{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T07:52:58Z","timestamp":1768031578381,"version":"3.49.0"},"publisher-location":"Cham","reference-count":20,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783031078019","type":"print"},{"value":"9783031078026","type":"electronic"}],"license":[{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022]]},"DOI":"10.1007\/978-3-031-07802-6_9","type":"book-chapter","created":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T11:04:18Z","timestamp":1654599858000},"page":"103-116","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Migrating CUDA to\u00a0oneAPI: A Smith-Waterman Case Study"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6937-3943","authenticated-orcid":false,"given":"Manuel","family":"Costanzo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6736-7358","authenticated-orcid":false,"given":"Enzo","family":"Rucci","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3470-1097","authenticated-orcid":false,"given":"Carlos","family":"Garc\u00eda-S\u00e1nchez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9127-3212","authenticated-orcid":false,"given":"Marcelo","family":"Naiouf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0687-3737","authenticated-orcid":false,"given":"Manuel","family":"Prieto-Mat\u00edas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,6,8]]},"reference":[{"key":"9_CR1","doi-asserted-by":"publisher","unstructured":"Christgau, S., Steinke, T.: Porting a legacy CUDA stencil code to oneAPI. In: 2020 IEEE IPDPSW, pp. 359\u2013367 (2020). https:\/\/doi.org\/10.1109\/IPDPSW50202.2020.00070","DOI":"10.1109\/IPDPSW50202.2020.00070"},{"key":"9_CR2","unstructured":"Costanzo, M., Rucci, E., Sanchez, C.G., Naiouf, M.: Early experiences migrating cuda codes to oneapi. In: Short papers of the 9th Conference on Cloud Computing Conference, Big Data & Emerging Topics. pp. 14\u201318 (2021). http:\/\/sedici.unlp.edu.ar\/handle\/10915\/125138"},{"key":"9_CR3","doi-asserted-by":"publisher","unstructured":"De Oilveira Sandes, E.F., Boukerche, A., De Melo, A.C.M.A.: Parallel optimal pairwise biological sequence comparison: algorithms, platforms, and classification. ACM Comput. Surv. 48(4) (2016). https:\/\/doi.org\/10.1145\/2893488","DOI":"10.1145\/2893488"},{"key":"9_CR4","first-page":"5","volume":"39","author":"N Hariharan","year":"2020","unstructured":"Hariharan, N., Mallady, R.K., Kapoor, A., O\u2019Leary, K.: Heterogeneous programming using oneapi. Parallel Universe 39, 5\u201318 (2020)","journal-title":"Heterogeneous programming using oneapi. Parallel Universe"},{"key":"9_CR5","unstructured":"Hasan, L., Al-Ars, Z.: Computational Biology and Applied Bioinformatics, chap. 9, pp. 187\u2013202. InTech, September 2011"},{"key":"9_CR6","doi-asserted-by":"publisher","unstructured":"Keryell, R., Yu, L.Y.: Early experiments using SYCL single-source modern C++ on Xilinx FPGA. In: Proceedings of the IWOCL 2018. ACM, New York (2018). https:\/\/doi.org\/10.1145\/3204919.3204937","DOI":"10.1145\/3204919.3204937"},{"issue":"19","key":"9_CR7","doi-asserted-by":"publisher","first-page":"2494","DOI":"10.1093\/bioinformatics\/btt410","volume":"29","author":"M Korpar","year":"2013","unstructured":"Korpar, M., Sikic, M.: SW# - GPU-enabled exact alignments on genome scale. Bioinformatics 29(19), 2494\u20132495 (2013). https:\/\/doi.org\/10.1093\/bioinformatics\/btt410","journal-title":"Bioinformatics"},{"key":"9_CR8","doi-asserted-by":"publisher","unstructured":"Korpar, M., Sosic, M., Blazeka, D., Sikic, M.: SWdb: GPU-accelerated exact sequence similarity database search. PLOS ONE 10(12), 1\u201311 (2016). https:\/\/doi.org\/10.1371\/journal.pone.0145857","DOI":"10.1371\/journal.pone.0145857"},{"issue":"2","key":"9_CR9","first-page":"64","volume":"3","author":"S Loukatou","year":"2014","unstructured":"Loukatou, S., et al.: Molecular dynamics simulations through GPU video games technologies. J. Mol. Biochem. 3(2), 64 (2014)","journal-title":"J. Mol. Biochem."},{"key":"9_CR10","doi-asserted-by":"publisher","DOI":"10.1145\/3465998.3466012","author":"E Marinelli","year":"2021","unstructured":"Marinelli, E., Appuswamy, R.: XJoin: portable, parallel hash join across diverse XPU architectures with OneAPI. ACM (2021). https:\/\/doi.org\/10.1145\/3465998.3466012","journal-title":"ACM"},{"issue":"2","key":"9_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00894-014-2067-1","volume":"20","author":"D Mrozek","year":"2014","unstructured":"Mrozek, D., Bro\u017cek, M., Ma\u0142ysiak-Mrozek, B.: Parallel implementation of 3d protein structure similarity searches using a GPU and the CUDA. J. Mol. Model. 20(2), 1\u201317 (2014)","journal-title":"J. Mol. Model."},{"key":"9_CR12","doi-asserted-by":"publisher","unstructured":"Nobile, M.S., Cazzaniga, P., Tangherloni, A., Besozzi, D.: Graphics processing units in bioinformatics, computational biology and systems biology. Briefings Bioinform. 18(5), 870\u2013885 (2016). https:\/\/doi.org\/10.1093\/bib\/bbw058","DOI":"10.1093\/bib\/bbw058"},{"key":"9_CR13","doi-asserted-by":"crossref","unstructured":"Ohue, M., Shimoda, T., Suzuki, S., Matsuzaki, Y., Ishida, T., Akiyama, Y.: Megadock 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers. Bioinformatics 30(22), 3281\u20133283 (2014)","DOI":"10.1093\/bioinformatics\/btu532"},{"key":"9_CR14","unstructured":"Robert Dow: GPU shipments increase year-over-year in Q3 (2021). https:\/\/www.jonpeddie.com\/press-releases\/gpu-shipments-increase-year-over-year-in-q3"},{"issue":"3","key":"9_CR15","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1177\/1094342016654215","volume":"32","author":"E Rucci","year":"2018","unstructured":"Rucci, E., Garcia, C., Botella, G., Giusti, A.E.D., Naiouf, M., Prieto-Matias, M.: Oswald: Opencl smith-waterman on altera\u2019s fpga for large protein databases. Int. J. High Perform. Comput. Appl. 32(3), 337\u2013350 (2018). https:\/\/doi.org\/10.1177\/1094342016654215","journal-title":"Int. J. High Perform. Comput. Appl."},{"key":"9_CR16","doi-asserted-by":"crossref","unstructured":"Rucci, E., Sanchez, C.G., Juan, G.B., De Giusti, A., Naiouf, M., Prieto-Matias, M.: Swimm 2.0: enhanced smith-waterman on intel\u2019s multicore and manycore architectures based on avx-512 vector extensions. Int. J. Parallel Programm. 47(2), 296\u2013316 (2019)","DOI":"10.1007\/s10766-018-0585-7"},{"issue":"1","key":"9_CR17","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"TF Smith","year":"1981","unstructured":"Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. J. Mol. Biol. 147(1), 195\u2013197 (1981)","journal-title":"J. Mol. Biol."},{"key":"9_CR18","unstructured":"The Khronos SYCL Working Group: SYCL Specification (2020). https:\/\/www.khronos.org\/registry\/SYCL\/specs\/sycl-2020\/pdf\/sycl-2020.pdf"},{"key":"9_CR19","doi-asserted-by":"crossref","unstructured":"Tsai, Y.M., Cojean, T., Anzt, H.: Porting a sparse linear algebra math library to intel gpus (2021)","DOI":"10.1007\/978-3-031-06156-1_5"},{"issue":"3","key":"9_CR20","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1145\/3024918","volume":"60","author":"M Zahran","year":"2017","unstructured":"Zahran, M.: Heterogeneous computing: here to stay. Commun. ACM 60(3), 42\u201345 (2017)","journal-title":"Commun. ACM"}],"container-title":["Lecture Notes in Computer Science","Bioinformatics and Biomedical Engineering"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-031-07802-6_9","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,26]],"date-time":"2024-09-26T15:30:32Z","timestamp":1727364632000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-031-07802-6_9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022]]},"ISBN":["9783031078019","9783031078026"],"references-count":20,"URL":"https:\/\/doi.org\/10.1007\/978-3-031-07802-6_9","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022]]},"assertion":[{"value":"8 June 2022","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"IWBBIO","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Work-Conference on Bioinformatics and Biomedical Engineering","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Gran Canaria","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Spain","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2022","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"27 June 2022","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"30 June 2022","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"9","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"iwbbio2022","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/iwbbio.ugr.es\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Single-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"212","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"75","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"0","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"35% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3,1","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"No","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}