Markus Fleischauer

SIRIUS 4.0.1 released

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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:
    • https://www.csi-fingerid.uni-jena.de/webapi/trainingstructures.csv?predictor=pos
    • https://www.csi-fingerid.uni-jena.de/webapi/trainingstructures.csv?predictor=neg

See our changelog for further details .

You can download SIRIUS with CSI:FingerID here.

Meet us at ASMS 2018

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Marcus is presenting ZODIAC on Monday at ASMS. This is our new method which enables comprehensive molecular formula identification on whole datasets.
The talk is “The whole is easier than the parts: Improving molecular formula identification using Gibbs sampling on fragmentation trees”.

SIRIUS 3 is not longer supported

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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.

Meet Kai and Marcus at Metabolomics 2017

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Kai and Marcus will give talks at Metabolomics conference 2017 in Brisbane on Wed, June 28th.
Kai will talk about CANOPUS, the new tool for compound category prediction. Marcus will discuss ZODIAC, a method for comprehensive molecular formula identification on complete LC/MS runs with tandem mass spectra.

SIRIUS+CSI:FingerID 3.5 released

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Our new version, Sirius 3.5, comes with several advancements. Download and use it here.
We have a new overview tab for CSI:FingerID hits which displays results of structure search for multiple molecular formulas.
You can examine the predicted fingerprint of each compound (and molecular formula) independently of any database.
We now offer the possibility to create and search in custom structure databases.
Besides, we have a new bayesian networks scoring function for CSI:FingerID which considers dependencies between different molecular properties.
This and much more.

SIRIUS+CSI:FingerID 3.4 released

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A new Sirius version is available. We included new features to enable a more intuitive workflow. We hope you’ll like it. Download and use it here.
We provide element prediction using isotope pattern. CSI:FingerID now predicts more molecular properties which improves structure identification.
Besides we fundamentally changed the structure of the result output generated by the command line tool to its final version. This means you might have to adjust  your workflow.

 

 

 

Sirius release 3.4 is coming soon

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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.

SIRIUS+CSI:FingerID for Mac OSX

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SIRIUS+CSI:FingerID is no available for Mac. You can download it here. A few highlights of the new version:

  • 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

Meet us at Metabolomics 2016

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Kai, Franziska and Marcus are visiting the Metabolomics in Dublin from Monday, 27 June 2016 to Thursday, 30 June 2016.

Franziska is giving a talk on  the Significance of metabolite identifications from searching mass spectral libraries.
Marcus will speak about our new Confidence score for CSI:FingerID identifications.
Kai will present the new SIRIUS 3.2 release.

Gastvorlesung Ivo Große

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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.