SIRIUS 4.8.0 is out and releases the COSMIC confidence score to the wild. For more details on COSMIC see here.
After 2 and a half successful years and over 35 million predicted fingerprints, SIRIUS 4.0.1 will reach its end of life on Friday the 30th of April 2021.
What does this mean for you? We will shut down the web service for CSI:FingerID, so no fingerprint prediction and structure database search will be possible with SIRIUS 4.0.1 anymore.
We are happy to announce that SIRIUS 4.7.0 is now available for download . This release is all about fixing bugs and performance optimization. To all who had problems with the ILP solvers, a freezing GUI, high memory consumption or long running times: This update should make your life way easier. For a full list of changes see the Changelog.
We further integrated the option to compute fragmentation trees only with our heuristic algorithm (no ILP involved) to speedup molecular formula identification for high mass compounds.
Together with applying timeouts on compound level this should make the processing of large datasets much more feasible.
We are happy to announce that the new online documentation for SIRIUS is now available at https://boecker-lab.github.io/docs.sirius.github.io/.
The content is completely written in Markdown which makes contributions by the community very easy. No programming skills required!
Help us with your contributions to make this documentation more comprehensive and useful for the community. See our GitHub repository for
detailed information on how to contribute.
Some of you may have noticed problems where SIRIUS 4.4 GUI did not start without reporting any error.
This might be due to old incompatible configs (.sirius directory) from version 4.0.1. SIRIUS 4.4.21 fixes this problem and now uses a separate config directory (.sirius-4.4). It is now possible to use version 4.0.1 and 4.4.x along on the same system without interfering each other.
Since we could fix the deadlocks of the SIRIUS GUI on Mac with build 4.4.18, the SIRIUS 4.4. GUI now also available for MacOS: https://bio.informatik.uni-jena.de/software/sirius/
It’s been a while since SIRIUS 4 received its last update. We are excited to announce that SIRIUS 4.4 is coming soon.
It comes with many new features, e.g.:
- Project-Space: A standardized persistence layer shared by CLI and GUI that makes both fully compatible.
- Redesigned Command Line Interface: SIRIUS is now a toolbox that contains different sub-tools that can be combined to “tool-chains”.
- New (and newly integrated) tools:
- ZODIAC: Improve Molecular Formula Identifications by re-ranking SIRIUS molecular formula annotations using Bayesian statistics. ZODIAC optimizes annotations on a whole dataset taking advantage of the fact that compounds usually co-occur in a network of derivatives.
- PASSATUTTO: Is now part of SIRIUS and allows you to generate dataset specific decoy spectral libraries from computed fragmentation trees.
- lcms-align: SIRIUS supports mzML/mzXML format to process whole LC-MS/MS runs. The lcms-align preprocessing tool performs feature detection and feature alignment based on the available MS/MS spectra.
- Other handy standalone tools, e.g. compound similarity calculation.
To provide user friendly but also flexible and customizable access to the different tools we completely redesigned the command line interface (CLI).
We know that this might break your workflows and therefore we provide you an early access version of the CLI that can be used for testing and adapting your workflows:
You will also find an updated version of the manual which is still work-in-progress but contains already an updated section on the new CLI.
No worries, even when SIRIUS 4.4. will be released (as soon as the GUI is ready) version 4.0.1 will still be available for some time.
If you find bugs or have any feedback feel free to open an issue on the SIRIUS GitHub repository or contact us via .
Meet Markus at the ISMB/ECCB 2019 in Basel.
On Tuesday, Markus will give a talk about “SIRIUS 4: turning tandem mass spectra into metabolite structure information”.
There is also a corresponding poster in Session A (J-06) which will be presented on Tuesday 6:00pm-8:00pm.
Meet Kai, Markus and Martin at ASMS 2019.
On Wednesday Kai presents a poster (WP-408) about SIRIUS 4 and how it turns tandem mass spectra into metabolite structure information.
Some of you might have noticed problems with the
Speaking of SIRIUS and CSI:FingerID are gathering interest in the community, the CSI:FingerID web service has processed more than ten million compound queries. Awesome!
A new version of SIRIUS 4 is available for download.
SIRIUS 4.0.1 brings many bugfixes, user interface polishing and improved stability of the CSI:FingerID backend.
- SIRIUS 4.0.1 now supports JAVA 9 and higher
- The structures used to train CSI:FingerID are now available via the web service:
See our changelog for further details .
You can download SIRIUS with CSI:FingerID here.
On July 8, 2018, the CSI:FingerID web service has passed five million compound queries. Awesome!
We found a major bug in the web service of SIRIUS 3 which can also affect the stability of the new SIRIUS 4. Therefore we decided to shut down the web service of SIRIUS 3 immediately.
Please contact us () if you need to finish work that can only be done with SIRIUS 3. We will try to find a solution then.
All news of our group are now available on Twitter: @boeckerlab
Build 4 contains some more bug fixes!
Build 2 fixes a major bug when the included GLPK ILP solver is used to calculate fragmentation trees.
During the next few days we will release Sirius 3.4
This will be a major release containing several changes on the command line interface.
You may have to adjust existing scripts to get them work with the finalized command line interface.
- Searching your tandem mass spectra in molecular databases using CSI:FingerId
- Restrict the SIRIUS molecular formula identification to formulas appearing in molecular databases – or search through the whole space of possible formulas. It’s up to you.
- Sort you identification results by confidence such that more reliable identifications (e.g. from high quality spectra or easy recognizable compounds) are separated from bogus identifications.
- Predict structural features and substructures from tandem mass spectra and visualize them in your candidate structure list.
Don’t hesitate to give us your feedback, report bugs or suggesting new features. Just write to
Ivo Große von der Universität Halle wird uns am 13. Januar besuchen und eine Gastvorlesung zum Thema Motif Finding und EM-Algorithmus halten – klassische Themen der Bioinformatik, die in Jena leider nicht mehr gelehrt werden.
Die Vorlesung findet am Mittwoch den 13. Januar von 9:30 bis 12:00 Uhr im Seminarraum 119, August-Bebel-Str. 4 statt.
Die Veranstaltung ist für alle Studierenden der Bioinformatik, insbesondere für alle Master-Studenten interessant. Alle Interessierten sind herzlich eingeladen.