{"id":"https://openalex.org/W4411490480","doi":"https://doi.org/10.1145/3732775.3733579","title":"Scalable Genomic Context Analysis with GCsnap2 on HPC Clusters","display_name":"Scalable Genomic Context Analysis with GCsnap2 on HPC Clusters","publication_year":2025,"publication_date":"2025-06-16","ids":{"openalex":"https://openalex.org/W4411490480","doi":"https://doi.org/10.1145/3732775.3733579"},"language":"en","primary_location":{"id":"doi:10.1145/3732775.3733579","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3732775.3733579","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3732775.3733579","source":null,"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Platform for Advanced Scientific Computing Conference","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3732775.3733579","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030468603","display_name":"Reto Krummenacher","orcid":null},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Reto Krummenacher","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0009-0005-6854-6004","affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074148783","display_name":"Osman Seckin Simsek","orcid":"https://orcid.org/0000-0002-2719-9174"},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Osman Seckin Simsek","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-2719-9174","affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002438847","display_name":"Mich\u00e8le Leemann","orcid":null},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Mich\u00e8le Leemann","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0009-0008-9641-8837","affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002042314","display_name":"Leila T. Alexander","orcid":"https://orcid.org/0000-0002-7594-2110"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Leila T. Alexander","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-7594-2110","affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049569891","display_name":"Torsten Schwede","orcid":"https://orcid.org/0000-0003-2715-335X"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Torsten Schwede","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-2715-335X","affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055373392","display_name":"Florina M. Ciorba","orcid":"https://orcid.org/0000-0002-2773-4499"},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Florina M. Ciorba","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-2773-4499","affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041584450","display_name":"Joana Pereira","orcid":"https://orcid.org/0000-0002-5588-6588"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Joana Pereira","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-5588-6588","affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5030468603"],"corresponding_institution_ids":["https://openalex.org/I1850255"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12466104,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9955000281333923,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9955000281333923,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.994700014591217,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9799000024795532,"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":0.7324602603912354},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6969633102416992},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6050117015838623},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.40741121768951416},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3981333374977112},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3953090310096741},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.16114071011543274},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13169819116592407}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7324602603912354},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6969633102416992},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6050117015838623},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.40741121768951416},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3981333374977112},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3953090310096741},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.16114071011543274},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13169819116592407},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3732775.3733579","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3732775.3733579","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3732775.3733579","source":null,"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Platform for Advanced Scientific Computing Conference","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:2505.02195","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2505.02195","pdf_url":"https://arxiv.org/pdf/2505.02195","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"}],"best_oa_location":{"id":"doi:10.1145/3732775.3733579","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3732775.3733579","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3732775.3733579","source":null,"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Platform for Advanced Scientific Computing Conference","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310466","display_name":"Universit\u00e4t Basel","ror":"https://ror.org/02s6k3f65"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320331322","display_name":"Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411490480.pdf","grobid_xml":"https://content.openalex.org/works/W4411490480.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1519646691","https://openalex.org/W1986555327","https://openalex.org/W2160763289","https://openalex.org/W2527672088","https://openalex.org/W2953008890","https://openalex.org/W3087148269","https://openalex.org/W3138507280","https://openalex.org/W3164436820","https://openalex.org/W4237139895","https://openalex.org/W4282934256","https://openalex.org/W4312247616","https://openalex.org/W4366768926","https://openalex.org/W4377087476","https://openalex.org/W4377968771","https://openalex.org/W4383198216","https://openalex.org/W4385693523","https://openalex.org/W4389665156","https://openalex.org/W4391281511","https://openalex.org/W4402703459","https://openalex.org/W6912177926"],"related_works":["https://openalex.org/W2389214306","https://openalex.org/W2965083567","https://openalex.org/W4235240664","https://openalex.org/W1838576100","https://openalex.org/W2095886385","https://openalex.org/W2889616422","https://openalex.org/W2089704382","https://openalex.org/W1983399550","https://openalex.org/W97075385","https://openalex.org/W4401278057"],"abstract_inverted_index":{"GCsnap2":[0,27],"Cluster":[1,28],"is":[2],"a":[3,30],"scalable,":[4],"high":[5],"performance":[6],"tool":[7],"for":[8,43,73,84],"genomic":[9,40],"context":[10,41],"analysis,":[11],"developed":[12],"to":[13,88],"overcome":[14],"the":[15,57,82],"limitations":[16],"of":[17,45,47,59,76],"its":[18],"predecessor,":[19],"GCsnap1":[20],"Desktop.":[21],"Leveraging":[22],"distributed":[23],"computing":[24],"with":[25],"mpi4py.futures,":[26],"achieved":[29],"22\u00d7":[31],"improvement":[32],"in":[33,50,65,92],"execution":[34],"time":[35],"and":[36,62],"can":[37],"now":[38],"perform":[39],"analysis":[42,101],"hundreds":[44],"thousands":[46],"input":[48],"sequences":[49],"HPC":[51],"clusters.":[52],"Its":[53],"modular":[54],"architecture":[55],"enables":[56],"creation":[58],"task-specific":[60],"workflows":[61],"flexible":[63],"deployment":[64],"various":[66],"computational":[67],"environments,":[68],"making":[69],"it":[70],"well":[71],"suited":[72],"bioinformatics":[74],"studies":[75],"large-scale":[77,99],"datasets.":[78],"This":[79],"work":[80],"highlights":[81],"potential":[83],"applying":[85],"similar":[86],"approaches":[87],"solve":[89],"scalability":[90],"challenges":[91],"other":[93],"scientific":[94],"domains":[95],"that":[96],"rely":[97],"on":[98],"data":[100],"pipelines.":[102]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
