Build 2 fixes a major bug when the included GLPK ILP solver is used to calculate fragmentation trees.
SIRIUS+CSI:FingerID 3.4 released
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
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.
Kerstin awarded Wissenschaftspreis für anwendungsorientierte Abschlussarbeit
Today, Kerstin was awarded the “Wissenschaftspreis für anwendungsorientierte Abschlussarbeit” (scientific award for application-oriented thesis) from the Wirtschaftsförderungsgesellschaft mbH and the FSU Jena, for her PhD thesis “Small molecules: From mass spectral fragmentation data to structural elucidation”. Congratulations!
meet Sebastian at the OpenMS user meeting 2016
Sebastian will give a talk on CSI:FingerID and SIRIUS at the OpenMS user meeting 2016 in Tübingen, 21-23 September 2016.
meet Sebastian at the de.NBI Summer School 2016
Sebastian will give a talk at the de.NBI Summer School 2016: From Big Data to Big Insights (Dagstuhl, 26-30 September 2016).
SIRIUS+CSI:FingerID for Mac OSX
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
SIRIUS+CSI:FingerID release
SIRIUS+CSI:FingerID leaves the alpha state. 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
SIRIUS+CSI:FingerID alpha release
The CASMI winner methods SIRIUS and CSI:FingerID are now available as a user interface. This allows users to batch process their spectra; which was not possible for the web application of CSI:FingerID.
You can try an early alpha version of SIRIUS+CSI:FingerID here.
Within the next three weeks we will release the final 3.1.4 version. Please report bugs to .
Meet us at Metabolomics 2016
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.
Besucht unseren Workshop beim MINT-Schülerkongress
Wir sind dabei, beim MINT-Schülerkongress 2016 des Schülerforschungszentrums Nordhessen in Kassel.
Alle weiteren Infos findet ihr hier.
CSI:FingerID: Best automated method in CASMI contest
CSI:FingerID participated in this year’s CASMI (Critical Assessment of Small Molecule Identification) contest for automated methods identifying compounds solely by mass spectral data without additional meta data (category 2). IOKR, the new prediction method within CSI:FingerID, won this category. Standard CSI:FingerId prediction method ranked 2nd best. For positive ionization, CSI:FingerID identified more than twice as much compounds than any other method.
We are pleased that SIRIUS and CSI:FingerID were successfully used by many other contestants in category 1.
You can try CSI:FingerID on http://www.csi-fingerid.org/. A commandline version as well as a user interface which allows batch processing of MS/MS data will be released soon. We will also integrate the new IOKR prediction method into the CSI:FingerID web interface.
de.NBI Summer School 2016: From Big Data to Big Insights
Das German Network for Bioinformatics Infrastructure (de.NBI) läd ein zur de.NBI Summer School 2016 unter dem Motto “From Big Data to Big Insights: Computational methods for the analysis and interpretation of mass-spectrometric high-throughput data”
Interessenten können sich noch bis zum 1. Juni bewerben.
Wir sind dabei beim Girls‘ Day 2016 am 28. April!
Mehr Infos gibt es hier.
Meet Betram and Franziska in Bled
Bertram and Franziska are visiting the 31st TBI Winterseminar in Bled from Sunday, 14 Feb 2016 to Friday, 19 Feb 2016. Bertram is giving a talk on Transcriptomics in Cyanobacteria.
Gastvorlesung Sebastian in Halle
Sebastian wird am Montag den 25.01.2016 zwei Vorlesungen zum Thema “Genome Rearrangements und Gene Clusters” an der Universität Halle halten.
Die Vorlesungen finden von 10:15 bis 12:00 Uhr in Seminarraum 1.30 sowie von 14:00 Uhr bis 15:15 Uhr in Seminarraum 0.04 des Institut für Informatik (Von-Seckendorff-Platz 1, Halle) statt.
Interessierte sind herzlich eingeladen.
Bioinformatik Blog jetzt online
Ab sofort wird Franziska auf ihrem Blog wöchentlich über Forschungsfelder, aktuelle Publikationen und Karrieremöglichkeiten aus der Bioinformatik berichten.
Gastvorlesung Ivo Große
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.
Sirius 3.1 is out and now ships with a graphical user interface!
It was announced for October, but as so often, it took longer than expected to do the last steps. But here it is: The newest release of SIRIUS ships with a graphical user interface that helps with importing the data and visualizing the results. You can download SIRIUS 3.1 here.
We have published a paper in PNAS
Our paper “Searching molecular structure databases with tandem mass spectra using CSI:FingerID” has just appeared in the online issue of Proceedings of the National Academy of Sciences USA. Also see the press release by the Friedrich-Schiller-University Jena (here for German). The metabolite search engine CSI:FingerID is available from http://www.csi-fingerid.org/. This is joint work with Juho Rousu and his group at Aalto University (Finland).