf174/63309645/btaf174.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:40408146","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40408146","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:pubmedcentral.nih.gov:12119135","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12119135","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf174","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf174","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf174/63309645/btaf174.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[{"display_name":"Life in Land","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G546781751","display_name":"London Interdisciplinary Doctoral Programme","funder_award_id":"BB/T008709/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410630208.pdf","grobid_xml":"https://content.openalex.org/works/W4410630208.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1960881728","https://openalex.org/W1966223820","https://openalex.org/W2012994611","https://openalex.org/W2035044764","https://openalex.org/W2071841602","https://openalex.org/W2078599166","https://openalex.org/W2081653606","https://openalex.org/W2104890139","https://openalex.org/W2126218947","https://openalex.org/W2165008361","https://openalex.org/W2413154614","https://openalex.org/W2561761056","https://openalex.org/W2589887861","https://openalex.org/W2597588799","https://openalex.org/W2762019694","https://openalex.org/W2883674512","https://openalex.org/W2955206482","https://openalex.org/W3002175424","https://openalex.org/W3087179384","https://openalex.org/W3092811517","https://openalex.org/W3121268133","https://openalex.org/W3139601120","https://openalex.org/W3176019422","https://openalex.org/W3184522930","https://openalex.org/W4292508558","https://openalex.org/W4294917890","https://openalex.org/W4295660562","https://openalex.org/W4310588941","https://openalex.org/W4379508096","https://openalex.org/W4401455176"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W2093262417","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4312626803","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W2123131699","https://openalex.org/W4287027380"],"abstract_inverted_index":{"SUMMARY:":[0],"The":[1,18,252],"study":[2],"of":[3,22,38,48,55,107,117,131,162],"microbial":[4,39,49,89,108,132,140,171],"communities":[5,109],"is":[6,156,180,190,199,271],"vital":[7],"for":[8,78,87,158,258,268],"understanding":[9,116],"their":[10,118],"impact":[11],"on":[12,210],"environmental,":[13],"health,":[14],"and":[15,20,36,42,70,95,127,146,151,160,168,173,198,204,217,221,236,247],"technological":[16],"domains.":[17],"Modelling":[19],"Inference":[21],"MICrobiomes":[23],"Project":[24],"(MIMIC)":[25],"introduces":[26],"a":[27,53,84,114],"Python":[28,193,212],"package":[29],"designed":[30,157],"to":[31,82,103,138,148,165],"advance":[32,139],"the":[33,45,101,105,129,184,224,234,238],"simulation,":[34],"inference,":[35],"prediction":[37],"community":[40],"interactions":[41],"dynamics.":[43,90],"Addressing":[44],"complex":[46,119],"nature":[47],"ecosystems,":[50],"MIMIC":[51,99,155,179,208,239],"integrates":[52],"suite":[54],"mathematical":[56],"models,":[57],"including":[58,214],"previously":[59],"used":[60],"approaches":[61],"such":[62],"as":[63,230],"Generalized":[64],"Lotka-Volterra":[65],"(gLV),":[66],"Gaussian":[67],"Processes":[68],"(GP),":[69],"Vector":[71],"Autoregression":[72],"(VAR)":[73],"plus":[74],"newly":[75],"developed":[76],"models":[77],"integrating":[79],"multi-omic":[80],"data,":[81,112],"offer":[83],"versatile":[85],"framework":[86],"analyzing":[88],"By":[91],"leveraging":[92],"Bayesian":[93],"inference":[94],"machine":[96],"learning":[97],"techniques,":[98],"provides":[100],"ability":[102],"infer":[104],"dynamics":[106],"from":[110],"empirical":[111],"facilitating":[113],"deeper":[115],"biological":[120],"processes,":[121],"unveiling":[122],"possible":[123],"unknown":[124],"ecological":[125],"interactions,":[126],"enabling":[128],"design":[130],"communities.":[133],"Such":[134],"insights":[135],"could":[136],"help":[137],"ecology":[141,172],"research,":[142],"optimizing":[143],"biotechnological":[144],"applications,":[145],"contribute":[147],"environmental":[149],"sustainability":[150],"public":[152],"health":[153],"strategies.":[154],"flexibility":[159],"ease":[161],"use,":[163],"aiming":[164],"support":[166],"researchers":[167],"practitioners":[169],"in":[170,192,233],"microbiome":[174],"research.":[175],"AVAILABILITY":[176],"AND":[177],"IMPLEMENTATION:":[178],"freely":[181,256],"available":[182,257,273],"under":[183],"MIT":[185],"License":[186],"at":[187,237,259,274],"https://github.com/ucl-cssb/MIMIC.":[188],"It":[189],"implemented":[191],"(version":[194],"3.7":[195],"or":[196],"higher)":[197],"compatible":[200],"with":[201,243],"Windows,":[202],"macOS,":[203],"Linux":[205],"operating":[206],"systems.":[207],"depends":[209],"standard":[211],"libraries":[213],"NumPy,":[215],"SciPy,":[216],"PyMC.":[218],"Comprehensive":[219],"examples":[220],"tutorials":[222],"(including":[223],"main":[225],"text":[226],"demonstrations)":[227],"are":[228],"provided":[229],"Jupyter":[231],"notebooks":[232],"examples/directory":[235],"Docs":[240],"website,":[241],"along":[242],"detailed":[244],"installation":[245],"instructions":[246],"real-world":[248],"data":[249],"use":[250],"cases.":[251],"software":[253],"will":[254],"remain":[255],"least":[260],"two":[261],"years":[262],"following":[263],"publication.":[264],"A":[265],"code":[266],"snapshot":[267],"this":[269],"publication":[270],"also":[272],"Zenodo:":[275],"https://doi.org/10.5281/zenodo.15149003.":[276]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
