Wir sind dabei, beim MINT-Schülerkongress 2016 des Schülerforschungszentrums Nordhessen in Kassel.
Alle weiteren Infos findet ihr hier.
News
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).
PNAS paper scheduled for Sep 21
We are thrilled that our paper in “Proceedings of the National Academy of Sciences USA” is scheduled for Sep 21, 2015 online issue. More details then.
Sebastian won the Teaching Award of the Faculty.
Sebastian has been presented with the Teaching Award of the Faculty at the Day of the Faculty.
Meet Sebastian at Metabolomics 2015
Sebastian will attend the Conference of the Metabolomics Society 2015 in San Franciso, and give a talk on “Searching molecular structure databases with tandem mass spectra using CSI:FingerID”. On Tuesday after 6 pm, Steffen Neumann and Sebastian will head the BoF meeting on Computational Mass Spectrometry.
Kinderuni am Freitag 19. Juni
Am Freitag 19. Juni 2015 wird Sebastian im Rahmen der KinderUni Jena einen Vortrag zum Thema “Auch Computer müssen aufräumen” halten. Start ist um 16:00 Uhr, Veranstaltungsort ist der Hörsaal 7 in der Carl Zeiss Straße 3 (neben der Mensa).
SIRIUS 3.0 release
We present SIRIUS 3.0, a java-based software for discovering a landscape of de-novo identification of metabolites using single and tandem mass spectrometry.
SIRIUS uses isotope pattern analysis for detecting the molecular formula and further analyses the fragmentation pattern of a compound using fragmentation trees.
The version 3.0 is a complete rewrite of our previous software. It uses faster algorithms for the fragmentation tree computation and a revised scoring based on Bayesian statistics.
A command line tool is available here. We will add a graphical user interface soon.
Promotionspreis der Dekanin
Franziska wird für ihre Promotion mit dem Preis der Dekanin ausgezeichnet.
We will present a paper at COCOON 2015
Our paper “Speedy Colorful Subtrees” will be presented at the International Computing and Combinatorics Conference (COCOON 2015) in Beijing, China.
Sebastian will give a talk at the Science Pub in Jena
Sebastian will give a talk at the Science Pub in Jena: “Was ist Bioinformatik und kann man mit Dreck Krebs heilen?” The talk is Mon April 13, 2015 at 20:oo, Cafe Wagner.
Meet Kai at RECOMB in Warsaw
Kai will give a talk at the 19th Annual International Conference on Research in Computational Molecular Biology in Warsaw, Poland.