{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T09:44:08Z","timestamp":1785404648983,"version":"3.56.0"},"posted":{"date-parts":[[2026,2,9]]},"group-title":"Biophysics","reference-count":42,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,2,9]],"date-time":"2026-02-09T00:00:00Z","timestamp":1770595200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["R35 GM153458"],"award-info":[{"award-number":["R35 GM153458"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,2,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  As high-performance computing provides the ability to generate and analyze ever larger simulation trajectories, the challenges in learning, applying, and sharing the best analytical practices become more salient. Extracting reproducible scientific insights from simulation requires a thorough understanding of many computing topics unrelated to the molecular systems being modeled and simulated. While the rapid development of the technologies used for analysis makes previously impossible studies into routine work, the growing repertoire of software combined with the specificity of the ecosystems that they rely on can easily break the programs used in older studies. In this work, we present ST-Analyzer, a simulation trajectory analysis suite with command-line (CLI) and graphical (GUI) user interfaces. ST-Analyzer is distributed freely as an open-source conda-forge package with support for macOS, Linux, and Windows (via WSL2). Besides facilitating several common analysis tasks, the GUI shows users the exact commands necessary to repeat the same tasks on the command-line. We demonstrate ST-Analyzer\u2019s capabilities by reproducing several results from previously published simulation studies on the lipid parameters of heterogeneous biomembranes and the behavior of a SARS-CoV-2 spike protein-antibody complex. We expect ST-Analyzer to be useful to experts for quickly setting up common analysis tasks and to nonexperts as a guided introduction to simulation analysis using both GUI and CLI. ST-Analyzer is freely available at\n                  <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/nk53\/stanalyzer\">https:\/\/github.com\/nk53\/stanalyzer<\/jats:ext-link>\n                  .\n                <\/jats:p>","DOI":"10.64898\/2026.02.06.704471","type":"posted-content","created":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T02:45:19Z","timestamp":1770691519000},"source":"Crossref","is-referenced-by-count":0,"title":["ST-Analyzer: A Packaged Web and Command-Line Interface for Simulation Trajectory Analysis"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0936-7274","authenticated-orcid":false,"given":"Nathan R.","family":"Kern","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4883-3031","authenticated-orcid":false,"given":"Soohyung","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4516-8689","authenticated-orcid":false,"given":"Yiwei","family":"Cao","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5642-6041","authenticated-orcid":false,"given":"Wonpil","family":"Im","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA"},{"name":"Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026021208551942000_2026.02.06.704471v1.1","doi-asserted-by":"publisher","DOI":"10.1145\/235815.235821"},{"key":"2026021208551942000_2026.02.06.704471v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.softx.2015.06.001"},{"key":"2026021208551942000_2026.02.06.704471v1.3","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"2026021208551942000_2026.02.06.704471v1.4","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21287"},{"key":"2026021208551942000_2026.02.06.704471v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2021.11.1368"},{"key":"2026021208551942000_2026.02.06.704471v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2015.08.015"},{"key":"2026021208551942000_2026.02.06.704471v1.7","doi-asserted-by":"publisher","DOI":"10.1021\/ct400341p"},{"key":"2026021208551942000_2026.02.06.704471v1.8","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23753"},{"key":"2026021208551942000_2026.02.06.704471v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2649-2"},{"key":"2026021208551942000_2026.02.06.704471v1.10","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0686-2"},{"key":"2026021208551942000_2026.02.06.704471v1.11","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20945"},{"key":"2026021208551942000_2026.02.06.704471v1.12","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.24660"},{"key":"2026021208551942000_2026.02.06.704471v1.13","doi-asserted-by":"publisher","DOI":"10.1063\/5.0012280"},{"key":"2026021208551942000_2026.02.06.704471v1.14","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00935"},{"key":"2026021208551942000_2026.02.06.704471v1.15","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23584"},{"key":"2026021208551942000_2026.02.06.704471v1.16","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.4774217"},{"key":"2026021208551942000_2026.02.06.704471v1.17","unstructured":"Ram\u00edrez, S. 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