{"id":45008057,"url":"https://github.com/sirius-ms/sirius","last_synced_at":"2026-07-08T02:00:35.833Z","repository":{"id":41879317,"uuid":"94561614","full_name":"sirius-ms/sirius","owner":"sirius-ms","description":"SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)","archived":false,"fork":false,"pushed_at":"2026-07-02T07:38:21.000Z","size":227820,"stargazers_count":155,"open_issues_count":85,"forks_count":36,"subscribers_count":8,"default_branch":"stable","last_synced_at":"2026-07-02T08:17:56.241Z","etag":null,"topics":["bioinformatics","cheminformatics","csi-fingerid","denovo","fingerid","fragmentation-trees","isotope-pattern","java","mass-spectra","mass-spectrometry","metabolomics","molecular-formulas","molecular-structures","ms-data","ms-spectra","science","sirius","structure-elucidation"],"latest_commit_sha":null,"homepage":"","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"agpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sirius-ms.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"COPYING.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2017-06-16T16:21:34.000Z","updated_at":"2026-06-30T10:18:28.000Z","dependencies_parsed_at":"2024-01-26T12:08:50.950Z","dependency_job_id":"2de7d622-f24c-47ff-958b-e740d0e985fc","html_url":"https://github.com/sirius-ms/sirius","commit_stats":null,"previous_names":["sirius-ms/sirius","boecker-lab/sirius"],"tags_count":112,"template":false,"template_full_name":null,"purl":"pkg:github/sirius-ms/sirius","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sirius-ms%2Fsirius","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sirius-ms%2Fsirius/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sirius-ms%2Fsirius/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sirius-ms%2Fsirius/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sirius-ms","download_url":"https://codeload.github.com/sirius-ms/sirius/tar.gz/refs/heads/stable","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sirius-ms%2Fsirius/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35248842,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-08T02:00:06.796Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","cheminformatics","csi-fingerid","denovo","fingerid","fragmentation-trees","isotope-pattern","java","mass-spectra","mass-spectrometry","metabolomics","molecular-formulas","molecular-structures","ms-data","ms-spectra","science","sirius","structure-elucidation"],"created_at":"2026-02-18T23:09:29.293Z","updated_at":"2026-07-08T02:00:35.823Z","avatar_url":"https://github.com/sirius-ms.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blueviolet.svg)](https://www.gnu.org/licenses/agpl-3.0)\n[![Generic badge](https://img.shields.io/badge/Version-6.3.7-informational.svg)](https://shields.io/)\n[![Build and Publish](https://github.com/sirius-ms/sirius/actions/workflows/distribute.yaml/badge.svg?branch=release-4-pre)](https://github.com/sirius-ms/sirius/actions/workflows/distribute.yaml)\n[![Join community chat at https://gitter.im/sirius-ms/general](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/sirius-ms/general?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge\u0026utm_content=badge)\n\n*\u003cspan style=\"color: #808080;\"\u003eOur methods are offered to the scientific community as freely available resources. (Re-)distribution of the\nmethods, in whole or in part, for commercial purposes is prohibited.\nThe SIRIUS web services (CSI:FingerID, CANOPUS, MSNovelist and others) hosted by the [Böcker group](https://bio.informatik.uni-jena.de/) are for academic research and education use only.\nPlease review the [terms of service](https://bio.informatik.uni-jena.de/terms-of-service-fsu-csi) of the academic version for details.\nFor non-academic users, the [Bright Giant GmbH](https://bright-giant.com) provides licenses and all related services.\nWe ask that users of our tools cite the corresponding papers in any resulting publications.\u003c/span\u003e*\n\nSIRIUS is a java-based software framework for the analysis of LC-MS/MS data of metabolites and other \"small molecules of biological interest\".\nSIRIUS integrates a collection of our tools, including CSI:FingerID (with [COSMIC](https://bio.informatik.uni-jena.de/software/cosmic/)), [ZODIAC](https://bio.informatik.uni-jena.de/software/zodiac/),\n[CANOPUS](https://bio.informatik.uni-jena.de/software/canopus/). In particular, both the\ngraphical user interface and the command line version of SIRIUS seamlessly integrate the CSI:FingerID, CANOPUS and MSNovelist web services.\n\nMain developers of SIRIUS are the [Böcker group](https://bio.informatik.uni-jena.de/) and the [Bright Giant GmbH](https://bright-giant.com)\n\n## Download Links\n\n### Documentation\n- [Online Documentation](https://v6.docs.sirius-ms.io/)\n- [Video tutorials](https://www.youtube.com/playlist?list=PL8R4DKiWsw-vBpvrhtKaZT8UX5Zt08x9h)\n- [Videos - Behind the scenes](https://www.youtube.com/playlist?list=PL57Jv_39fTddhuGqIlX6OIfzhtMBabrGi)\n- [Demo data](https://github.com/sirius-ms/sirius/raw/refs/heads/stable/data/demo-data.zip?download=)\n- [Logos for publications and presentations](https://bio.informatik.uni-jena.de/software/sirius/sirius-logos/)\n\n\u003c!--begin download--\u003e\n\n### SIRIUS+CSI:FingerID GUI and CLI - Version 6.3.7 (2026-05-23)\n##### These versions include the Java Runtime Environment, so there is no need to install Java separately! Just download, install/unpack and execute.\n- for Windows (x86-64/amd64/x64): [msi](https://github.com/sirius-ms/sirius/releases/download/v6.3.7/sirius-6.3.7-win-x64.msi) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.3.7/sirius-6.3.7-win-x64.zip)\n- for Mac (x86-64/amd64/x64): [pkg](https://github.com/sirius-ms/sirius/releases/download/v6.3.7/sirius-6.3.7-macos-x64.pkg) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.3.7/sirius-6.3.7-macos-x64.zip)\n- for Mac (arm64/aarch64/apple silicon): [pkg](https://github.com/sirius-ms/sirius/releases/download/v6.3.7/sirius-6.3.7-macos-arm64.pkg) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.3.7/sirius-6.3.7-macos-arm64.zip)\n- for Linux (x86-64/amd64/x64): [zip](https://github.com/sirius-ms/sirius/releases/download/v6.3.7/sirius-6.3.7-linux-x64.zip)\n- for Linux (arm64/aarch64): [zip](https://github.com/sirius-ms/sirius/releases/download/v6.3.7/sirius-6.3.7-linux-arm64.zip)\n\n\n\u003c!--end download--\u003e\n\nAll (including previous) releases can be found [here](https://github.com/sirius-ms/sirius/releases).\n\n### [Installation](https://v6.docs.sirius-ms.io/install)\nFor Windows and MacOS, the installer version of SIRIUS (msi/pkg) should be preferred but might require administrator permissions.\nThese installer packages are signed by [Bright Giant](https://bright-giant.com) to verify the package provider’s identity, and should therefore trigger no or only mild security warnings from the operating system during installation.\nSee the [documentation](https://v6.docs.sirius-ms.io/install) for details.\n\n\n### [Creating a user account](https://v6.docs.sirius-ms.io/account-and-license/)\nUser accounts can be created directly via the SIRIUS GUI. Please, use your **institutional email address**. SIRIUS\nweb services are free for academic use. Usually academic institutions are identified by their\nemail domain and access will be granted automatically. In some cases, further validation of your academic may be required.\n[See also SIRIUS Documentation – Account and License](https://v6.docs.sirius-ms.io/account-and-license/).\n\n### [Sources on GitHub](https://github.com/sirius-ms)\n- [SIRIUS](https://github.com/sirius-ms/sirius)\n- [SIRIUS-API SDKs](https://github.com/sirius-ms/sirius-client-openAPI)\n- [SIRIUS-API Java SDK](sirius-sdk/README.md)\n\n### [Changelog](https://v6.docs.sirius-ms.io/changelog/)\n\n### Contact\n- To get news, help or ask questions please join our [Gitter Community `#sirius-ms:gitter.im`](https://matrix.to/#/#sirius-ms:gitter.im).\n- For bug reports or feature request please use the issues on our [GitHub](https://github.com/sirius-ms/sirius/issues). Or check the [documentation](https://v6.docs.sirius-ms.io/bugs/) for further information about this topic.\n\n### Integration of CSI:FingerID, CANOPUS and MSNovelist\n\nFragmentation trees and spectra can be directly uploaded from SIRIUS to the CSI:FingerID, CANOPUS and MSNovelist web services.\nResults are retrieved from the web service and can be displayed in the SIRIUS graphical user interface. This functionality is\nalso available for the SIRIUS command-line tool. Training structures for CSI:FingerID's predictors are available through the CSI:FingerID web API:\n\u003c!--begin training--\u003e\n\n- https://www.csi-fingerid.uni-jena.de/v3.0/api/fingerid/trainingstructures?predictor=1 (training structures for positive ion mode)\n- https://www.csi-fingerid.uni-jena.de/v3.0/api/fingerid/trainingstructures?predictor=2 (training structures for negative ion mode)\n\n\u003c!--end training--\u003e\n\n### Fragmentation Tree Computation\n\nThe manual interpretation of tandem mass spectra is time-consuming and\nnon-trivial. SIRIUS analyses the fragmentation pattern resulting in\na hypothetical fragmentation tree, in which nodes are annotated with\nmolecular formulas of the fragments and arcs (edges) represent fragmentation\nevents (losses). SIRIUS allows for the automated and high-throughput analysis of\nsmall-compound MS data beyond elemental composition without requiring\ncompound structures or a mass spectral database.\n\n### Isotope Pattern Analysis\n\nSIRIUS deduces molecular formulas of small compounds by ranking isotope\npatterns from mass spectra of high resolution. After preprocessing, the\noutput of a mass spectrometer is a list of peaks which corresponds to\nthe masses of the sample molecules and their abundance. In principle,\nelemental compositions of small molecules can be identified using only\naccurate masses. However, even with very high mass accuracy, many\nformulas are obtained in higher mass regions. High resolution mass\nspectrometry allows us to determine the isotope pattern of sample\nmolecule with outstanding accuracy and apply this information to\nidentify the elemental composition of the sample molecule. SIRIUS can be\ndownloaded either as graphical user interface (see Sirius GUI) or as\ncommand-line tool.\n\n\u003c!--begin cite--\u003e\n## Main citations\n\nKai Dührkop, Markus Fleischauer, Marcus Ludwig, Alexander A. Aksenov, Alexey V. Melnik, Marvin Meusel, Pieter C. Dorrestein, Juho Rousu and Sebastian Böcker.\n[SIRIUS 4: Turning tandem mass spectra into metabolite structure information.](https://doi.org/10.1038/s41592-019-0344-8)\n*Nature Methods* 16, 299–302, 2019.\n\n---\nMichael A. Stravs and Kai Dührkop, Sebastian Böcker and Nicola Zamboni.\n[MSNovelist: De novo structure generation from mass spectra.](https://doi.org/10.1038/s41592-022-01486-3)\n*Nature Methods* 19, 865–870, 2022. (Cite if you are using: MSNovelist)\n\nMartin A. Hoffmann, Louis-Félix Nothias, Marcus Ludwig, Markus Fleischauer, Emily C. Gentry, Michael Witting, Pieter C. Dorrestein, Kai Dührkop and Sebastian Böcker.\n[High-confidence structural annotation of metabolites absent from spectral libraries.](https://doi.org/10.1038/s41587-021-01045-9)\n*Nature Biotechnology* 40, 411–421, 2022. (Cite if you are using: *CSI:FingerID*, *COSMIC*)\n\nKai Dührkop, Louis-Félix Nothias, Markus Fleischauer, Raphael Reher, Marcus Ludwig, Martin A. Hoffmann, Daniel Petras, William H. Gerwick, Juho Rousu, Pieter C. Dorrestein and Sebastian Böcker.\n[Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra.](https://doi.org/10.1038/s41587-020-0740-8)\n*Nature Biotechnology*, 2021. (Cite if you are using *CANOPUS*)\n\nYannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner, David S. Wishart.\n[ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.](https://doi.org/10.1186/s13321-016-0174-y)\n*Journal of Cheminformatics* 8, 61, 2016. (*ClassyFire* publication; cite this if you are using *CANOPUS*)\n\nMarcus Ludwig, Louis-Félix Nothias, Kai Dührkop, Irina Koester, Markus Fleischauer, Martin A. Hoffmann, Daniel Petras, Fernando Vargas, Mustafa Morsy, Lihini Aluwihare, Pieter C. Dorrestein, Sebastian Böcker.\n[Database-independent molecular formula annotation using Gibbs sampling through ZODIAC.](https://doi.org/10.1038/s42256-020-00234-6)\n*Nature Machine Intelligence* 2, 629–641, 2020. (Cite if you are using *ZODIAC*)\n\nKai Dührkop and Sebastian Böcker.\n[Fragmentation trees reloaded.](http://dx.doi.org/10.1007/978-3-319-16706-0_10)\n*Journal of Cheminformatics* 8, 5, 2016. (Cite this for *fragmentation pattern analysis and fragmentation tree computation*)\n\nKai Dührkop, Huibin Shen, Marvin Meusel, Juho Rousu, and Sebastian Böcker.\n[Searching molecular structure databases with tandem mass spectra using CSI:FingerID](http://dx.doi.org/10.1073/pnas.1509788112).\n*Proceedings of the National Academy of Sciences U S A* 112(41), 12580-12585, 2015. (cite this when *using CSI:FingerID*)\n\nSebastian Böcker, Matthias C. Letzel, Zsuzsanna Lipták and Anton Pervukhin.\n[SIRIUS: decomposing isotope patterns for metabolite identification.](http://bioinformatics.oxfordjournals.org/content/25/2/218.full)\n*Bioinformatics* 25(2), 218-224, 2009. (Cite this for *isotope pattern analysis*)\n\n### Additional citations\n\nDavid S Wishart , Siyang Tian , Dana Allen , Eponine Oler , Harrison Peters , Vicki W Lui , Vasuk Gautam , Yannick Djoumbou-Feunang , Russell Greiner , Thomas O Metz.\n[BioTransformer 3.0—a web server for accurately predicting metabolic transformation products](https://doi.org/10.1093/nar/gkac313)\nNucleic Acids Research, 50(W1), W115–W123, 2022. (Cite if you are using: Biotransformer for structure database generation)\n\nShipei Xing, Sam Shen, Banghua Xu, Xiaoxiao Li and Tao Huan.\n[BUDDY: molecular formula discovery via bottom-up MS/MS interrogation.](https://doi.org/10.1038/s41592-023-01850-x)\n*Nature Methods* 20, 881–890, 2023. (Cite if you are using: Bottom-up molecular formula generation)\n\nMarcus Ludwig, Kai Dührkop and Sebastian and Böcker.\n[Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints.](http://doi.org/10.1093/bioinformatics/bty245)\n*Bioinformatics*, 34(13): i333-i340. 2018. Proc. of Intelligent Systems for Molecular Biology (ISMB 2018). (Cite for CSI:FingerID Scoring)\n\nW. Timothy J. White, Stephan Beyer, Kai Dührkop, Markus Chimani and\nSebastian Böcker. [Speedy Colorful\nSubtrees.](http://dx.doi.org/10.1007/978-3-319-16706-0_10) In *Proc. of\nComputing and Combinatorics Conference (COCOON 2015)*, volume 9198 of\n*Lect Notes Comput Sci*, pages 310-322. Springer, Berlin, 2015. (cite\nthis on *why computations are swift*, even on a laptop computer)\n\nHuibin Shen, Kai Dührkop, Sebastian Böcker and Juho Rousu. [Metabolite\nIdentification through Multiple Kernel Learning on Fragmentation\nTrees.](http://dx.doi.org/10.1093/bioinformatics/btu275)\n*Bioinformatics*, 30(12):i157-i164, 2014. Proc. of *Intelligent Systems\nfor Molecular Biology* (ISMB 2014). (Introduces *the machinery behind\nCSI:FingerID*)\n\nImran Rauf, Florian Rasche, François Nicolas and\nSebastian Böcker. [Finding Maximum Colorful Subtrees in\npractice.](http://dx.doi.org/10.1089/cmb.2012.0083) *J Comput Biol*,\n20(4):1-11, 2013. (More, earlier work on *why computations are swift*\ntoday)\n\nHeinonen, M.; Shen, H.; Zamboni, N.; Rousu, J. [Metabolite\nidentification and molecular fingerprint prediction through machine\nlearning](http://dx.doi.org/10.1093/bioinformatics/bts437).\n*Bioinformatics*, 2012. Vol. 28, nro 18, pp. 2333-2341. (Introduces the\n*idea of predicting molecular fingerprints* from tandem MS data)\n\nFlorian Rasche, Aleš Svatoš, Ravi Kumar Maddula, Christoph Böttcher, and\nSebastian Böcker. [Computing Fragmentation Trees from Tandem Mass\nSpectrometry\nData](http://pubs.acs.org/doi/abs/10.1021/ac101825k). *Analytical\nChemistry* (2011) 83 (4): 1243–1251. (Cite this for *introduction of\nfragmentation trees* as used by SIRIUS)\n\nSebastian Böcker and Florian Rasche. [Towards de novo identification of metabolites by analyzing\ntandem mass\nspectra](http://bioinformatics.oxfordjournals.org/content/24/16/i49.abstract).\n*Bioinformatics* (2008) 24 (16): i49-i55. (The very *first paper to\nmention fragmentation trees* as used by SIRIUS)\n\n\u003c!--end cite--\u003e\n\n## License\n\nStarting with version 4.4.27, SIRIUS is licensed under the [GNU Affero General\nPublic License (GPL)](https://www.gnu.org/licenses/agpl-3.0.txt). If you integrate SIRIUS into other software, we\nstrongly encourage you to make the usage of SIRIUS as well as the literature to cite transparent to the user.\n\n## Acknowledgements\n#### Thanks for supporting the development of SIRIUS!\n[![MSCJ Logo](https://www.mscj.uni-jena.de/wp-content/uploads/2015/05/logo-svg-text-horizontal.svg)](https://www.mscj.uni-jena.de)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsirius-ms%2Fsirius","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsirius-ms%2Fsirius","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsirius-ms%2Fsirius/lists"}