{"id":12104,"date":"2023-07-06T16:04:43","date_gmt":"2023-07-06T14:04:43","guid":{"rendered":"https:\/\/new.sano.science\/?post_type=people&p=12104"},"modified":"2026-01-31T20:29:51","modified_gmt":"2026-01-31T19:29:51","slug":"piotr-kica","status":"publish","type":"people","link":"https:\/\/sano.science\/people\/piotr-kica\/","title":{"rendered":"Piotr Kica"},"excerpt":{"rendered":"

PhD Student in Extreme-scale Data and Computing<\/p>\n","protected":false},"featured_media":25154,"template":"","people_teams":[19,34,37],"class_list":["post-12104","people","type-people","status-publish","has-post-thumbnail","hentry","people_teams-research","people_teams-extreme-scale-data-and-computing","people_teams-scientific-programmers"],"yoast_head":"\nPiotr Kica - Centre for Computational Personalized Medicine<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sano.science\/people\/piotr-kica\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Piotr Kica\" \/>\n<meta property=\"og:description\" content=\"PhD Student in Extreme-scale Data and Computing\" \/>\n<meta property=\"og:url\" content=\"https:\/\/sano.science\/people\/piotr-kica\/\" \/>\n<meta property=\"og:site_name\" content=\"Centre for Computational Personalized Medicine\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/sano.science\/\" \/>\n<meta property=\"article:modified_time\" content=\"2026-01-31T19:29:51+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/sano.science\/wp-content\/uploads\/2023\/07\/Piotr_Kica_Sano.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"350\" \/>\n\t<meta property=\"og:image:height\" content=\"350\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@sanoscience\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/sano.science\\\/people\\\/piotr-kica\\\/\",\"url\":\"https:\\\/\\\/sano.science\\\/people\\\/piotr-kica\\\/\",\"name\":\"Piotr Kica - 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An advocate of an active lifestyle\u2014both physical (bouldering, team sports) and mental (chess).<\/p>\n<p>In his free time, he enjoys listening to audiobooks and attending orchestral concerts.<\/p>\n","email":"","social_media":[{"icon":{"ID":11992,"id":11992,"title":"orcid","filename":"orcid.svg","filesize":15590,"url":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/orcid.svg","link":"https:\/\/sano.science\/people\/maciej-malawski\/orcid\/","alt":"","author":"5","description":"","caption":"","name":"orcid","status":"inherit","uploaded_to":531,"date":"2023-07-06 11:21:29","modified":"2023-07-06 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2025","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"accelerating-cloud-based-transcriptomics-performance-analysis-and-optimization-of-the-star-aligner-workflow","to_ping":"","pinged":"","post_modified":"2026-01-31 20:24:54","post_modified_gmt":"2026-01-31 19:24:54","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=28615","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":28622,"post_author":"8","post_date":"2026-01-31 20:27:39","post_date_gmt":"2026-01-31 19:27:39","post_content":"<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-2Pi2d5\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">J. Meizner, P. Kica, S. Licho\u0142ai, M. Malawski<br><\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"20px\",\"epAnimationGeneratedClass\":\"edplus_anim-1zPQcu\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_697e57c573194\",\"name\":\"acf\/button\",\"data\":{\"title\":\"Read\/Download\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/events.plgrid.pl\/event\/70\/attachments\/143\/364\/PROCEEDINGS%202025_na%20www%20bez%20notatek.pdf\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_self\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-kY6bTP\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><\/p>\n<!-- \/wp:paragraph -->","post_title":"Analysis of Index Access Pattern in STAR RNA-seq Aligner","post_excerpt":"Conference abstract: Seventeenth ACC Cyfronet AGH HPC Users\u2019 Conference (KUKDM 2025), 2025","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"analysis-of-index-access-pattern-in-star-rna-seq-aligner","to_ping":"","pinged":"","post_modified":"2026-02-06 11:42:54","post_modified_gmt":"2026-02-06 10:42:54","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=28622","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":14937,"post_author":"5","post_date":"2024-01-16 13:33:06","post_date_gmt":"2024-01-16 12:33:06","post_content":"<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-G1GWMI\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\">Piotr Kica, Magdalena Otta, Krzysztof Czechowicz, Karol Zaj\u0105c, Piotr Nowakowski, Andrew Narracott, Ian Halliday, Maciej Malawski<\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-vSoDxU\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-sGaBCh\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Digital twins are virtual representations of physical objects or systems used for the purpose of analysis, most often via computer simulations, in many engineering and scientific disciplines. Recently, this approach has been introduced to computational medicine, within the concept of Digital Twin in Healthcare (DTH). Such research requires verification and validation of its models, as well as the corresponding sensitivity analysis and uncertainty quantification (VVUQ). From the computing perspective, VVUQ is a computationally intensive process, as it requires numerous runs with variations of input parameters. Researchers often use high-performance computing (HPC) solutions to run VVUQ studies where the number of parameter combinations can easily reach tens of thousands. However, there is a viable alternative to HPC for a substantial subset of computational models - serverless computing. In this paper we hypothesize that using the serverless computing model can be a practical and efficient approach to selected cases of running VVUQ calculations. We show this on the example of the EasyVVUQ library, which we extend by providing support for many serverless services. The resulting library - CloudVVUQ - is evaluated using two real-world applications from the computational medicine domain adapted for serverless execution. Our experiments demonstrate the scalability of the proposed approach.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-vSoDxU\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_65a6776af10b8\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/www.computer.org\/csdl\/proceedings-article\/ccgrid\/2023\/011900a627\/1OFrjleAbTy\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_blank\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"Serverless Approach to Sensitivity Analysis of Computational Models","post_excerpt":"In: CCGrid2023, 2023.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"serverless-approach-to-sensitivity-analysis-of-computational-models","to_ping":"","pinged":"","post_modified":"2024-01-16 13:33:06","post_modified_gmt":"2024-01-16 12:33:06","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=14937","menu_order":27,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":28570,"post_author":"8","post_date":"2026-01-31 20:02:26","post_date_gmt":"2026-01-31 19:02:26","post_content":"<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-as2Mby\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Dorota Studzi\u0144ska, Sabina Licho\u0142ai, Kamil Polok, Hanna Plutecka, Piotr Kica, Piotr Grazda, Maciej Chwa\u0142a, Marek Sanak, Wojciech Szczeklik<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"20px\",\"epAnimationGeneratedClass\":\"edplus_anim-TLD5gM\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-LWwApb\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">The relationship between Th17-related immune mechanisms and miRNA regulation in the development of abdominal aortic aneurysm (AAA) is still not fully understood. This prospective study aimed to investigate the potential role of miR-21-5p in mediating Th17 pathway alterations contributing to AAA formation.<br>Samples were obtained from patients with infrarenal AAA undergoing elective open surgery and from a control group of peripheral arterial disease (PAD) patients without aneurysms, both at the time of surgical admission. Aneurysmal tissue fragments were collected intraoperatively. Total RNA was isolated, and miR-21-5p expression together with Th17-related markers were quantified using RT-qPCR and Luminex assays. Additionally, an in vitro model using human endothelial cells transfected with a synthetic miR-21-5p mimic was employed to study mechanistic effects.<br>A total of 60 participants were included\u201430 AAA cases and 30 matched controls. Circulating miR-21-5p levels were markedly elevated in AAA patients. Functional analysis revealed that miR-21-5p downregulates genes essential for endothelial development, vascular permeability regulation, and endothelial response to growth factors. Th17-associated cytokine levels were also increased in AAA patients and were particularly elevated in the midsection of the aneurysmal wall.<br><\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-LWwApb\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">These findings suggest that elevated miR-21-5p contributes to endothelial dysfunction and inflammation, key processes driving the progression of abdominal aortic aneurysm.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"20px\",\"epAnimationGeneratedClass\":\"edplus_anim-TLD5gM\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-d0Kp5N\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>Keywords<\/strong>: Abdominal aortic aneurysm, miR-21-5p, Th17 pathway, Interleukin 17A, Interleukin 21<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"20px\",\"epAnimationGeneratedClass\":\"edplus_anim-vDgWfZ\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-d0Kp5N\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Journal Issue: IJC Heart & Vasculature<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-7ZR1O2\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>Published by:<\/strong>\u00a0Elsevier<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"20px\",\"epAnimationGeneratedClass\":\"edplus_anim-vDgWfZ\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_697e520726a24\",\"name\":\"acf\/button\",\"data\":{\"title\":\"Read more\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2352906725002246?via%3Dihub\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_self\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"Role of miR-21-5p in the pathogenesis of abdominal aortic aneurysm regarding the Th17 pathway","post_excerpt":"Journal article: IJC Heart & Vasculature, Published by: Elsevier, 2025","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"role-of-mir-21-5p-in-the-pathogenesis-of-abdominal-aortic-aneurysm-regarding-the-th17-pathway","to_ping":"","pinged":"","post_modified":"2026-01-31 20:04:20","post_modified_gmt":"2026-01-31 19:04:20","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=28570","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":28581,"post_author":"8","post_date":"2026-01-31 20:09:05","post_date_gmt":"2026-01-31 19:09:05","post_content":"<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-OIukPr\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><br>Jonathan Bader, Jim Belak, Matthew Bement, Matthew Berry, Robert Carson, Daniela Cassol, Stephen Chan, John Coleman, Kastan Day, Alejandro Duque, Kjiersten Fagnan, Jeff Froula, Shantenu Jha, Daniel S. Katz, Piotr Kica, Volodymyr Kindratenko, Edward Kirton, Ramani Kothadia, Daniel Laney, Fabian Lehmann, Ulf Leser, Sabina Licho\u0142ai, Maciej Malawski, Mario Melara, Elais Player, Matt Rolchigo, Setareh Sarrafan, Seung-Jin Sul, Abdullah Syed, Lauritz Thamsen, Mikhail Titov, Matteo Turilli, Silvina Caino-Lores, and Anirban Mandal<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"20px\",\"epAnimationGeneratedClass\":\"edplus_anim-vEGtJv\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-TIIdxt\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Conference: Proceedings of the SC '23 Workshops<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"20px\",\"epAnimationGeneratedClass\":\"edplus_anim-vEGtJv\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_697e53803e5f8\",\"name\":\"acf\/button\",\"data\":{\"title\":\"Read\/Download\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/hal.science\/hal-04385285\/file\/WORKS23_Abstract_Papers.pdf\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_self\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"Novel Approaches Toward Scalable Composable Workflows in Hyper-Heterogeneous Computing Environments","post_excerpt":"Conference: Proceedings of the SC '23 Workshops, 2023","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"novel-approaches-toward-scalable-composable-workflows-in-hyper-heterogeneous-computing-environments","to_ping":"","pinged":"","post_modified":"2026-01-31 20:10:12","post_modified_gmt":"2026-01-31 19:10:12","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=28581","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":28592,"post_author":"8","post_date":"2026-01-31 20:14:34","post_date_gmt":"2026-01-31 19:14:34","post_content":"<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-0300LX\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Piotr Kica, Sabina Licho\u0142ai, Micha\u0142 Orzechowski, Maciej Malawski<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-cotKU2\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Conference:\u00a0IEEE International Conference on Cluster Computing Workshops<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"20px\",\"epAnimationGeneratedClass\":\"edplus_anim-y0RYas\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_697e545904169\",\"name\":\"acf\/button\",\"data\":{\"title\":\"Read\/Download\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/arxiv.org\/pdf\/2409.05886\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_self\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"Optimizing STAR Aligner for High Throughput Computing in the Cloud","post_excerpt":"Conference manuscript: IEEE International Conference on Cluster Computing Workshops, 2024","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"optimizing-star-aligner-for-high-throughput-computing-in-the-cloud","to_ping":"","pinged":"","post_modified":"2026-01-31 20:15:39","post_modified_gmt":"2026-01-31 19:15:39","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=28592","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":28602,"post_author":"8","post_date":"2026-01-31 20:17:46","post_date_gmt":"2026-01-31 19:17:46","post_content":"<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-msySbD\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Piotr Kica, Micha\u0142 Orzechowski, Maciej Malawski<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-5oCaBe\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Aligning RNA sequences to a reference genome is essential for analyzing gene expression, detecting genetic variations, and conducting transcriptomic research. Among the most efficient and accurate tools for this purpose is the STAR aligner , a computationally demanding yet widely adopted solution in modern transcriptomics.<br>Serverless computing models such as Function-as-a-Service (FaaS) and Container-as-a-Service (CaaS) have emerged as flexible frameworks for executing diverse workloads, including batch and event-driven tasks . These architectures offer key advantages over conventional infrastructure\u2014mainly high scalability, minimal maintenance, and cost efficiency through pay-per-use billing. Nonetheless, each service type comes with its own constraints, which may influence their suitability for running STAR-based RNA sequence processing.<br>Previous studies have demonstrated the feasibility of executing lightweight aligners, such as HiSat2, within serverless environments . By partitioning input FASTQ files into smaller chunks, researchers effectively parallelized computations, achieving notable performance improvements. Despite this progress, STAR remains superior in both alignment accuracy and potential processing speed .<br>Deploying STAR efficiently in a serverless setup poses several challenges, primarily due to its reliance on a large prebuilt genome index that must reside in memory during execution. For the human genome, this index typically occupies around 30\u202fGB of space\u2014surpassing memory limits imposed by many cloud services.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-5oCaBe\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><br><strong>The objectives of this study include<\/strong>:<br>\u2022 Identifying serverless platforms capable of supporting STAR alignment tasks,<br>\u2022 Conducting performance tests of the STAR aligner in a serverless environment,<br>\u2022 Comparing cost-efficiency between serverless and conventional computing models,<br>\u2022 Exploring optimization strategies for resource management,<br>\u2022 Proposing practical scenarios for deploying STAR in serverless settings.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"20px\",\"epAnimationGeneratedClass\":\"edplus_anim-ST7ouf\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_697e559d04556\",\"name\":\"acf\/button\",\"data\":{\"title\":\"Read\/Download\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/arxiv.org\/pdf\/2504.05078\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_self\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"Serverless Approach to Running Resource-Intensive STAR Aligner","post_excerpt":"Conference manuscript: CCGrid2025, 2025","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"serverless-approach-to-running-resource-intensive-star-aligner","to_ping":"","pinged":"","post_modified":"2026-01-31 20:21:16","post_modified_gmt":"2026-01-31 19:21:16","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=28602","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"}]},"_links":{"self":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12104","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people"}],"about":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/types\/people"}],"version-history":[{"count":14,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12104\/revisions"}],"predecessor-version":[{"id":28629,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12104\/revisions\/28629"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media\/25154"}],"wp:attachment":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media?parent=12104"}],"wp:term":[{"taxonomy":"people_teams","embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people_teams?post=12104"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}