{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T09:07:26Z","timestamp":1791018446338,"version":"4.1.0"},"posted":{"date-parts":[[2026,7,15]]},"group-title":"Bioinformatics","reference-count":43,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T00:00:00Z","timestamp":1784073600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"award":["U01HL122700"],"award-info":[{"award-number":["U01HL122700"]}],"id":[{"id":"https:\/\/ror.org\/012pb6c26","id-type":"ROR","asserted-by":"publisher"}]},{"award":["U01HL148861"],"award-info":[{"award-number":["U01HL148861"]}],"id":[{"id":"https:\/\/ror.org\/012pb6c26","id-type":"ROR","asserted-by":"publisher"}]},{"award":["U01HL122703"],"award-info":[{"award-number":["U01HL122703"]}],"id":[{"id":"https:\/\/ror.org\/012pb6c26","id-type":"ROR","asserted-by":"publisher"}]},{"award":["U01HL148860"],"award-info":[{"award-number":["U01HL148860"]}],"id":[{"id":"https:\/\/ror.org\/012pb6c26","id-type":"ROR","asserted-by":"publisher"}]},{"award":["U01HL175451"],"award-info":[{"award-number":["U01HL175451"]}],"id":[{"id":"https:\/\/ror.org\/012pb6c26","id-type":"ROR","asserted-by":"publisher"}]},{"award":["U54HL165443"],"award-info":[{"award-number":["U54HL165443"]}],"id":[{"id":"https:\/\/ror.org\/001d55x84","id-type":"ROR","asserted-by":"publisher"}]},{"award":["U01DK114920"],"award-info":[{"award-number":["U01DK114920"]}],"id":[{"id":"https:\/\/ror.org\/00adh9b73","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"United States Department of Energy","doi-asserted-by":"crossref","award":["DE-AC05\u201376RLO01830"],"award-info":[{"award-number":["DE-AC05\u201376RLO01830"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Multi-omics and spatial-omics technologies are exploding in use, producing increasingly complex datasets. Existing bioinformatics tools are developing rapidly but fail to fully enforce the FAIR principles, leaving the field vulnerable to escalating issues in computational reproducibility. Here, we introduce a reproducible-by-design paradigm represented in an omics data processing package, RomicsProcessor. At its core, the \u201cRomics_object\u201d, which is a self-contained digital artifact that encapsulates the full history of the data from the original data to the fully processed state, capturing the details of the transformative steps and the required dependencies. This architecture ensures that computational workflows are fully portable and reproducible. In this manuscript, we demonstrate RomicProcessor\u2019s computational capabilities and scalability on diverse datasets, including bulk proteomics, large-scale multiplexed immunofluorescence, and multi-batch mass spectrometry imaging. Providing a robust framework for truly FAIR Data Principles-based analysis, RomicsProcessor is a blueprint for the next generation of reproducible bioinformatics tools that can dramatically accelerate discovery in multi-omics biology in the era of artificial intelligence.<\/jats:p>","DOI":"10.64898\/2026.07.09.737600","type":"posted-content","created":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T09:45:12Z","timestamp":1784108712000},"source":"Crossref","is-referenced-by-count":1,"title":["Reproducible-by-design: Romics Processor, a FAIR ecosystem for multi-omics and spatial-omics analysis"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5087-3606","authenticated-orcid":false,"given":"Brittney L.","family":"Gorman","sequence":"first","affiliation":[{"name":"Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, WA 99352, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4291-9870","authenticated-orcid":false,"given":"Harsh","family":"Bhotika","sequence":"additional","affiliation":[{"name":"Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, WA 99352, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-7735-4024","authenticated-orcid":false,"given":"Matthew","family":"Jehrio","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7636-4992","authenticated-orcid":false,"given":"Jeffrey M.","family":"Purkerson","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frederic","family":"Carlin","sequence":"additional","affiliation":[{"name":"UMR408 SQPOV, INRAE, Avignon, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4056-2695","authenticated-orcid":false,"given":"Ernesto","family":"Nakayasu","sequence":"additional","affiliation":[{"name":"Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, WA 99352, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew M.","family":"Dylag","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1352-4378","authenticated-orcid":false,"given":"Ravi S.","family":"Misra","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0399-0700","authenticated-orcid":false,"given":"Joshua","family":"Adkins","sequence":"additional","affiliation":[{"name":"Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, WA 99352, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6170-1033","authenticated-orcid":false,"given":"Christopher R.","family":"Anderton","sequence":"additional","affiliation":[{"name":"Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, WA 99352, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9185-3994","authenticated-orcid":false,"given":"Gloria","family":"Pryhuber","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0478-8520","authenticated-orcid":false,"given":"Geremy","family":"Clair","sequence":"additional","affiliation":[{"name":"Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, WA 99352, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026071805500419000_2026.07.09.737600v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-023-00580-2"},{"key":"2026071805500419000_2026.07.09.737600v1.2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biodatasci-102523-103640"},{"key":"2026071805500419000_2026.07.09.737600v1.3","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002870"},{"key":"2026071805500419000_2026.07.09.737600v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-025-06142-x"},{"key":"2026071805500419000_2026.07.09.737600v1.5","doi-asserted-by":"publisher","DOI":"10.1126\/science.abq4964"},{"key":"2026071805500419000_2026.07.09.737600v1.6","doi-asserted-by":"publisher","DOI":"10.3390\/metabo10070286"},{"key":"2026071805500419000_2026.07.09.737600v1.7","doi-asserted-by":"publisher","DOI":"10.1007\/s10827-018-0702-z"},{"key":"2026071805500419000_2026.07.09.737600v1.8","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2296-x"},{"key":"2026071805500419000_2026.07.09.737600v1.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgg.2025.09.003"},{"key":"2026071805500419000_2026.07.09.737600v1.10","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-01033-y"},{"key":"2026071805500419000_2026.07.09.737600v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02565-3"},{"key":"2026071805500419000_2026.07.09.737600v1.12","doi-asserted-by":"publisher","DOI":"10.1038\/sdata.2016.18"},{"key":"2026071805500419000_2026.07.09.737600v1.13","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2025.100845"},{"key":"2026071805500419000_2026.07.09.737600v1.14","doi-asserted-by":"publisher","DOI":"10.1016\/j.yrtph.2021.105020"},{"key":"2026071805500419000_2026.07.09.737600v1.15","first-page":"255","article-title":"Advancing reproducible research by publishing R markdown notebooks as interactive sandboxes using the learnr package","volume":"14","year":"2022","journal-title":"The R Journal"},{"key":"2026071805500419000_2026.07.09.737600v1.16","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giad113"},{"key":"2026071805500419000_2026.07.09.737600v1.17","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1008316"},{"key":"2026071805500419000_2026.07.09.737600v1.18","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz278"},{"key":"2026071805500419000_2026.07.09.737600v1.19","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01767-y"},{"key":"2026071805500419000_2026.07.09.737600v1.20","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac299"},{"key":"2026071805500419000_2026.07.09.737600v1.21","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4256"},{"key":"2026071805500419000_2026.07.09.737600v1.22","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1511"},{"key":"2026071805500419000_2026.07.09.737600v1.23","doi-asserted-by":"publisher","DOI":"10.1021\/jasms.0c00039"},{"key":"2026071805500419000_2026.07.09.737600v1.24","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.202008-3303OC"},{"key":"2026071805500419000_2026.07.09.737600v1.25","doi-asserted-by":"publisher","DOI":"10.1016\/j.kint.2021.08.026"},{"key":"2026071805500419000_2026.07.09.737600v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/s41551-025-01423-7"},{"key":"2026071805500419000_2026.07.09.737600v1.27","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-31640-x"},{"key":"2026071805500419000_2026.07.09.737600v1.28","doi-asserted-by":"publisher","DOI":"10.1101\/2024.06.17.599411"},{"key":"2026071805500419000_2026.07.09.737600v1.29","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.165515"},{"key":"2026071805500419000_2026.07.09.737600v1.30","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2022.02.003"},{"key":"2026071805500419000_2026.07.09.737600v1.31","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.9b03349"},{"key":"2026071805500419000_2026.07.09.737600v1.32","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giad115"},{"key":"2026071805500419000_2026.07.09.737600v1.33","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giaa144"},{"key":"2026071805500419000_2026.07.09.737600v1.34","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6976.2008.00112.x"},{"key":"2026071805500419000_2026.07.09.737600v1.35","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M000027-MCP201"},{"key":"2026071805500419000_2026.07.09.737600v1.36","doi-asserted-by":"publisher","DOI":"10.3390\/toxins12110701"},{"key":"2026071805500419000_2026.07.09.737600v1.37","doi-asserted-by":"publisher","DOI":"10.1016\/j.kint.2024.11.008"},{"key":"2026071805500419000_2026.07.09.737600v1.38","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adu3730"},{"key":"2026071805500419000_2026.07.09.737600v1.39","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01094-0"},{"key":"2026071805500419000_2026.07.09.737600v1.40","doi-asserted-by":"crossref","unstructured":"Lovric, M. in International Encyclopedia of Statistical Science (ed Miodrag Lovric ) 1356-1374 (Springer Berlin Heidelberg, 2025).","DOI":"10.1007\/978-3-662-69359-9_328"},{"key":"2026071805500419000_2026.07.09.737600v1.41","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1382-0"},{"key":"2026071805500419000_2026.07.09.737600v1.42","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01358-2"},{"key":"2026071805500419000_2026.07.09.737600v1.43","doi-asserted-by":"publisher","DOI":"10.1101\/2021.12.16.473007"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.07.09.737600","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T12:50:16Z","timestamp":1784379016000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.07.09.737600"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,15]]},"references-count":43,"URL":"https:\/\/doi.org\/10.64898\/2026.07.09.737600","relation":{},"subject":[],"published":{"date-parts":[[2026,7,15]]},"subtype":"preprint"}}