{"id":"https://openalex.org/W2976770895","doi":"https://doi.org/10.1515/jib-2019-0057","title":"The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development","display_name":"The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development","publication_year":2019,"publication_date":"2019-09-01","ids":{"openalex":"https://openalex.org/W2976770895","doi":"https://doi.org/10.1515/jib-2019-0057","mag":"2976770895","pmid":"https://pubmed.ncbi.nlm.nih.gov/31560649"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2019-0057","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2019-0057","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2019-0057/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.degruyter.com/document/doi/10.1515/jib-2019-0057/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059487495","display_name":"Bj\u00f6rn Sommer","orcid":"https://orcid.org/0000-0003-1514-9898"},"institutions":[{"id":"https://openalex.org/I165526535","display_name":"Royal College of Art","ror":"https://ror.org/01egahc47","country_code":"GB","type":"education","lineage":["https://openalex.org/I165526535"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Bjorn Sommer","raw_affiliation_strings":["Royal College of Art, School of Design, Innovation Design Engineering , London SW7 2EU , UK"],"affiliations":[{"raw_affiliation_string":"Royal College of Art, School of Design, Innovation Design Engineering , London SW7 2EU , UK","institution_ids":["https://openalex.org/I165526535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5059487495"],"corresponding_institution_ids":["https://openalex.org/I165526535"],"apc_list":null,"apc_paid":null,"fwci":0.0852,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.47313094,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"16","issue":"3","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":0.9836999773979187,"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":0.9836999773979187,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9735000133514404,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9496999979019165,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/java","display_name":"Java","score":0.8095821142196655},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7146612405776978},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5785107016563416},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.5575096011161804},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.541935384273529},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5151799917221069},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5031852126121521},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.4787099361419678},{"id":"https://openalex.org/keywords/software-development","display_name":"Software development","score":0.43358325958251953},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4080408811569214},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2923247814178467}],"concepts":[{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.8095821142196655},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7146612405776978},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5785107016563416},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.5575096011161804},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.541935384273529},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5151799917221069},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5031852126121521},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.4787099361419678},{"id":"https://openalex.org/C529173508","wikidata":"https://www.wikidata.org/wiki/Q638608","display_name":"Software development","level":3,"score":0.43358325958251953},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4080408811569214},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2923247814178467},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000266","qualifier_name":"history","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000266","qualifier_name":"history","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000266","qualifier_name":"history","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000266","qualifier_name":"history","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000266","qualifier_name":"history","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000266","qualifier_name":"history","is_major_topic":false},{"descriptor_ui":"D049673","descriptor_name":"History, 20th Century","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049673","descriptor_name":"History, 20th Century","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049673","descriptor_name":"History, 20th Century","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049674","descriptor_name":"History, 21st Century","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049674","descriptor_name":"History, 21st Century","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049674","descriptor_name":"History, 21st Century","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1515/jib-2019-0057","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2019-0057","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2019-0057/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31560649","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31560649","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:researchonline.rca.ac.uk:4193","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402545","display_name":"Royal College of Art Research Repository (Royal College of Art)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165526535","host_organization_name":"Royal College of Art","host_organization_lineage":["https://openalex.org/I165526535"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:doaj.org/article:c137398c0df34b9b8153598c78c39a64","is_oa":true,"landing_page_url":"https://doaj.org/article/c137398c0df34b9b8153598c78c39a64","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 16, Iss 3, Pp e201302014-64 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6798854","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6798854","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Integr Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1515/jib-2019-0057","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2019-0057","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2019-0057/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.47999998927116394,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320971","display_name":"Monash University","ror":"https://ror.org/02bfwt286"},{"id":"https://openalex.org/F4320323389","display_name":"Universit\u00e4t Bielefeld","ror":"https://ror.org/02hpadn98"},{"id":"https://openalex.org/F4320326505","display_name":"Universit\u00e4t Konstanz","ror":"https://ror.org/0546hnb39"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2976770895.pdf","grobid_xml":"https://content.openalex.org/works/W2976770895.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1552632109","https://openalex.org/W1908357622","https://openalex.org/W1974035453","https://openalex.org/W1992928135","https://openalex.org/W2003949305","https://openalex.org/W2020227650","https://openalex.org/W2021520922","https://openalex.org/W2024038403","https://openalex.org/W2029088347","https://openalex.org/W2034346243","https://openalex.org/W2037947871","https://openalex.org/W2042382087","https://openalex.org/W2056402029","https://openalex.org/W2062476751","https://openalex.org/W2064697628","https://openalex.org/W2068146784","https://openalex.org/W2093775834","https://openalex.org/W2095716650","https://openalex.org/W2101791557","https://openalex.org/W2108227345","https://openalex.org/W2130479394","https://openalex.org/W2140498353","https://openalex.org/W2140831051","https://openalex.org/W2147470832","https://openalex.org/W2162144833","https://openalex.org/W2167279371","https://openalex.org/W2291468715","https://openalex.org/W2556901799","https://openalex.org/W2571805434","https://openalex.org/W2588096604","https://openalex.org/W2618506555","https://openalex.org/W2746496230","https://openalex.org/W2792585663","https://openalex.org/W2831736488","https://openalex.org/W2842599072","https://openalex.org/W2915257269","https://openalex.org/W4212920271","https://openalex.org/W4254025072","https://openalex.org/W4254867703"],"related_works":["https://openalex.org/W2121696621","https://openalex.org/W2109693630","https://openalex.org/W3005935371","https://openalex.org/W1964405022","https://openalex.org/W2113128227","https://openalex.org/W632256878","https://openalex.org/W4211197663","https://openalex.org/W2491403535","https://openalex.org/W3123068371","https://openalex.org/W2479811461"],"abstract_inverted_index":{"For":[0],"more":[1],"than":[2],"one":[3],"decade,":[4],"CELLmicrocosmos":[5],"tools":[6,30,120,145],"are":[7],"being":[8,32],"developed.":[9],"Here,":[10],"we":[11],"discus":[12],"some":[13],"of":[14,37,55,98,118,133],"the":[15,48,51,68,71,74,77,91,105,115],"technical":[16],"and":[17,40,46,76,101,153],"administrative":[18],"hurdles":[19],"to":[20,95,140],"keep":[21],"a":[22,35,122],"software":[23],"suite":[24],"running":[25],"so":[26],"many":[27],"years.":[28,52],"The":[29,53],"were":[31],"developed":[33],"during":[34],"number":[36],"student":[38],"projects":[39],"theses,":[41],"whereas":[42],"main":[43],"developers":[44,132],"refactored":[45],"maintained":[47],"code":[49],"over":[50],"focus":[54,124],"this":[56,129,148],"publication":[57,149],"is":[58],"laid":[59],"on":[60,125],"two":[61],"Java-based":[62],"Open":[63],"Source":[64],"Software":[65],"frameworks.":[66],"Firstly,":[67],"CellExplorer":[69],"with":[70,121],"PathwayIntegration":[72],"combines":[73],"mesoscopic":[75],"functional":[78],"level":[79],"by":[80],"mapping":[81],"biological":[82],"networks":[83],"onto":[84],"cell":[85],"components":[86],"using":[87,104],"database":[88],"integration.":[89],"Secondly,":[90],"MembraneEditor":[92],"enables":[93],"users":[94],"generate":[96],"membranes":[97],"different":[99],"lipid":[100],"protein":[102],"compositions":[103],"PDB":[106],"format.":[107],"Technicalities":[108],"will":[109],"be":[110,138,151],"discussed":[111,146],"as":[112,114],"well":[113],"historical":[116],"development":[117],"these":[119],"special":[123],"group-based":[126],"development.":[127],"In":[128],"way,":[130],"university-associated":[131],"Integrative":[134],"Bioinformatics":[135],"applications":[136],"should":[137],"inspired":[139],"go":[141],"similar":[142],"ways.":[143],"All":[144],"in":[147],"can":[150],"downloaded":[152],"installed":[154],"from":[155],"https://www.CELLmicrocosmos.org.":[156]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
