- GUI: Better progress information for running jobs
- more bugfixes ;-)
- fix: prevent Nullpointer in CANOPUS View filter box
- improvement: allow to store projectspace copy as directory (not compressed)
- fix: error when using external path for custom dbs in the CLI (#4)
- fix: wrong log directory that might prevent SIRIUS from starting.
- 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
--db=BIOis 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
- critical-fix: custom database importer wrote cache files to working directory instead to the usual casche dir
- fix: problems with the deletion and creation of custom databases (GUI)
- improvement: local database cached can be cleare from the settings panel (GUI)
- 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)
- fix: intensity bug in FBMN export
- fix: CONFIG already exists error during background computations (FBMN export, custom-db import)
.ceffile extension missing in file import dialog
java.util.ConcurrentModificationExceptionwhen computing subtool separately with the CLI
- fix: fixed missing jar/zip provider in bundled jre -> Zipped project-spaces are now working again
- fix: fixed ignored
custom.configand config inheritance
- feature: Heuristic computation for fragmentation trees to improve running times for high mass compounds (no ILP has to be computed)
- feature/improvement: Summaries
- fix: inconsistent ranking in
- 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
- 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
- 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
- feature: standalone subtool (
ftree-export) to export fragmentation trees from CLI
--noCitecommand 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
- fix: ZODIAC crash caused by empty spectra
- fix: invalid project-space (not importable) due to empty detected adducts
- fix: uncatched exception during adduct resolution (GitHub issue #9)
- Merry X-Mas
- 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
- 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 (
retentionTimeInSeconds) have been added to project wide summary files such as
- breaking: column names in
breaking: column names describing scores now use camel case instead of underscores:
- 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.
- fix: Error when parsing FragTree json with non numeric double values
- fix: layout of screener progress bar on Mac
- 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
- 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
- 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
- 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
- feature: ms2 istotope scorer now available in cli and gui
- 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
- 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
- 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
- fix: some more fixes on MacOS GUI freezes
- 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
- 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
- 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
- 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.
- 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
- 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
- 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
- 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
- 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
- fix missing MS2 data error
- MacOSX compatible start script
- add proxy settings, bug reporter, feature request
- new GUI look
- 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
- fix bug with penalizing molecular formulas on intrinsically charged mode
- fix critical bug in CSV reader
- 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
- fix crash when using GLPK solver
- fix bug: SIRIUS uses the old scoring system by default when -p parameter is not given
- fix some minor bugs
- 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
- release version