SIRIUS 5

5.6.2 (2022-11-03)

  • fix: bug that prevents accepting license terms caused by mising content-length header in the request.

    5.6.1 (2022-10-28)

  • feature: improved progress information for background computations.
  • feature: new scheduling of remote jobs that reduces computation time and improves local cpu utilization.
  • feature: A Beta version of the new SIRIUS background service is now included in the respective build (service suffix).
  • feature: support for MS1 only data in GUI (Isotope Pattern analysis only).
    • MS1 only data from Agilent CEF format can now be imported
  • feature: command line autocompletion support for Linux and MacOS. See sirius --help for details.
  • feature: allow to write uncompressed (legacy) project-spaces via --no-compression pearameter
  • improvement: improvements on feature finding and feature alignment
  • improvement: more robust custom database importer. Support to import existing DBs into the GUI.
  • fix: fixed bug in feature finding that changed negative ion mode data to positive ion mode
  • fix: fixed inconsistent indexing of aligned and not aligned mzml/mzxml data that caused an invalid FBMN output.
    • possibly breaking change: SIRIUS internal compound index does now start at 1 instead of 0
  • fix: several smaller fixes and improvements

5.5.2

  • fix: Collsion energy parsing bug
  • feature: Update checker

5.4.1

  • breaking: User Authentication. A user account and license is now needed to user the online features of SIRIUS. The license is free and automatically available for non-commercial use, details here.
  • breaking: New project-space compression. Method level directories are now compressed archives to reduce number of files and save storage.
  • breaking: Summary writing has been moved to a separate sub-tool (write-summaries). Som summary files have slightly changed. Usually just additional columns if at all.
  • breaking: The fingerid/structure sub-tool has been split into a fingerprint (fingerprint prediction) and a structure (structure db search) sub-tool. This allows the user to recompute the database search without having to recompute the fingerprint and compound class predictions. It further allows to compute canopus compound class prediction without having to perform structure db search.
  • breaking: Updated Fingerprint vector. Fingerprint related results of SIRIUS 4 projects might have to be recomputed to perform some modification (e.g. recompute db-search). Reading the projects is still possible and formula results do not affected.
  • breaking: Custom database format has changed. Custom databases need to be re-imported

  • feature: Tool - El Gordo lipid class annotation.
  • feature: GUI Tool - Epimetheus sub-structure annotation. Combinatorial fragmentation of CSI:FingerID candidates to assign fragment peaks to sub-structures of the candidate.
  • feature: GUI View - New feature rich spectrum viewer. Mirror-plot to compare Isotope pattern and Simulated isotope pattern (e.g. ).
  • feature: GUI View - LC-MS view to review chromatographic peak and data quality report for a given feature/compound
  • feature: CANOPUS now fully supports NPC classes (prediction, GUI and output)
  • feature: GUI advanced filtering options
  • feature: GUI scaling factor can be defined by the user (setting panel)
  • feature: Additional file formats for spectrum import supported (.msp, massbank, .mat)

SIRIUS 4

4.9.3

  • fix: prevent Null-pointer in CANOPUS View filter box
  • improvement: allow storing project-space copy as directory (not compressed)

4.9.2

  • fix: error when using external path for custom dbs in the CLI (#4)

4.9.1

  • fix: wrong log directory that might prevent SIRIUS from starting.

4.9.0

  • feature: improved filtering options for the compound list in the GUI
  • feature: MS1 only data can now be imported using the CLI (--allow-ms1-only) to perform isotope pattern based molecular formula identification #28.
  • change: changed tanimoto algorithm form probabilistic to rounded to dramatically reduce running time for large structure candidate lists, see #43
  • change: --db=BIO is now the default in the CLI, see #43
  • fix: wrong adduct for adduct switch annotated spectra in project-space output.

  • dev feature: hidden parameter to skip project validation for testing purposes see, #42

  • minor bug fixes and improvementss

4.8.2

  • critical-fix: custom database importer wrote cache files to working directory instead to the usual casche dir

4.8.1

  • fix: problems with the deletion and creation of custom databases (GUI)
  • improvement: local database cached can be cleare from the settings panel (GUI)

4.8.0

  • feature: COSMIC - confidence score
  • improvement: new Object storage baackend
  • improvement: resizeable compound list (GUI)
  • improvement: CSI:FingerID and SIRIUS/ZODIAC scores in formula selector (GUI)
  • fix: new CLP dll should improve compatibility on windows (NO Solver found problem)

4.7.4

  • fix: intensity bug in FBMN export
4.7.3
  • fix: CONFIG already exists error during background computations (FBMN export, custom-db import)
  • fix: .cef file extension missing in file import dialog

4.7.2

  • fix: java.util.ConcurrentModificationException when computing subtool separately with the CLI

4.7.1

  • fix: fixed missing jar/zip provider in bundled jre -> Zipped project-spaces are now working again
  • fix: fixed ignored custom.config and config inheritance

4.7.0

  • feature: Heuristic computation for fragmentation trees to improve running times for high mass compounds (no ILP has to be computed)
  • feature/improvement: Summaries
    • new formula_identifications_adducts.tsv summary file
    • new canopus_summary_adducts.tsv summary file
    • added fromulaRank to compound_identifications.tsv and compound_identifications_adducts.tsv
    • fix: inconsistent ranking in compound_identifications.tsv and compound_identifications_adducts.tsv
  • improvement: more information about running jobs (compound information), improved log panel
  • improvement: All SIRIUS distros ship with start scripts that should handle env variables properly
  • improvement: rounded values for similarity matrix output
  • improvement: better progress information during import
  • improvement: CSI:FingerID adn CANOPUS summaries with multiple adducts (like the formula summary)
  • improvement/fix: Multithreading and performance issues of integrated CLP ILP solver
  • improvement/fix: GUI Job cancelling now works properly, even under high load
  • improvement/fix: improved caching and update mechanisms prevents GUI freezes and reduces GUI memory consumption when computing large data sets
  • improvement/fix: much lower memory consumption when writing summaries

  • fix: memory leak in jjob job manager lib - dramatically improves performance on large datasets.
  • fix: correct handling of CHARGE=-0 in mgf
  • fix: corrupted project-space caused by empty adduct detection results after mgf import
  • fix: empty project dir after wrong command
  • fix: wrong compound name in compound edit panel
  • fix: invalid valence filter error when computing positive and negative ion mode together fix: compound timeout not working reliable
  • fix: Commercial ILP solver not detected correctly even if the correct env variable was set
  • fix: CEF format import - “No proper interval given” error
  • fix: multiOS build architecture now OpenMS compatible
  • several minor bug fixes

  • upgrade: SIRIUS ships now with JRE-15 which should fix jvm crashes during heavy multi threading on linux

4.6.1

  • fix: CSI:FingerID results were not refreshed correctly after recomputing with different parameters in the GUI
  • fix: Parameters were not always handled correctly when recomputing with the GUI
  • fix: Index bug in fragmentation tree scoring

4.6.0

  • feature: standalone subtool (ftree-export) to export fragmentation trees from CLI
  • feature: --noCite command to disable bibliography print in CLI
  • improvement: bibliography is not printed when showing help message or command parsing error
  • fix: another problem with un-importable projects due to detected adducts

4.5.3

  • fix: ZODIAC crash caused by empty spectra

4.5.2

  • fix: invalid project-space (not importable) due to empty detected adducts
  • fix: uncatched exception during adduct resolution (GitHub issue #9)
  • Merry X-Mas

4.5.1

  • improvement: CLP native libs are now compatible with glibc 2.12+ (instead of 2.18+)
  • fix: project-space with outdated fingeprint versions (e.g. from SIRIUS 4.4) are now handled correctly and can be converted.
  • fix: database formulas could be used if candidates even if they were incompatible with the adduct
  • fix: mzml/mzxml files are now shown in input file selector

4.5.0

  • feature: CANOPUS: for negative ion mode data
  • feature: Bayesian (individual tree) scoring is now the default for ranking structure candidates
  • update: Structure DB update due to major changes in PubChem standardization since the last one.
    • feature: COCONUT, NORMAN and Super Natural are now officially supported
  • feature: Custom-DB importer View (GUI)

  • feature: mgf export for Feature Based Molecular Networking is now available in the GUI

  • breaking: additional columns (ionMass, retentionTimeInSeconds) have been added to project wide summary files such as formula_identifications.tsv, compound_identifications.tsv and compound_identifications_adducts.tsv
  • breaking: column names in formula_candidates.tsv have changed: massError(ppm) to massErrorPrecursor(ppm), explainedPeaks to numExplainedPeaks, medianAbsoluteMassError(ppm) to medianAbsoluteMassErrorFragmentPeaks(ppm)
  • breaking: column names describing scores now use camel case instead of underscores: ConfidenceScore, SiriusScore, ZodiacScore,TreeScore,IsotopeScore, CSI:FingerIDScore

  • fix: incompatibility with recent MaOSX version caused by gatekeeper. We now provide an installable packages.
  • fix: missing SCANS annotation in mgf-export subtool - creates now a valid input for FBMN
  • fix: un-parsed retention times in CEF format.
  • fix: Structure DB linking (wrong ids, missing link flags, duplicate entries, etc.)
  • fix: reduced memory consumption of CLI and GUI

  • JRE is now included in all version of SIRIUS
  • Many more bug fixes and performance improvements

NOTE: SIRIUS versions will now follow semantic versioning (all upcoming releases) regarding the command line interface and project-space output.

4.4.29

  • fix: Error when parsing FragTree json with non numeric double values
  • fix: layout of screener progress bar on Mac

4.4.28

  • feature: Retention time will now be imported by SIRIUS
    • RT is shown in the Compound list in the SIRUS GUI and the list can be sorted by RT
    • RT is part of the compound.info file in the project-space
  • feature: Loglevel can now be changed from CLI
  • feature: Summaries can not be written without closing SIRIUS GUI
    • Improvement: Better progress reporting when Summary writing summaries (GUI)
  • fix: Agilent CEF files without CE can now be imported

4.4.27

  • feature: coin-or ilp solver (CLP) is now included. This allows parallel computation of FragTrees without the need for a commercial solver.
  • improvement: Compounds without given charge are can now be imported. SIRIUS tries to guess the charge from the name (keyword: pos/neg) or falls back to positive.
  • improvement: additional parameters in compute dialog
  • improvement: commands of the ‘show command’ dialog can now be copied
  • fix: error when writing/reading fragmentation trees with new Jackson parser
  • fix: mgf exporter (CLI) now outputs feature name properly
  • fix: deadlock during connection check without internet connection
  • fix: tree rendering bug on non linux systems
  • fix: crash when aborting recompute dialog
  • upgrade (GUI): included JRE to zulu11.41.23-ca-fx-jre11.0.8

4.4.26

  • fix: deadlock and waiting time due to webservice connections
  • fix/improvement: Adduct Settings and Adduct detection
  • fix: memory leak in third party json lib -> Zodiac memory consumption has been reduced dramatically
  • fix: several minor bug fixes in the sirius libs

4.4.25

  • fix: removed spring boot packaging to
    • solve several class not found issues,
    • solve github issue #7
    • errors when importing and aligning mzml files.
    • improve startup time
  • fix: cosine similarity tool ignores instances without spectra (failed before)
  • fix: mgf-export tool skips invalid instances if possible (failed before)
  • instance validation after lcms-align tool

4.4.24

  • feature: ms2 istotope scorer now available in cli and gui

4.4.23

  • fix: wrong missing value handling in xlogp filter (some candidates were invisible)
  • improvement: less cores for computations if gui is running to have mor cpu time for GUI tasks
  • improvement: show deviation to target ion in FragTree root if precursor is missing in MS/MS

4.4.22

  • fix: Classloader exceptions when using CLI from the GUI version
  • fix: Wrong mass deviation for trees with adducts
  • fix: misplaced labels when exporting svg/pdf fragtrees
  • fix: some minor GUI bugs

4.4.21

  • fix: incompatibilities with existing configs from previous versions (.sirius)
  • fix: CANOPUS detail view has size zero
  • fix: failing CSI:FingerID computation with Zodiac re-ranking and existing Adducts
  • improvement: errors that occur before GUI is started are now reported
  • improvement: minor GUI improvements

4.4.20

  • fix: some more fixes on MacOS GUI freezes

4.4.18

  • fix: GUI Deadlock on MacOS X fixed. Mac version is now available.
  • improvement: Character separated files in project-space have now .tsv extension for better excel compatibility.
  • feature: Windows headless executable respects %JAVA_HOME% as JRE location.
  • improvement: Improved packaging and startup of the GUI version
  • fixes GitHub issues: 4 and 6

4.4.16

  • feature: CSI:FingerID for negative ion mode is available
    • NOTE: CANOPUS for negative mode data is not ready yet and will still take some time.
  • fix: Too small Heapsize on Windows
  • improvement: better GUI performance

4.4.15

  • feature: CLI Sub-Tool to export projects to mgf.
  • feature: multiple candidate number for Zodiac.
  • fix: zodiac score rendering.
  • fix: deadlock project-space import
  • fixes: tree rendering
  • improvement: import and deletion performance
  • improvement: import progress now shown

4.4.14

  • fix: MacOS included JRE not found.
  • fix: ignored parameters.
  • fix: recompute does not correctly invalidate and delete previous results.
  • fix: UI now correctly update when data will by deleted by the computations.

4.4.(0-13)

  • New (and newly integrated) tools:
    • CANOPUS:: A tool for the comprehensive annotation of compound classes from MS/MS data.
    • ZODIAC: Builds upon the SIRIUS molecular formula identifications and uses, say, its top 50 molecular formula annotations as candidates for one compound. It then re-ranks molecular formula candidates using Bayesian statistics.
    • PASSATUTTO: Is now part of SIRIUS and allows you to generate dataset specific decoy databases from computed fragmentation trees.
    • Other handy standalone tools e.g. compound similarity calculation, mass decomposition, custom-db creation and project-space manipulation.
  • Project-Space: A standardized persistence layer shared by CLI and GUI that makes both fully compatible.
    • Save and reimport your projects with all previously calculated results.
    • Review your results computed with the CLI in the GUI.
    • Handy project-space summary CSV and mzTab-M files for downstream analysis.
    • Preojects can be stored and modified as directory structure or as compressed archive.
  • LCMS-Runs: SIRIUS can now handle full LCMS-Runs given in mzML/mzXML format and performs automatic feature detection.
    • The lcms-align preprocessing tool performs feature detection and feature alignment for multiple LCMS-Runs based on the available the MS/MS spectra.
  • Redesigned Command line interface: SIRIUS is now a toolbox containing many subtools that may be combined to ToolChains based on the project-space.

  • CSI:FingerID had some massive updates, including more and larger molecular properties.
    • Structure DBs New version of the CSI:FingerID PubChem copy that now uses PubChem standardized structures.
    • NORMAN is now available as search DB
    • All available database filters can now be combined to arbitrary subsets for searching (even with custom databases).
  • Interactive fragmentation tree viewer with vector graphics export in the GUI.
  • New REST service with openAPI specification and Swagger-UI.
  • Java 11 or higher is now mandatory
    • GUI version ships with an integrated JRE
  • Many minor improvements and Bugfixes

4.0.1

  • Java 9 and higher are now supported
  • CSI:FingerID trainings structures available
    • Trainings structures available via WebAPI.
    • Trainings structures are flagged in CSI:FingerID candidate list.
  • SMARTS filter for candidate list (GUI)
  • Molecular Property filter for candidate list (GUI)
  • Available prediction workers of the CSI:FingerID webservice can be listed from SIRIUS
  • Improved connection handling and auto reconnect to Webservice
  • Improved error messaged
  • Improved stability and load balancing of the CSI:FingerID webservice
  • Several bug fixes

4.0

  • Fragmentation tree heuristics
  • Negative ion mode data is now supported
  • Polished and more informative GUI
    • Sirius Overview: Explained intensity, number of explained peaks, median mass deviation
    • Fragmentation trees: Color coding of nodes by intensity/mass deviation, more informative Fragmentation tree nodes
    • CSI:FingerID Overview: Number of Pubmed publication with pubmed linking for each Candidate, Visualization of CSI:FingerID score.
    • Predicted Fingerprints: Visualisation of prediction (posterior probability), predictor quality (F1) and number of training examples.
    • Several small improvements
  • CPLEX ILP solver support
  • Consider a specific list of ionizations for Sirius
  • Consider a specific list of adducts for CSI:FingerID
  • Custom ionizations/adducts can be specified (CLI and GUI)
  • Full-featured standalone command line version (headless version)
  • Improved parallelization and task management
  • Improved stability of the CSI:FingerID webservice
  • Time limit for fragmentation tree computations
  • Specify fields to import name and ID from .sdf into a custom database (GUI).
  • CSI:FingerID results can be filtered by Custom databases (GUI).
  • Better filtering performance (GUI)
  • Bug fix in Database filtering view (GUI)
  • Error Reporter bug fixed (GUI)
  • Logging bugs fixed
  • Many minor bug fixes

    SIRIUS 3

    3.5

  • Custom databases can be imported by hand or via csv file. You can manage multiple databases within Sirius.
  • New Bayesian Network scoring for CSI:FingerID which takes dependencies between molecular properties into account.
  • CSI:FingerID Overview which lists results for all molecular formulas.
  • Visualization of the predicted fingerprints.
  • ECFP fingerprints are now also in the CSI:FingerID database and do no longer have to be computed on the users side.
  • Connection error detection and refresh feature. No restart required to apply Sirius internal proxy settings anymore.
  • System wide proxy settings are now supported.
  • Many minor bug fixes and small improvements of the GUI

3.4

  • element prediction using isotope pattern
  • CSI:FingerID now predicts more molecular properties which improves structure identification
  • improved structure of the result output generated by the command line tool to its final version

3.3

  • fix missing MS2 data error
  • MacOSX compatible start script
  • add proxy settings, bug reporter, feature request
  • new GUI look

3.2

  • integration of CSI:FingerID and structure identification into SIRIUS
  • it is now possible to search formulas or structures in molecular databases
  • isotope pattern analysis is now rewritten and hopefully more stable than before

3.1.3

  • fix bug with penalizing molecular formulas on intrinsically charged mode
  • fix critical bug in CSV reader

3.1.0

  • Sirius User Interface
  • new output type -O sirius. The .sirius format can be imported into the User Interface.
  • Experimental support for in-source fragmentations and adducts

3.0.3

  • fix crash when using GLPK solver

3.0.2

  • fix bug: SIRIUS uses the old scoring system by default when -p parameter is not given
  • fix some minor bugs

3.0.1

  • if MS1 data is available, SIRIUS will now always use the parent peak from MS1 to decompose the parent ion, instead of using the peak from an MS/MS spectrum
  • fix bugs in isotope pattern selection
  • SIRIUS ships now with the correct version of the GLPK binary

3.0.0

  • release version