{"id":"https://openalex.org/W7160342812","doi":"https://doi.org/10.21105/joss.07943","title":"Zarrtraj: A Python package for streaming molecular dynamics trajectories from cloud services","display_name":"Zarrtraj: A Python package for streaming molecular dynamics trajectories from cloud services","publication_year":2026,"publication_date":"2026-05-02","ids":{"openalex":"https://openalex.org/W7160342812","doi":"https://doi.org/10.21105/joss.07943"},"language":null,"primary_location":{"id":"doi:10.21105/joss.07943","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.07943","pdf_url":null,"source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"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 Open Source Software","raw_type":"journal-article"},"type":"software-paper","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://doi.org/10.21105/joss.07943","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Lawson Woods","orcid":"https://orcid.org/0009-0003-0713-4167"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lawson Woods","raw_affiliation_strings":["School of Computing and Augmented Intelligence, Arizona State University, Tempe, Arizona, United States of America","School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States of America"],"raw_orcid":"https://orcid.org/0009-0003-0713-4167","affiliations":[{"raw_affiliation_string":"School of Computing and Augmented Intelligence, Arizona State University, Tempe, Arizona, United States of America","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States of America","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hugo MacDermott-Opeskin","orcid":"https://orcid.org/0000-0002-7393-7457"},"institutions":[{"id":"https://openalex.org/I40695006","display_name":"Open Geospatial Consortium","ror":"https://ror.org/00fsdxs93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40695006"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hugo MacDermott-Opeskin","raw_affiliation_strings":["Open Molecular Software Foundation, Davis, CA, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-7393-7457","affiliations":[{"raw_affiliation_string":"Open Molecular Software Foundation, Davis, CA, United States of America","institution_ids":["https://openalex.org/I40695006"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Edis Jakupovic","orcid":"https://orcid.org/0000-0001-8813-6356"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edis Jakupovic","raw_affiliation_strings":["Center for Biological Physics, Arizona State University, Tempe, AZ, United States of America","Department of Physics, Arizona State University, Tempe, Arizona, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-8813-6356","affiliations":[{"raw_affiliation_string":"Center for Biological Physics, Arizona State University, Tempe, AZ, United States of America","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"Department of Physics, Arizona State University, Tempe, Arizona, United States of America","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yuxuan Zhuang","orcid":"https://orcid.org/0000-0003-4390-8556"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuxuan Zhuang","raw_affiliation_strings":["Department of Computer Science, Stanford University, Stanford, CA 94305, USA","Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA"],"raw_orcid":"https://orcid.org/0000-0003-4390-8556","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Richard J Gowers","orcid":"https://orcid.org/0000-0002-3241-1846"},"institutions":[{"id":"https://openalex.org/I4210113093","display_name":"CTI BioPharma (United Kingdom)","ror":"https://ror.org/01cyatv27","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210101701","https://openalex.org/I4210113093"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard J Gowers","raw_affiliation_strings":["Charm Therapeutics, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-3241-1846","affiliations":[{"raw_affiliation_string":"Charm Therapeutics, London, United Kingdom","institution_ids":["https://openalex.org/I4210113093"]}]},{"author_position":"last","author":{"id":null,"display_name":"Oliver Beckstein","orcid":"https://orcid.org/0000-0003-1340-0831"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Oliver Beckstein","raw_affiliation_strings":["Center for Biological Physics, Arizona State University, Tempe, AZ, United States of America","Department of Physics, Arizona State University, Tempe, Arizona, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-1340-0831","affiliations":[{"raw_affiliation_string":"Center for Biological Physics, Arizona State University, Tempe, AZ, United States of America","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"Department of Physics, Arizona State University, Tempe, Arizona, United States of America","institution_ids":["https://openalex.org/I55732556"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"11","issue":"121","first_page":"7943","last_page":"7943"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.3677999973297119,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.3677999973297119,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.0544000007212162,"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/T10101","display_name":"Cloud Computing and Resource Management","score":0.04780000075697899,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8978000283241272},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.7214000225067139},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5863999724388123},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.33000001311302185}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8978000283241272},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7760000228881836},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.7214000225067139},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5863999724388123},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.49459999799728394},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.4099000096321106},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3707999885082245},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.33000001311302185},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.31790000200271606},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.3176000118255615},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.30489999055862427},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.27639999985694885}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.21105/joss.07943","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.07943","pdf_url":null,"source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"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 Open Source Software","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.21105/joss.07943","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.07943","pdf_url":null,"source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"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 Open Source Software","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1966326070","https://openalex.org/W2081287834","https://openalex.org/W2140628770","https://openalex.org/W2510475640","https://openalex.org/W2949033096","https://openalex.org/W2957177175","https://openalex.org/W2974666250","https://openalex.org/W3035965352","https://openalex.org/W3042198040","https://openalex.org/W3179717569","https://openalex.org/W3202105317","https://openalex.org/W4224910107","https://openalex.org/W4230804723","https://openalex.org/W4385230480","https://openalex.org/W4385627674","https://openalex.org/W4386897003","https://openalex.org/W4401102549","https://openalex.org/W6949974677","https://openalex.org/W6958302479"],"related_works":[],"abstract_inverted_index":null,"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2026-03-02T00:00:00"}
