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# Lehrstuhl Bioinformatik Jena

Friedrich-Schiller-Universität Jena, Fakultät für Mathematik und Informatik

## Sitemaps

- [XML Sitemap](https://bio.informatik.uni-jena.de/sitemap.xml): Contains all public & indexable URLs for this website.

## Posts

- [News](https://bio.informatik.uni-jena.de/news/)
- [Back from ASMS 2023](https://bio.informatik.uni-jena.de/2023/06/back-from-asms-2023/) - Markus, Martin and Marcus have been at ASMS 2023 in Houston, USA. Thanks everyone for the great discussions at our poster.
- [Meet Leopold at the NII Shonan Meeting and the International Conference on Machine Learning 2026](https://bio.informatik.uni-jena.de/2026/06/meet-leopold-at-the-nii-shonan-meeting-and-the-international-conference-on-machine-learning-2026/) - Leopold will be at the NII Shonan Meeting at the Shonan Village Center in Japan from June 29 to July 2, and at the International Conference on Machine Learning (ICML) 2026 in Seoul, South Korea, from July 6 to July 11. Come by, have a chat, and talk some science! 🔬
- [Our PySirius protocol for untargeted metabolomics is now available in STAR Protocols](https://bio.informatik.uni-jena.de/2026/08/our-pysirius-protocol-for-untargeted-metabolomics-is-now-available-in-star-protocols/) - We are happy to announce that our paper “Protocol for untargeted LC-MS/MS metabolomics annotation and differential abundance analysis using the SIRIUS Python client” is now available in STAR Protocols. Untargeted LC-MS/MS metabolomics workflows often involve several tools and intermediate files, making complete analyses difficult to reproduce. In our new protocol, we demonstrate how to carry
- [FragTree Viewer, our interface for fragmentation trees visualization, is now available as a web service!](https://bio.informatik.uni-jena.de/2026/08/fragtree-viewer-our-interface-for-fragmentation-trees-visualization-is-now-available-as-a-web-service/) - Try out here: https://tree-viewer.boeckerlab.uni-jena.de
- [Fleming successfully defended his thesis on “Transferable Liquid Chromatography Retention Time Prediction” on Thursday, June 18!](https://bio.informatik.uni-jena.de/2026/06/fleming-successfully-defended-his-thesis-on-transferable-liquid-chromatography-retention-time-prediction-on-thursday-june-18/) - Congratulations Fleming!
- [How many small molecules could be out there?](https://bio.informatik.uni-jena.de/2025/06/how-many-small-molecules-could-be-out-there/) - Every (put a large number here) days I stumble over the question, "how large is the universe of small molecules?" in a publication or a blog. Not the number of small molecules that we already "know" - those are covered in databases such as HMDB, PubChem or ZINC. (Although many compounds in PubChem etc. are
- [2-step, our method for transferable retention time prediction, is now available as a web service!](https://bio.informatik.uni-jena.de/2026/06/2-step-our-method-for-transferable-retention-time-prediction-is-now-available-as-a-web-service/) - Try out here: 2-step.boeckerlab.uni-jena.deMore about the method: bio.informatik.uni-jena.de/software/2-step/
- [Meet Nils and Andrés at Metabolomics 2026 in Buenos Aires](https://bio.informatik.uni-jena.de/2026/06/meet-nils-and-andres-at-metabolomics-2026-in-buenos-aires/) - Nils and Andrés will be at the Metabolomics Conference in Buenos Aires, Argentina. Come have a chat and talk some science!
- [Meet Sebastian at the SMAP conference in Lille](https://bio.informatik.uni-jena.de/2024/09/meet-sebastian-at-the-smap-conference-in-lille/) - Sebastian will give a plenary talk at the conference on Mass Spectrometry and Proteomic Analysis (SMAP), which will be held from September 16 to 19, 2024.
- [We co-author a paper at ISMB](https://bio.informatik.uni-jena.de/2014/05/we-co-author-a-paper-at-ismb/) - Our joint paper with Huibin Shen and Juho Rousu (Aalto University, Helsinki, Finland), "Metabolite Identification through Multiple Kernel Learning on Fragmentation Trees", will be presented by Huibin at the Intelligent Systems for Molecular Biology (ISMB 2014) conference in Boston.
- [We will present a paper at RECOMB 2015](https://bio.informatik.uni-jena.de/2015/01/we-will-present-a-paper-at-recomb-2015/) - Our paper "Fragmentation Trees reloaded" will be presented at the Research in Computational Biology (RECOMB 2015) conference in Warsaw, Poland.
- [Meet us at ISMB/ECCB in Berlin](https://bio.informatik.uni-jena.de/2013/07/meet-us-at-ismbeccb-in-berlin/) - Martin, Markus, Franziska, Purva and Kai will attend 21st Annual International Conference on Systems and Molecular Biology in Berlin. We will present three posters (B21, K07, and O064).
- [Meet us at ISMB 2012](https://bio.informatik.uni-jena.de/2012/07/meet-us-at-ismb-2012/) - Franziska, Kerstin, and Sebastian will attend the Intelligent Systems for Molecular Biology (ISMB 2012) conference in Long Beach, California (July 15-17, 2012). Franziska will present a regular paper, Kerstin will present a poster, and Sebastian will present a highlight paper.
- [We will present a paper at ISMB 2012](https://bio.informatik.uni-jena.de/2012/03/we-will-present-a-paper-at-ismb-2012/) - We will present a paper on "Fast alignment of fragmentation trees" at the Intelligent Systems for Molecular Biology (ISMB 2012) conference in Long Beach, California. Acceptance rate has been only 13% this year, so we are thrilled.
- [Highlights paper at ISMB 2012](https://bio.informatik.uni-jena.de/2012/04/highlights-paper-at-ismb-2012/) - We will present a highlights paper on “Identifying the unknowns by aligning fragmentation trees” (Anal. Chem., 2012, in press, doi:10.1021/ac300304u) at the Intelligent Systems for Molecular Biology (ISMB 2012) conference in Long Beach, California. I already mentioned that we are thrilled...
- [Sebastian is now a Humboldt fellow](https://bio.informatik.uni-jena.de/2010/12/sebastian-is-now-a-humboldt-fellow/) - The Alexander von Humboldt Foundation maintains a network of more than 24,000 Humboldtians from all disciplines in over 130 countries worldwide.
- [Workshop "Introduction to mass spectrometry techniques and analysis" at MPI-CE](https://bio.informatik.uni-jena.de/2026/04/workshop-introduction-to-mass-spectrometry-techniques-and-analysis-at-mpi-ce/) - We are part of the second iteration of the Introduction to mass spectrometry techniques and analysis workshop from 4th to 5th of June - hosted by and in the Max Planck Institute for Chemical Ecology! This three-part workshop includes a basic introduction to MS principles and instrumentation, Preprocessing with MZmine as well as Feature annotation
- [PhD and postdoc positions within the ERC project BindingShadows are still open](https://bio.informatik.uni-jena.de/2025/11/phd-and-postdoc-positions-within-the-erc-project-bindingshadows-are-still-open/) - Update: This posting is now closed. Thank you for your interest. A quick reminder: The PhD and postdoc positions within the ERC project BindingShadows are still open! We’ve just moved into a brand-new building, and during the transition our servers and website were occasionally down, meaning we might not have received some applications. So once
- [Meet us at Mittelerde 2026 in Halle](https://bio.informatik.uni-jena.de/2026/03/meet-us-at-mittelerde-2026-in-halle/) - We are at the 7th Central German Meeting on Bioinformatics (also known as Mittelerde) in Halle from 26/03/2026 to 27/03/2026! Sebastian will hold a keynote about small molecule machine learning. Fleming will talk about retention time prediction. Nils, Andres, Leopold and Jonas will have posters to come and look at during the poster session.
- [Small server downtimes at the 24th and 25th](https://bio.informatik.uni-jena.de/2025/11/small-server-downtimes-at-the-24th-and-25th/) - On the 24th and 25th of November 2025, our website and our Mattermost instance will be unavailable for multiple hours. Estimated downtimes are: Mo, 24. November: 13-17 Tue, 25. November: 15-19
- [Our barcode-free screening platform for early drug discovery appeared in Nature Communications](https://bio.informatik.uni-jena.de/2025/11/our-barcode-free-screening-platform-for-early-drug-discovery-appeared-in-nature-communications/) - Our paper "Barcode-free hit discovery from massive libraries enabled by automated small molecule structure annotation" has finally been published in Nature Communications. This first publication from our joint project with Sebastian Pomplun (Leiden University and Oncode Institute) presents a barcode-free self-encoded library (SEL) platform that enables the screening of over half a million small molecules
- [We finally moved!](https://bio.informatik.uni-jena.de/2025/11/we-finally-moved/) - We moved! After several weeks of home office, we finally moved into our brand-new building!Apologies for the occasional downtime of our servers and website over the past two months. Everything is back up and should run smoothly from now on!
- [Website and Mattermost will be down again on 20th and 21st](https://bio.informatik.uni-jena.de/2025/10/website-and-mattermost-will-be-down-again-on-20th-and-21st/) - On the 20th and 21st of October 2025, our website and our Mattermost instance will not be available. This is due to stress testing of the compute infrastructure at our new building. The SIRIUS services like CSI:FingerID will stay up and running. We hope to be back at full operation on Wednesday and should stay
- [We are back](https://bio.informatik.uni-jena.de/2025/10/we-are-back/) - After three weeks, our web server (and many other things) are back online. We made sure that CSI:FingerID etc are up and running, but somehow forgot that there is more than that. Sorry in case this caused any troubles.
- [PhD and postdoc positions as part of the ERC project BindingShadows](https://bio.informatik.uni-jena.de/2025/09/phd-and-postdoc-positions-as-part-of-the-erc-project-bindingshadows/) - The official site is up! So, if you are skilled in bioinformatics and/or machine learning and want to work on mind-boggling new computational methods for analyzing small molecule mass spec data, please apply! The project is running for 5 years, there are 2 postdoc and 2 PhD positions, minimum. We are right now moving into
- [Why we do not use metascores](https://bio.informatik.uni-jena.de/2022/02/why-we-do-not-use-metascores/) - ...and why you should also be very careful when doing so Hi all, I (Sebastian) have recorded a talk about metascores which is now available from our YouTube channel at https://www.youtube.com/watch?v=mkfG6-ZqD0s. With "metascores", I mean scores that are not based on the actual data (or metadata!) but rather on side information such as citation counts
- [MAD HATTER correctly annotates 98% of small molecule MS/MS searching in PubChem](https://bio.informatik.uni-jena.de/2022/12/mad-hatter-correctly-annotates-98-of-small-molecule-ms-ms-searching-in-pubchem/) - We are thrilled to announce that our newest tool MAD HATTER can correctly annotate 98% of small molecule tandem mass spectra, when searching in PubChem! We are extremely excited about this massive breakthrough! MAD HATTER combines CSI:FingerID results with information from the searched structure database via a metascore, using viable compound information such as the
- [Visualizing the universe of small biomolecules](https://bio.informatik.uni-jena.de/2023/07/visualizing-the-universe-of-small-biomolecules/) - Have you ever wanted to look at the universe of biomolecules (small molecules of biological interest, including metabolites and toxins)? Have you ever wondered how your own dataset fits into this universe? In our preprint, we introduce a method to do just that, using MCES distances to create a UMAP visualization. Onto this visualization, any
- [Bioinformatische Methoden in der Genomforschung im WiSe 25/26](https://bio.informatik.uni-jena.de/2025/08/bioinformatische-methoden-in-der-genomforschung-im-wise-25-26/) - Im kommenden Wintersemester 2025/2026 wird wieder das Modul Bioinformatische Methoden in der Genomforschung angeboten. Im Sommersemester 2026 wird dann wieder das Modul Sequenzanalyse zu hören sein.
- [Retention time prediction is dead, long live retention order index prediction!](https://bio.informatik.uni-jena.de/2025/08/retention-time-prediction-is-dead-long-live-retention-order-index-prediction/) - We just solved a problem that I never wanted to solve: That is, transferable retention time prediction of small molecules. They say that the best king is someone who does not want to be king; so maybe, the best problem solver is someone who does not want to solve the problem? Not sure about that.
- [One billion queries served](https://bio.informatik.uni-jena.de/2025/07/one-billion-queries-served/) - Now, that number deserves a celebration: Our web services have served a billion queries! In detail, the CSI:FingerID web service processed 759 million queries, the CANOPUS web service 228 million, and MSNovelist has 17 million queries. During the last 12 months, 3816 users have processed their data using our web services. Excellent! Remember when Gangnam Style
- [Sebastian will receive an ERC advanced grant](https://bio.informatik.uni-jena.de/2025/07/sebastian-will-receive-an-erc-advanced-grant/) - Excellent news: Sebastian will receive an ERC Advanced Grant from the European Research Council! In the project BindingShadows, we will develop machine learning models that predict whether some query molecule has a particular bioactivity (say, toxicity) or is binding to a certain protein, where the only information we have about the query molecule is its
- [SIRIUS 6.1.0 is Here!](https://bio.informatik.uni-jena.de/2025/01/sirius-6-1-0-is-here/) - We’re excited to announce the latest version of SIRIUS designed to improve your small molecule analysis workflow with a refreshed interface, streamlined processes, and several important fixes that ensure smoother performance and better data handling. Highlights: ? New Color Scheme: A consistent and intuitive look throughout the entire identification process.⚡ Streamlined Workflows: Tools are now
- [Meet Markus and Jonas at the 4th International Summer School in Non-Targeted Metabolomics Data Mining](https://bio.informatik.uni-jena.de/2025/07/meet-markus-and-jonas-at-the-4th-international-summer-school-in-non-targeted-metabolomics-data-mining-for-exposomics-and-natural-products-research/) - Markus and Jonas will contribute to the summer school with a workshop about SIRIUS. For all interested, it takes place 18. to 22. August 2025 in Copenhagen, Denmark. We hope to meet many of you there!
- [Bad Clade Deletion supertrees -- swift and accurate, but project has ended](https://bio.informatik.uni-jena.de/2018/06/bad-clade-deletion-supertrees-swift-and-accurate-but-project-has-ended/) - With the publication of the beam search variant of BCD supertrees (Fleischauer and Böcker, PeerJ 2018), this project has come to an end. BCD supertrees shows an outstanding performance for a supertree method with guaranteed polynomial running time, and is usually on par or even better than established supertree methods such as MRP or SuperFine.
- [How good is the new SIRIUS? (update)](https://bio.informatik.uni-jena.de/2018/02/how-good-is-the-new-sirius/) - With the release of the new SIRIUS version (and, behind the scenes, a new version of CSI:FingerID), we want to share some numbers so you know if it was worth the hassle. We use CASMI 2016 data, to allow you to compare our results against those of other methods. We use the candidate structures provided
- [CASMI 2017 results are out](https://bio.informatik.uni-jena.de/2017/11/casmi-2017-results-are-out/) - CASMI (Critical Assessment of Small Molecule Identification) 2017 results are finally out! Kai participated with SIRIUS/CSI:FingerID, and won categories 1 (Best Structure Identification on Natural Products), 2 (Best Automatic Structural Identification - In Silico Fragmentation Only), and 4 (Best Automatic Candidate Ranking). He did not participate in category 3. For category 4 (in silico methods
- [GCB 2012 in Jena](https://bio.informatik.uni-jena.de/2011/11/gcb-2012-in-jena/) - The German Conference on Bioinformatics is coming to Jena in September 2012.
- [GCB 2012 in Jena will start shortly!](https://bio.informatik.uni-jena.de/2012/09/gcb-2012-in-jena-will-start-shortly/) - Hope to see you all in Jena at the GCB 2012, September 19-22, 2012! The conference features six international invited speakers, about 20 regular and highlight presentations, almost 100 posters and already more than 200 registered attendees. So come and join us for a wonderful conference!
- [Analysing tandem mass spectra of metabolites on SIRIUS: First fragmentation trees planted!](https://bio.informatik.uni-jena.de/2009/07/analysing-tandem-mass-spectra-of-metabolites-on-sirius-first-fragmentation-trees-planted/) - Version 0.7 of SIRIUS is shipped with completely new starburst functionality for de-novo identification of molecular formulas using Tandem MS data. SIRIUS downloads are available here.
- [EPoS 0.8 released!](https://bio.informatik.uni-jena.de/2008/07/epos-0-8-released/) - We released the new version of EPoS,our modular software framework for phylogenetic analysis and visualization. Downloads are available here.
- [False Discovery Rates for metabolite annotation: Why accurate estimation is impossible, and why this should not stop us from trying](https://bio.informatik.uni-jena.de/2024/07/false-discovery-rates-for-metabolite-annotation/) - I recently gave a talk at the conference of the Metabolomics society. After the talk, Oliver Fiehn asked, "when will we finally have FDR estimation in metabolite annotation?" This is a good question: False Discovery Rates (FDR) and FDR estimation have been tremendously helpful in genomics, transcriptomics and proteomics. In particular, FDRs have been extremely
- [Yet another blog](https://bio.informatik.uni-jena.de/2025/05/yet-another-blog/) - Hi all, I thought I put my blog post (singular) into its own category. Not sure about the title, that may change. Why another blog when there is already this great blog on metabolomics and mass spectrometry? Because here I may talk about computational stuff as well, such as failed evaluations of machine learning methods
- [Algorithmische Phylogenetik statt Sequenzanalyse im SoSe 2025](https://bio.informatik.uni-jena.de/2025/03/algorithmische-phylogenetik-statt-sequenzanalyse-im-sose-2025/) - Im kommenden Semester wird statt Sequenzanalyse das Modul Algorithmische Phylogenetik angeboten. Sequenzanalyse wird dann wieder im SoSe 2026 zu hören sein.
- [Times are changing but order matters](https://bio.informatik.uni-jena.de/2024/12/times-are-changing-but-order-matters/) - Our preprint Times are changing but order matters: Transferable prediction of small molecule liquid chromatography retention times is finally available on chemRxiv! Congratulations to Fleming and all authors. In short, we show that prediction of retention times is a somewhat ill-posed problem, as retention times vary substantially even for nominally identical condition. Next, we show
- [Meet Jonas at the IMPRS course on mass spectrometry in the MPI for Chemical Ecology](https://bio.informatik.uni-jena.de/2024/11/meet-jonas-at-the-imprs-course-on-mass-spectrometry-in-the-mpi-for-chemical-ecology/) - Jonas will give a lecture on SIRIUS at the IMPRS course "Introduction to mass spectrometry techniques and analysis" (2-4 December) in the Max Planck Institute for Chemical Ecology.
- [Chair is awarded Thuringian Research Prize 2022 for applied research](https://bio.informatik.uni-jena.de/2022/04/chair-is-awarded-thuringian-research-prize-2022-for-applied-research/) - Today (06 April), Prof. Sebastian Böcker, Dr. Kai Dührkop, Dr. Markus Fleischauer, Dr. Marcus Ludwig and Martin Hoffmann were awarded the Thuringian Research Prize 2022 for applied research. This was announced by Thuringia’s Science Minister Wolfgang Tiefensee in a video presentation. The price recognizes the development of machine learning methods for identifying small molecules, including
- [meet Sebastian at the de.NBI Summer School 2016](https://bio.informatik.uni-jena.de/2016/08/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).
- [Meet Sebastian at APRS in Salzburg](https://bio.informatik.uni-jena.de/2014/07/meet-sebastian-at-aprs-in-salzburg/) - Sebastian will give a plenary talk at the Austrian Proteomic Research Symposium (September 22-24, 2014) in Salzburg. Title of the talk is "Elementary, my dear Watson: Fingerprint search in molecular structure databases".
- [Meet Sebastian at Trends in Metabolomics in Frankfurt](https://bio.informatik.uni-jena.de/2014/06/meet-sebastian-at-trends-in-metabolomics-in-franfurt/) - Sebastian will give a talk at the Dechema meeting "Trends in Metabolomics" in Frankfurt, June 4-5, 2014. Title of the talk is "Searching PubChem with MS2 data: Teaming fragmentation trees and molecular fingerprint prediction".
- [Special issue on Computational Mass Spectrometry](https://bio.informatik.uni-jena.de/2011/03/special-issue-on-computational-mass-spectrometry/) - Advances in Bioinformatics has an open call for papers for its special issue on Computational Mass Spectrometry. See here for the pdf version.
- [Introducing COSMIC to assign confidence to annotations](https://bio.informatik.uni-jena.de/2021/03/introducing-cosmic-to-assign-confidence-to-annotations/) - We are happy to introduce COSMIC, a tool for that allows you to assign confidence to structure annotations. For every structure annotated by CSI:FingerID, COSMIC provides a confidence score (a number between 0 and 1) that tells you how likely it is that this annotation is correct. This is similar in spirit to what is
- [Meet us at GCB 2024 in Bielefeld](https://bio.informatik.uni-jena.de/2024/09/meet-us-at-gcb-2024-in-bielefeld/) - At GCB 2024 (30th Sep. - 2nd Oct.), Fleming will give a presentation about RepoRT. Jonas, Leopold and Roberto will show their posters in the poster session.
- [Meet Sebastian at the SETAC Asia-Pacific Biennial Meeting in Tianjin](https://bio.informatik.uni-jena.de/2024/09/meet-sebastian-at-the-setac-asia-pacific-biennial-meeting-in-tianjin/) - Sebastian will give a plenary talk at the SETAC Asia-Pacific 14th Biennial Meeting (September 21 to 25, 2024).
- [New Web-App for RepoRT](https://bio.informatik.uni-jena.de/2024/08/new-web-app-for-report/) - To make the submission process to RepoRT easier, we have launched a web app, available under https://rrt.boeckerlab.uni-jena.de. Submitters can upload their data without having to adhere to specific formatting requirements. Metadata and gradient information can be entered directly online. Part of the data validation happens during the uploading process, providing immediate feedback when something is
- [Meet Sebastian at IWOCA 2011](https://bio.informatik.uni-jena.de/2011/07/meet-sebastian-at-iwoca-2011/) - Sebastian will present a paper at the International Workshop on Combinatorial Algorithms in Victoria, Canada, June 20-22, 2011.
- [Meet Markus at the ASMS conference in Anaheim](https://bio.informatik.uni-jena.de/2024/05/meet-markus-at-the-asms-conference-in-california/) - Meet Markus at the ASMS conference 2024 in Anaheim between June 2-6!
- [Meet Sebastian, Kai and Fleming at the Metabolomics conference in Osaka](https://bio.informatik.uni-jena.de/2024/06/meet-sebastian-kai-and-fleming-at-the-osaka-metabolomics/) - At the Metabolomics 2024 (16-20 June), Sebastian will give a keynote presentation. Kai and Fleming will hold a workshop on SIRIUS 6.
- [Meet Jonas at the Computational Metabolomics Workshop in Aberdeen](https://bio.informatik.uni-jena.de/2024/06/meet-jonas-at-computational-metabolomics-workshop-in-aberdeen/) - At the Computational Mass Spectrometry Workshop (19-21 June 2024), Jonas will hold a presentation on SIRIUS 6.
- [Meet Sebastian at the Okinawa Workshop for Computational Mass Spectrometry](https://bio.informatik.uni-jena.de/2024/06/meet-sebastian-at-the-okinawa-workshop-for-computational-mass-spectrometry/) - On June 24, Sebastian will give a presentation on SIRIUS 6 at the Okinawa Workshop for Computational Mass Spectrometry.
- [Meet Andrés and Nils at the European School of Metabolomics in Granada](https://bio.informatik.uni-jena.de/2024/04/meet-andres-and-nils-at-the-european-school-of-metabolomics-in-granada/) - Meet us at the EUSM 2024 in Granada! Nils will give a hands-on session on SIRIUS.
- [Prague workshop will be streamed](https://bio.informatik.uni-jena.de/2024/04/prague-workshop-will-be-streamed/) - Good news for those who want to attend the Prague workshop but were not admitted: The Prague workshop on computational mass spectrometry will be streamed, see here. You should get the necessary software installed beforehand if you want to join in.
- [IMPRS call for PhD student](https://bio.informatik.uni-jena.de/2024/03/imprs-call-for-phd-student/) - The International Max Planck Research School at the Max Planck Institute for Chemical Ecology in Jena is looking for PhD students. One of the projects (Project 7) is from our group on "rethinking molecular networks". Application deadline is April 19, 2024. Mass spectrometry (MS) is the analytical platforms of choice for high-throughput screening of small
- [Prague workshop on computational MS overbooked](https://bio.informatik.uni-jena.de/2024/02/prague-workshop-on-computational-ms-overbooked/) - Unfortunately, the Prague Workshop on Computational Mass Spectrometry (April 15-17, 2024) is heavily overbooked. The organizers will try to stream the workshop and the recorded sessions will be made available online, so check there regularly. The workshop is organized by Tomáš Pluskal and Robin Schmid (IOCB Prague). Marcus Ludwig (Bright Giant) and Sebastian will give
- [Meet Sebastian at the DGMS conference in Freising](https://bio.informatik.uni-jena.de/2024/02/meet-sebastian-at-the-dgms-conference-in-freising/) - Meet Sebastian at the conference of the Deutsche Gesellschaft für Massenspektrometrie (DGMS 2024) in Freising! The conference is March 10-13, and Sebastian will give a keynote talk on Tuesday, March 12. BTW, another keynote will be given by our close collaboration partner Michael Witting, also on March 12.
- [RepoRT has appeared in Nature Methods](https://bio.informatik.uni-jena.de/2024/01/report-has-appeared-in-nature-methods/) - Our paper "RepoRT: a comprehensive repository for small molecule retention times" has just appeared in Nature Methods. This is joint work with Michael Witting (Helmholtz Zentrum München) as part of the DFG project "Transferable retention time prediction for Liquid Chromatography-Mass Spectrometry-based metabolomics". Congrats to Fleming, Michael and all co-authors! In case you do not have
- [HUMAN EU PhD position is still open](https://bio.informatik.uni-jena.de/2023/09/human-eu-phd-position-is-still-open/) - Unfortunately, we have not been able to fill the PhD position for the HUMAN EU project so far. In case you are interested, please contact us! Update: The position has been filled.
- [Bioinformatische Methoden in der Genomforschung muss leider ausfallen](https://bio.informatik.uni-jena.de/2023/09/bioinformatische-methoden-in-der-genomforschung-muss-leider-ausfallen/) - Nach aktuellem Kenntnisstand muss das Modul "Bioinformatische Methoden in der Genomforschung" im WS 23/24 leider ausfallen. Wir dürfen die Mitarbeiterstelle nicht besetzen, die wir dafür zwingend brauchen. Wir haben gekämpft und argumentiert und alles getan was wir konnten, aber am Ende war es leider vergeblich. Das Modul findet voraussichtlich das nächste Mal im WS 25/26
- [Neues Video zum Studium Bioinformatik](https://bio.informatik.uni-jena.de/2023/09/neues-video-zum-studium-bioinformatik/) - Im Rahmen des MINT Festivals in Jena hat Sebastian ein neues Video zum Studium der Bioinformatik aufgenommen: "Kleine Moleküle. Was uns tötet, was uns heilt". Es richtet sich vom Vorwissen her an Schüler aus der Oberstufe, aber vielleicht können auch Schüler aus den Jahrgangsstufen darunter etwas mitnehmen. Das Video ist erst mal nur über diese
- [Meet Sebastian (remotely) and Fleming at the Swedish TB meeting](https://bio.informatik.uni-jena.de/2023/08/meet-sebastian-remotely-and-fleming-at-the-swedish-tb-meeting/) - Sebastian and Fleming will participate in the Swedish National Tuberculosis meeting: Sebastian will give a talk remotely and Fleming will be on site in Umeå to give a hands-on session on SIRIUS.
- [Meet Sebastian at the Korean Metabolomics Society Meeting](https://bio.informatik.uni-jena.de/2023/03/meet-sebastian-at-the-korean-metabolomics-society-meeting/) - Meet Sebastian at the annual symposium of the Korean Metabolomics Society (April 5-7). Sebastian will give a keynote lecture on April 7.
- [Meet Nils, Wei, Fleming and Sebastian at GCB 2023](https://bio.informatik.uni-jena.de/2023/09/meet-nils-wei-fleming-and-sebastian-at-gcb-2023/) - Meet us at the GCB 2023 in Hamburg! Nils, Wei and Fleming are going to present posters, and Sebastian will give a keynote talk.
- [Meet Sebastian at the Munich Metabolomics Meeting](https://bio.informatik.uni-jena.de/2023/09/meet-sebastian-at-the-munich-metabolomics-meeting/) - Sebastian will give a tutorial on using SIRIUS and beyond at the Munich Metabolomics Meeting 2023.
- [Retention time repository preprint out now](https://bio.informatik.uni-jena.de/2023/07/retention-time-repository-preprint-out-now/) - The RepoRT (well, Repository for Retention Times, you guessed it) preprint is available now. It has been a massive undertaking to get to this point; honestly, we did not expect it to be this much work. It is about diverse reference compounds measured on different columns with different parameters and in different labs. At present,
- [Most wanted: Tanaka and HSM parameters for RP columns](https://bio.informatik.uni-jena.de/2023/04/most-wanted-tanaka-and-hsm-parameters-for-rp-columns/) - A few years ago, Michael Witting and I joined forces to get a transferable prediction of retention times going: That is, we want to predict retention times (more precisely, retention order) for a column even if we have no training data for that column. Yet, to describe a column to a machine learning model, you
- [MZmine 3 has appeared in Nature Biotechnology](https://bio.informatik.uni-jena.de/2023/03/mzmine-3-has-appeared-in-nature-biotechnology/) - Congratulations to Robin Schmid, Steffen Heuckeroth and Ansgar Korf: The article “Integrative analysis of multimodal mass spectrometry data in MZmine 3” has appeared in Nature Biotechnology, and we are very happy to be part of this research. I don't assume I have to explain what MZmine is. If you are doing small molecule LC-MS/MS, you
- [Project Harvester about to start](https://bio.informatik.uni-jena.de/2023/02/project-harvester-about-to-start/) - The Deutsche Forschungsgemeinschaft has provided us with funding for our project Harvester. The problem in many areas of small molecule machine learning is the available training data and how slowly more data become available. This is also true for MS/MS data, where doubling time is a decade or two, possibly more. To this end, a
- [PhD position for EU HUMAN doctoral network](https://bio.informatik.uni-jena.de/2022/12/phd-positions-for-eu-human-doctoral-networks/) - As part of the EU HUMAN doctoral network, my group is looking for a PhD student from bioinformatics, computer science or cheminformatics for the computational analysis of mass spectrometry data. The PhD student is expected to have experience with and interest in the development and evaluation of computational methods and machine learning models. The project
- [Martin has successfully defended his thesis on Monday](https://bio.informatik.uni-jena.de/2022/12/martin-has-successfully-defended-his-thesis-on-monday/) - Congratulations!
- [DFG project on retention time/order prediction granted](https://bio.informatik.uni-jena.de/2019/06/dfg-project-on-retention-time-order-prediction-granted/) - The Deutsche Forschungsgemeinschaft has granted a project on retention time and order prediction for liquid chromatography. This is a joint project with Michael Witting, Helmholtz Zentrum München. The idea of the project is to integrate retention times from liquid chromatography into the SIRIUS/CSI:FingerID identification pipeline. Literally hundreds of papers have been published on the topic
- [meet Sebastian at the OpenMS user meeting 2016](https://bio.informatik.uni-jena.de/2016/08/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.
- [SIRIUS 4 End Of Life](https://bio.informatik.uni-jena.de/2022/11/sirius-4-end-of-life/) - SIRIUS 4 will reach its end of life on 2022-12-31. Fingerprint prediction, structure db search and compound class prediction will not be possible anymore.
- [We are part of the EU HUMAN doctoral network](https://bio.informatik.uni-jena.de/2022/10/we-are-part-of-the-eu-human-doctoral-network/) - We are part of EU HUMAN (Harmonising and Unifying Blood Metabolomic Analysis Networks) doctoral network, and we will be searching for a PhD student shortly.
- [SIRIUS email account verification failed, what now?](https://bio.informatik.uni-jena.de/2022/07/sirius-email-account-verification-failed-what-now/) - Dear SIRIUS users, when creating a new SIRIUS account the link checkers of some email tools seem to execute the verification link before the user can click the link manually. In such cases the link will already be used (invalid) when the user is clicking it manually and the server returns an error message. In
- [IMPRS application call for PhD students](https://bio.informatik.uni-jena.de/2018/03/imprs-application-call-for-phd-students/) - The International Max Planck Research School at the MPI for Chemical Ecology in Jena is looking for PhD students, and one of the projects is on "making SIRIUS and CSI:FingerID GCMS-ready". Only a half position is being paid by the IMPRS, but this can be supplemented by funding from our chair. We are searching for
- [Kai received FaBI prize for best PhD thesis in bioinformatics](https://bio.informatik.uni-jena.de/2019/09/kai-received-fabi-prize-for-best-phd-thesis-in-bioinformatics/) - At the German Conference on Bioinformatics 2019 in Heidelberg, Kai was awarded the prize for best PhD thesis in bioinformatics by the Fachgruppe Bioinformatik. Congratulations!!!
- [MSNovelist has appeared in Nature Methods](https://bio.informatik.uni-jena.de/2022/05/msnovelist-has-appeared-in-nature-methods/) - Congratulations to Michael "Michele" Stravs from the group of Nicola Zamboni at ETH Zürich: The article “MSNovelist: De novo structure generation from mass spectra” has appeared in Nature Methods, and we are thrilled to be part of this research. In short, MSNovelist is a computational method that transforms the tandem mass spectrum of a small
- [SIRIUS 5 is released!](https://bio.informatik.uni-jena.de/2022/05/sirius-5-is-released/) - We are happy to announce that a major version upgrade of SIRIUS is available! Scroll to the bottom to get a visual impression of the changes. SIRIUS 5 now includes the following new features and improvements: Lipid class annotation with El Gordo: Lipid structures that have the same molecular formula (usually belonging to the same lipid
- [CSI:FingerID successfully applied to dAPCI GC-MS data](https://bio.informatik.uni-jena.de/2018/06/csifingerid-successfully-applied-to-dapci-gc-ms-data/) - Larson et al. (J. Am. Soc. Mass Spectrom., 2018) have applied CSI:FingerID to dopant-assisted atmospheric pressure chemical ionization (dAPCI) gas chromatography mass spectrometry (GC-MS) data. They identified almost three times as many compounds with SIRIUS and CSI:FingerID as when searching in the NIST spectral library. Find their study here.
- [SIRIUS 4.0.1 released](https://bio.informatik.uni-jena.de/2018/09/sirius-4-0-1-released/) - 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 .
- [We have published a paper in PNAS](https://bio.informatik.uni-jena.de/2015/09/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
- [COSMIC has appeared in Nature Biotechnology](https://bio.informatik.uni-jena.de/2021/10/cosmic-has-appeared-in-nature-biotechnology/) - Our article "High-confidence structural annotation of metabolites absent from spectral libraries" has just appeared in Nature Biotechnology. Congrats to Martin and all co-authors! In short, COSMIC allows you to assign confidence to structure annotations. For every structure annotated by CSI:FingerID, COSMIC provides a confidence score (a number between 0 and 1) that tells you how
- [SIRIUS 4.5 released](https://bio.informatik.uni-jena.de/2020/11/sirius-4-5-released/) - We are happy to announce that a new version of SIRIUS is available. With that, CANOPUS now supports negative ion mode data. Additionally, we included more structure databases CSI:FingerID can search in, such as COCONUT (Sorokina & Steinbeck, 2020) and NORMAN (Brack et al., 2012). And in case an important database is missing: With the
- [Tag der Forschung: Die Digitale Gesellschaft](https://bio.informatik.uni-jena.de/2014/06/tag-der-forschung-die-digitale-gesellschaft/) - Am Mittwoch 11. Juni 2014 von 14 bis 21 Uhr findet im Foyer der Carl-Zeiss-Straße 3 sowie den angrenzenden Hörsälen der diesjährige Tag der Forschung zum Thema "Die Digitale Gesellschaft" statt. Gezeigt werden unter anderem Elektrofahrzeuge, Quadrocopter, 3D-Drucker sowie Demos aus den Bereichen Computer Vision und Biodiversität. Die Bioinformatik wird dort ebenfalls vertreten sein. Mehr
- [Meet Sebastian at Metabolomics 2015](https://bio.informatik.uni-jena.de/2015/06/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.
- [CANOPUS behind the scenes talk](https://bio.informatik.uni-jena.de/2021/07/canopus-behind-the-scenes-talk/) - A "behind the scenes" talk for CANOPUS and compound class prediction is now available from our YouTube channel. As usual, this is not a talk which demonstrates how to use our software; rather, this talk explains what design decisions went into CANOPUS, why we did things this way and not that way, what performance you
- [Call for Tutorials: SIRIUS and CSI:FingerID](https://bio.informatik.uni-jena.de/2017/12/call-for-tutorials-sirius-and-csifingerid/) - During the Dagstuhl seminar on Computational Metabolomics a few days ago, there was a session on "bridging the gap" between methods developers and experimentalists, which resulted in a long list of what method developers should do to bridge the gap (develop GUIs, provide example data, manuals, tutorials, etc) but rather little that experimentalists can do.
- [Happy 25 million queries, CANOPUS!](https://bio.informatik.uni-jena.de/2021/06/happy-25-million-queries-canopus/) - We are fully aware that this post is far less interesting to you than it is to us; but sometimes, proud parents just have to do what proud parents have to do: CANOPUS has passed 25 million queries! Congratulations! Wow, that was fast, the preprint appeared on bioRxiv only 14 months ago. In this context,
- [COSMIC now available!](https://bio.informatik.uni-jena.de/2021/04/cosmic-now-available/) - SIRIUS 4.8.0 is out and releases the COSMIC confidence score to the wild. For more details on COSMIC see here.
- [SIRIUS 4.0.1 End Of Life](https://bio.informatik.uni-jena.de/2021/04/sirius-4-0-1-end-of-life/) - 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 4.7.0 Released](https://bio.informatik.uni-jena.de/2021/03/sirius-4-7-0-released/) - 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
- [Lehre im Wintersemester 2020/21](https://bio.informatik.uni-jena.de/2020/10/lehre-im-wintersemester-2020-21/) - Auch im Wintersemester hat uns Corona noch im Griff; deshalb werden die meisten Lehrveranstaltungen online erfolgen. Hier ein paar Details, was Sie erwartet (Achtung, diese news ist eine sticky note; wir werden sie aktualisieren, wenn es weitere Informationen gibt): NEU: Das Seminar Beruf und Karriere (ASQ) findet als Blockveranstaltung in der Woche vom 22. bis
- [Video Behind the Scenes: CSI:FingerID](https://bio.informatik.uni-jena.de/2020/12/video-behind-the-scenes-csifingerid/) - There is a new video available and it is finally explaining CSI:FingerID in much detail -- possibly too much detail, the video is more than 2 hours. Covers everything from general thoughts and considerations about in silico methods and methods evaluation, to the details of molecular fingerprints, FingerID and, finally, CSI:FingerID. I am sorry for
- [SIRIUS online documentation now available!](https://bio.informatik.uni-jena.de/2020/12/sirius-online-documentation-now-available/) - 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
- [Video tutorials for SIRIUS and beyond](https://bio.informatik.uni-jena.de/2020/12/video-tutorials-for-sirius-and-beyond/) - We have started to collect video tutorials that explain how to use our software (thanks to Martin) or that allow you to look behind the scenes. We will continue to add videos, so check for updates.
- [Studieninformationsseite für Schüler](https://bio.informatik.uni-jena.de/2014/04/studieninformationsseite-fur-schuler/) - Unter http://www.uni-jena.de/bioinformatik finden sich Informationen zum Studium der Bioinformatik in Jena. Alle Studieninteressierten mögen dort vorbei schauen!
- [Classes for the masses: CANOPUS has appeared in Nature Biotechnology](https://bio.informatik.uni-jena.de/2020/11/classes-for-the-masses-canopus-has-appeared-in-nature-biotechnology/) - Our article "Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra" has just appeared in Nature Biotechnology. Congrats to Kai and all co-authors! In short: CANOPUS is a computational tool for systematic compound class annotation. It uses a deep neural network to predict 2,497 compound classes from fragmentation spectra, including all biologically relevant classes.
- [ZODIAC has appeared in Nature Machine Intelligence](https://bio.informatik.uni-jena.de/2020/10/zodiac-has-appeared-in-nature-machine-intelligence/) - Our article "Database-independent molecular formula annotation using Gibbs sampling through ZODIAC" has just appeared in Nature Machine Intelligence. Congrats to Marcus and all co-authors! In short: Annotating the molecular formula of a small molecule is the first step towards its structural elucidation but remains highly challenging, particularly for "large compounds" above 500 Daltons. ZODIAC is
- [Qemistree has appeared in Nature Chemical Biology](https://bio.informatik.uni-jena.de/2020/11/qemistree-has-appeared-in-nature-chemical-biology/) - Congratulations to Anupriya Tripathi from the group of Pieter Dorrestein: The article “Chemically informed analyses of metabolomics mass spectrometry data with Qemistree” has appeared in Nature Chemical Biology, and we are happy to be part of this research. In short, Qemistree is a data exploration strategy based on the hierarchical organization of molecular fingerprints predicted
- [Feature-Based Molecular Networking appeared in Nature Methods](https://bio.informatik.uni-jena.de/2020/09/feature-based-molecular-networking-appeared-in-nature-methods/) - Congratulations to Louis-Félix Nothias from the group of Pieter Dorrestein: The article "Feature-based molecular networking in the GNPS analysis environment" has appeared in Nature Methods, and we are happy to be part of this research. (We are lacking behind a little bit with our news.) In short, FBMN introduces chromatography separation into the molecular networking
- [Meet Sebastian at Metabolomics 2014](https://bio.informatik.uni-jena.de/2014/05/meet-sebastian-at-metabolomics-2014/) - Sebastian will give a talk at the Metabolomics 2014 meeting in Tsuruoka, Japan.
- [Marcus has successfully defended his thesis last Tuesday](https://bio.informatik.uni-jena.de/2020/07/marcus-has-successfully-defended-his-thesis-last-tuesday/) - Congratulations!
- [SIRIUS 4.4 is coming soon!](https://bio.informatik.uni-jena.de/2020/01/sirius-4-4-is-coming-soon/) - We are excited to announce that SIRIUS 4.4 is coming soon and provide you an early access version of the SIRIUS 4.4 command line tool for testing.
- [SIRIUS 4.4.21 - Can now be used along with 4.0.1](https://bio.informatik.uni-jena.de/2020/05/sirius-4-4-21-can-now-be-used-along-with-4-0-1/) - 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
- [SIRIUS 4.4 GUI for MacOS X now available](https://bio.informatik.uni-jena.de/2020/05/sirius-gui-for-macos-x-now-available/) - 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/
- [SIRIUS 4.4 released](https://bio.informatik.uni-jena.de/2020/04/sirius-4-4-released/) - We are happy to announce that SIRIUS 4.4 is finally released. (Unfortunately, the MacOS version will have to wait a few more days.) There have been numerous changes and improvements, only few of which can be mentioned here. Probably the biggest change is that SIRIUS 4.4 now reads mzML files (“centroided” data) and processes complete
- [SIRIUS 4.4 beta released](https://bio.informatik.uni-jena.de/2020/04/sirius-4-4-beta-released/) - Some of you may have noticed that yesterday, April 17, the SIRIUS 4.4 beta has been released. This update is huge so we are particularly careful not to break too many things. (We will definitely break some things so please report bugs using the SIRIUS GitHub repository or sirius@uni-jena.de.) Some facts of what you can
- [Introducing CANOPUS for comprehensive compound class annotation](https://bio.informatik.uni-jena.de/2020/04/introducing-canopus-for-comprehensive-compound-class-annotation/) - We are happy to introduce CANOPUS, a tool for the comprehensive annotation of compound classes from MS/MS data (certain restrictions apply, see below). In principle, CANOPUS is doing something similar as CSI:FingerID: Whereas CSI:FingerID can tell you what substructures are part of the query compound, CANOPUS does so for compound classes. The differences between both
- [Kinderuni am Freitag 19. Juni](https://bio.informatik.uni-jena.de/2015/06/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).
- [Trinity workflow video tutorial](https://bio.informatik.uni-jena.de/2017/02/trinity-workflow-video-tutorial/) - SIRIUS and CSI:FingerID are part of the Trinity workflow, and Louis-Felix Nothias-Scaglia (UCSD) has prepared a wonderful video tutorial how to use Optimus, SIRIUS & CSI:FingerID and GNPS together - enjoy!
- [We will present a paper at COCOON 2015](https://bio.informatik.uni-jena.de/2015/04/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.
- [Shonan seminar on exact algorithms for bioinformatics research](https://bio.informatik.uni-jena.de/2014/01/shonan-seminar-on-exact-algorithms-for-bioinformatics-research/) - Sebastian is one of the organizers of the Shonan seminar "Towards the ground truth: Exact algorithms for bioinformatics research". The seminar will take place in Tokyo, Japan from March 16th to March 20th. If you are interested in participating, please contact one of the organizers.
- [Sebastian will give a talk at the Science Pub in Jena](https://bio.informatik.uni-jena.de/2015/04/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.
- [We will present a paper at RECOMB 2012](https://bio.informatik.uni-jena.de/2011/12/we-will-present-a-paper-at-recomb-2012/) - Meet Florian and Sebastian at RECOMB 2012 in Barcelona, Spain.
- [New Junior Professorship „Bioinformatics for High Throughput Technologies“](https://bio.informatik.uni-jena.de/2009/11/new-junior-professorship-bioinformatics-for-high-throughput-technologies/) - The Institute of Computer Science at the Friedrich-Schiller University Jena, funded by the Carl-Zeiss-Stiftung, offers a Junior Professorship in Bioinformatics. An appointment as junior professor is time-limited to four years, and allows for a prolongation up to six years. The Junior Professorship comes with an additional staff position. Read the announcement.
- [New DFG project 3AGC funded, one position available](https://bio.informatik.uni-jena.de/2009/12/new-dfg-project-3agc-funded-one-position-available/) - We will receive funding from the Deutsche Forschungsgemeinschaft for our project "Algorithms for the Analysis of Approximate Gene Clusters". One Postdoc/PhD position is available as part of this project. The order of genes in genomes can be used to determine the function of unknown genes, as well as the phylogenetic history of the organisms. In
- [New PostDoc or PhD student position](https://bio.informatik.uni-jena.de/2009/11/new-postdoc-or-phd-student-position/) - We are offering a PostDoc or PhD student position as part of the DFG project “Parameterized Algorithms for Bioinformatics Problems”.
- [New DFG project IDUN funded, 2 positions available](https://bio.informatik.uni-jena.de/2009/12/new-dfg-project-idun-funded-2-positions-available/) - We will receive funding from the Deutsche Forschungsgemeinschaft for our project "Identifying the Unknowns: Towards structural elucidation of small molecules using mass spectrometry". Two Postdoc/PhD positions are available as part of this project. Rapid identification of small compounds from small amounts of substance is of interest in many areas of biology and medicine such as
- [Introducing ZODIAC for improved molecular formula annotations](https://bio.informatik.uni-jena.de/2020/04/introducing-zodiac-for-improved-molecular-formula-annotations/) - We are happy to introduce ZODIAC, a tool for the comprehensive annotation of molecular formulas for complete LC-MS/MS runs. SIRIUS 4 is currently best-of-class for this task (as far as we know); but ZODIAC can do better. Different from SIRIUS which considers one compound at a time, ZODIAC considers a complete dataset, assuming that all
- [Hiccup of FSU computer network](https://bio.informatik.uni-jena.de/2020/04/hiccup-of-fsu-computer-network/) - Yesterday (27 April 2020) our university computer network experienced some issues and was unavailable for several hours. Not unexpectedly, this also resulted in the unavailability of the CSI:FingerID web service, website etc. As usual, computer problems cause more computer problems: It looks like today (28 April 2020) we still have certain issues restarting the CSI:FingerID
- [IMPRS application call for PhD students](https://bio.informatik.uni-jena.de/2020/04/imprs-application-call-for-phd-students-3/) - The International Max Planck Research School at the Max Planck Institute for Chemical Ecology in Jena is looking for PhD students. One of the projects is from our group on "making SIRIUS and CSI:FingerID GCMS-ready". Deadline is May 08, 2020. SIRIUS and CSI:FingerID are the best-of-class tools for MS-based compound identification in metabolomics, natural products
- [Preprint of ZODIAC now on bioRxiv](https://bio.informatik.uni-jena.de/2019/11/preprint-of-zodiac-now-on-biorxiv/) - A preprint of our paper "ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules." is now available: https://doi.org/10.1101/842740 ZODIAC takes advantage of the fact that an organism produces related metabolites. ZODIAC builds upon SIRIUS and reranks molecular formula candidates, optimizing annotations on whole datasets. By applying ZODIAC to multiple datasets we greatly
- [SIRIUS and CSI:FingerID user meeting?](https://bio.informatik.uni-jena.de/2019/01/sirius-and-csifingerid-user-meeting/) - With SIRIUS and CSI:FingerID gathering interest in the community, we are thinking about a SIRIUS and CSI:FingerID user meeting (a SIRIUS user meeting, so to say) in Jena. This would be a 2-3 day come-together with the possibility to show what your are doing with our tools, discuss with the developers, give us feedback on
- [Meet us at GCB 2019](https://bio.informatik.uni-jena.de/2019/09/meet-us-at-gcb-2019/) - Sebastian, Kai, Martin and Marcus are attending the German Conference on Bioinformatics in Heidelberg. We look forward to a great conference.
- [HowTo for SIRIUS 4 and CSI:FingerID](https://bio.informatik.uni-jena.de/2019/09/howto-for-sirius-4-and-csifingerid/) - Marcus (with the help of The People) wrote a not-too-short, not-too-shabby HowTo document on, well, how to use SIRIUS 4 and CSI:FingerID. This will be published as a book chapter in a few months, but check out a preprint here.
- [New version of Lecture Notes on Algorithmic MS](https://bio.informatik.uni-jena.de/2019/09/new-version-of-lecture-notes-on-algorithmic-ms/) - I have just uploaded a new version (0.8.3) of the Lecture Notes on Algorithmic Mass Spectrometry. As expected, I did not have too much time to work on it (them?) during lecture time, which is luckily over now. It is a lot of small improvements. Also, Magnus Palmblad was so kind and had an expert
- [Meet us at ISMB 2019](https://bio.informatik.uni-jena.de/2019/07/meet-us-at-ismb-2019/) - 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 us at Metabolomics 2019](https://bio.informatik.uni-jena.de/2019/06/meet-us-at-metabolomics-2019/) - Meet Marcus and Sebastian at the conference of the Metabolomics Society 2019. On Monday and Tuesday, Marcus will present a poster (539) about SIRIUS 4 and turning tandem mass spectra into metabolite structure information.
- [Meet us at ASMS 2019](https://bio.informatik.uni-jena.de/2019/06/meet-us-at-asms-2019/) - 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.
- [CSI:FingerID: Negative mode fingerprint prediction back to normal.](https://bio.informatik.uni-jena.de/2019/04/csifingerid-negative-mode-fingerprint-prediction-back-to-normal/) - Some of you might have noticed problems with the pediction of negative ionized data within in last few days. These problems should be fixed now. Further SIRIUS 4.0.1 build 8 fixes some problem with the workspace export.
- [IMPRS application call for PhD students](https://bio.informatik.uni-jena.de/2019/04/imprs-application-call-for-phd-students-2/) - The International Max Planck Research School at the Max Planck Institute for Chemical Ecology in Jena is looking for PhD students. One of the projects is from our group on "making SIRIUS and CSI:FingerID GCMS-ready". Deadline is May 24, 2019. SIRIUS and CSI:FingerID are the best-of-class tools for MS-based compound identification in metabolomics, natural products
- [Lecture notes on Algorithmic Mass Spectrometry are online](https://bio.informatik.uni-jena.de/2019/03/lecture-notes-on-algorithmic-mass-spectrometry-are-online/) - Is it a script? Is it a textbook? Or maybe, lecture notes? See all the details at https://bio.informatik.uni-jena.de/textbook-algoms/! Version 0.7 is now available and contains chapters on p-value calculation and decoy databases. The previous version was not publicly announced because I hoped to get some feedback first; but somehow, it did not work out this
- [Our SIRIUS 4 paper is now available at Nature Methods](https://bio.informatik.uni-jena.de/2019/03/our-sirius-4-paper-is-now-available-at-nature-methods/) - We are happy to announce that our paper "SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information" is now available online at Nature Methods. K. Dührkop, M. Fleischauer, M. Ludwig, A. A. Aksenov, A. V. Melnik, M. Meusel, P. C. Dorrestein, J. Rousu, and S. Böcker, “Sirius 4: Turning tandem
- [Dagstuhl seminar on Computational Metabolomics filling up quickly](https://bio.informatik.uni-jena.de/2019/03/dagstuhl-seminar-on-computational-metabolomics-filling-up-quickly/) - Another Dagstuhl seminar on Computational Metabolomics will be held in January 2020. The seminar is filling up quickly: Less than a month ago, invitations have been send out; but 25 people have already accepted the invitation! That is a lot, considering that it is still 10 months to go. The title of the Dagstuhl seminar
- [CSI:FingerID passed 10 million compound queries](https://bio.informatik.uni-jena.de/2019/01/csifingerid-passed-10-million-compound-queries/) - 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!
- [Kai has successfully defended his thesis last Thursday](https://bio.informatik.uni-jena.de/2018/09/kai-has-successfully-defended-his-thesis-last-thursday/) - ...but only today, he finished the last important step of becoming a PhD. (Darned fall fair.) Congratulations!
- [Purva has successfully defended her thesis today](https://bio.informatik.uni-jena.de/2018/09/purva-has-successfully-defended-her-thesis-today/) - Congratulations!
- [AC broken, CSI:FingerID will be shutdown](https://bio.informatik.uni-jena.de/2018/08/ac-broken-csifingerid-will-be-shutdown/) - We have to shutdown the CSI:FingerID webservice. We will restart the service as soon as the AC is fixed. UPDATE: All up and running again.
- [CSI:FingerID passed 5 million compound queries](https://bio.informatik.uni-jena.de/2018/07/csifingerid-passed-5-million-compound-queries/) - On July 8, 2018, the CSI:FingerID web service has passed five million compound queries. Awesome!
- [Markus has successfully defended his thesis today](https://bio.informatik.uni-jena.de/2018/06/markus-has-successfully-defended-his-thesis-today/) - Congratulations! ...and we forgot to applaud Martin E who defended on May 4th - (late) congratulations to him, too!
- [Sebastian wins prize for best talk in Mittelerde](https://bio.informatik.uni-jena.de/2018/06/sebastian-wins-prize-for-best-talk-in-mittelerde/) - Sebastian was awarded the prize for best contributed talk at Mittelerde (Central German Meeting on Bioinformatics) 2018 at the Hochschule Mittweida. Many thanks!
- [Meet us at ASMS 2018](https://bio.informatik.uni-jena.de/2018/06/meet-us-at-asms-2018/) - 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".
- [The first million is always the hardest...](https://bio.informatik.uni-jena.de/2018/05/the-first-million-is-always-the-hardest/) - On May 9, 2018, the CSI:FingerID web service has passed two million compound queries. Nice.
- [SIRIUS fix for compounds in negative ion mode](https://bio.informatik.uni-jena.de/2018/04/sirius-fix-for-compounds-in-negative-ion-mode/) - We have fixed a bug in SIRIUS when analyzing compounds in negative ion mode. These were wrongly treated as intrinsically charged. If you have analyzed negative ion mode data with SIRIUS 4 and CSI:FingerID, you might want to reanalyze the data with the newest version.
- [Stress test on April 12: 260k compound queries on a single day](https://bio.informatik.uni-jena.de/2018/04/stress-test-on-april-12-260k-compound-queries-on-a-single-day/) - Some of you might have experienced problems to reach the CSI:FingerID web service on Thursday, April 12, 2018. The reason is: After a "relatively quiet" Wednesday with "only" 120k compound queries (irony warning), the CSI:FingerID web service had to handle a real-world stress test on Thursday, with 260k compound queries submitted on a single day.
- [SIRIUS 3 is not longer supported](https://bio.informatik.uni-jena.de/2018/03/sirius-3-not-longer-supported/) - 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 (sirius@uni-jena.de) if you need to finish work that can only be done with SIRIUS 3. We
- [SIRIUS 4.0 released](https://bio.informatik.uni-jena.de/2018/02/sirius-4-0-released/) - A new version of SIRIUS and CSI:FingerID is available for download. SIRIUS 4.0 supports structure elucidation for negative ion mode spectra and computes fragmentation trees up to 40 times faster. For positive ion mode spectra, CSI:FingerID shows an improved identification rate due to new training data and several methodical enhancements. We also fixed a lot
- [One million compound queries for CSI:FingerID](https://bio.informatik.uni-jena.de/2018/02/one-million-compound-queries-for-csifingerid/) - The CSI:FingerID web service has now processed more than one million compound queries. (In fact, we are already 50k queries beyond that.) We are thrilled, and hope that you made some interesting discoveries. ;-)
- [Juho Rousu will visit us Aug to Sep 2018](https://bio.informatik.uni-jena.de/2018/01/juho-rousu-will-visit-us-aug-to-sep-2018/) - Juho Rousu (Aalto University, Finland) will visit our group August to September 2018. We are excited to have him with us again: During his last visit, we jointly laid the foundations for CSI:FingerID; let us see what comes out this time!
- [Hello World: We are now on Twitter](https://bio.informatik.uni-jena.de/2017/11/hello-world-we-are-now-on-twitter/) - All news of our group are now available on Twitter: @boeckerlab
- [Our paper on FDR estimation has finally appeared in Nature Communications](https://bio.informatik.uni-jena.de/2017/11/our-paper-on-fdr-estimation-has-finally-appeared-in-nature-communications/) - Our paper "Significance estimation for large scale metabolomics annotations by spectral matching" (joined work with the group of Pieter Dorrestein) has finally appeared in Nature Communications; you can find it here.
- [Meet Kai and Marcus at Metabolomics 2017](https://bio.informatik.uni-jena.de/2017/06/meet-kai-and-marcus-at-metabolomics-2017/) - 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](https://bio.informatik.uni-jena.de/2017/06/siriuscsifingerid-3-5/) - 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
- [CSI:FingerID has processed 500,000 query compounds](https://bio.informatik.uni-jena.de/2017/06/csifingerid-500000-queries/) - The CSI:FingerID web service has just passed the mark of processing data from 500,000 query compounds -- congratulations to CSI:FingerID, and thank you for your interest in our tools! (Be reminded that CSI:FingerID should be accessed via the SIRIUS application, not via the web page.)
- [SIRIUS license change to GNU GPL](https://bio.informatik.uni-jena.de/2017/02/sirius-license-change-to-gnu-gpl/) - Since version 3.4, SIRIUS is licensed under the GNU General Public License (GNU GPL). If you need SIRIUS under a different license, please contact us.
- [CSI:FingerID: Best automated method in CASMI contest](https://bio.informatik.uni-jena.de/2016/05/csifingerid-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
- [SIRIUS+CSI:FingerID alpha release](https://bio.informatik.uni-jena.de/2016/06/siriuscsifingerid-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
- [SIRIUS+CSI:FingerID release](https://bio.informatik.uni-jena.de/2016/07/siriuscsifingerid-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
- [SIRIUS+CSI:FingerID for Mac OSX](https://bio.informatik.uni-jena.de/2016/08/siriuscsifingerid-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
- [SIRIUS+CSI:FingerID 3.4 released](https://bio.informatik.uni-jena.de/2017/02/siriuscsifingerid-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
- [SIRIUS+CSI:FingerID  3.4 build 2](https://bio.informatik.uni-jena.de/2017/02/siriuscsifingerid-3-4-build-2/) - Build 2 fixes a major bug when the included GLPK ILP solver is used to calculate fragmentation trees.
- [SIRIUS+CSI:FingerID  3.4 build 4](https://bio.informatik.uni-jena.de/2017/02/siriuscsifingerid-3-4-build-4/) - Build 4 contains some more bug fixes!
- [SIRIUS hotfix](https://bio.informatik.uni-jena.de/2017/02/sirius-hotfix/) - We released a patch for SIRIUS+CSI:FingerID (now version 3.4.1) that fixes some critical bugs. We recommend everybody to download the newest version of SIRIUS.
- [Sirius release 3.4 is coming soon](https://bio.informatik.uni-jena.de/2017/01/sirius-release-at-270117/) - 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 3.0 release](https://bio.informatik.uni-jena.de/2015/05/sirius3/) - 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.
- [Sirius 3.1 is out and now ships with a graphical user interface!](https://bio.informatik.uni-jena.de/2015/11/sirius-3-1-is-out-and-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.
- [Meet us at Metabolomics 2016](https://bio.informatik.uni-jena.de/2016/06/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.
- [Kerstin awarded Wissenschaftspreis für anwendungsorientierte Abschlussarbeit](https://bio.informatik.uni-jena.de/2016/11/kerstin-awarded-wissenschaftspreis-fur-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!
- [Besucht unseren Workshop beim MINT-Schülerkongress](https://bio.informatik.uni-jena.de/2016/06/besucht-unseren-workshop-beim-mint-schulerkongress/) - Wir sind dabei, beim MINT-Schülerkongress 2016 des Schülerforschungszentrums Nordhessen in Kassel. Alle weiteren Infos findet ihr hier.
- [de.NBI Summer School 2016: From Big Data to Big Insights](https://bio.informatik.uni-jena.de/2016/05/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!](https://bio.informatik.uni-jena.de/2016/04/wir-sind-dabei-beim-girls-day-2016-am-28-april/) - Mehr Infos gibt es hier.
- [Meet Betram and Franziska in Bled](https://bio.informatik.uni-jena.de/2016/01/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.
- [Sirius² is here](https://bio.informatik.uni-jena.de/2011/08/sirius²-is-here/) - Finally we present the first release of our renewed mass spectrometry software framework Sirius2, offering better user experiences. Sirius2 now combines a powerful graphical user interface with a plug-in system, allowing for persistent data storage and easy integration of new algorithms. Please visit our homepage for more information or download Sirius2 directly here.
- [New version of Sirius²](https://bio.informatik.uni-jena.de/2012/03/new-version-of-sirius²/) - We present the second release of our mass spectrometry software framework Sirius2. With Sirius2 version 1.0 you can now analyze MSn data and load full LCMS runs. Please visit our homepage for more information or download Sirius2 directly here.
- [Gastvorlesung Sebastian in Halle](https://bio.informatik.uni-jena.de/2016/01/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](https://bio.informatik.uni-jena.de/2016/01/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](https://bio.informatik.uni-jena.de/2016/01/gastvorlesung-ivo-grose/) - 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
- [PNAS paper scheduled for Sep 21](https://bio.informatik.uni-jena.de/2015/09/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.](https://bio.informatik.uni-jena.de/2015/06/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.
- [Promotionspreis der Dekanin](https://bio.informatik.uni-jena.de/2015/04/promotionspreis-der-dekanin/) - Franziska wird für ihre Promotion mit dem Preis der Dekanin ausgezeichnet.
- [FIFI ist jetzt online](https://bio.informatik.uni-jena.de/2015/05/fifi-ist-jetzt-online/) - Der Förderverein des Instituts für Informatik (kurz FIFI) ist jetzt online und nimmt schon Mitgliederanträge entgegen!
- [Meet Kai at RECOMB in Warsaw](https://bio.informatik.uni-jena.de/2015/04/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.
- [COCONUT released!](https://bio.informatik.uni-jena.de/2015/02/coconut-released/) - We present the first release of our renewed tool for estimating the composition distribution from mass spectra of synthetic copolymers. COCONUT provides an easy-to-use graphical user interface and can be downloaded here.
- [Gecko3  released!](https://bio.informatik.uni-jena.de/2015/01/gecko3-released/) - We released the new version of Gecko -- our software for finding gene clusters. Gecko3 offers an easy-to-use graphical user interface, but can also be used as a command line tool in an analysis pipeline. Downloads are available here.
- [Meet Sebastian at the CeBiTec symposium in Bielefeld](https://bio.informatik.uni-jena.de/2015/01/meet-sebastian-at-the-cebitec-symposium-in-bielefeld/) - Sebastian will given a talk on Computational Mass Spectrometry in Metabolomics at the CeBiTec symposium on "Bioinformatics for Biotechnology and Biomedicine" in Bielefeld.
- [GCB 2012 website has been moved](https://bio.informatik.uni-jena.de/2015/01/gcb-2012-website-has-been-moved/) - The website of the German Conference on Bioinformatics 2012 has been moved from http://www.gcb2012-jena.de/ to https://bio.informatik.uni-jena.de/gcb2012/. The content will be made available permanently under the new URL.
- [Manja Marz will start her Juniorprofessorship at the FSU Jena shortly](https://bio.informatik.uni-jena.de/2012/01/manja-marz-will-start-her-juniorprofessorship-at-the-fsu-jena-shortly/) - Dr. Manja Marz (bisher Uni Marburg) tritt in Kürze ihre Juniorprofessur "Bioinformatik für Hochdurchsatzmethoden" (gefördert durch die Carl-Zeiss-Stiftung) an der Friedrich-Schiller-Universität Jena an. Wir freuen uns, sie in Jena begrüßen zu dürfen!
- [Meet Kai at the ASMS conference in Baltimore](https://bio.informatik.uni-jena.de/2014/06/meet-kai-at-the-asms-conference-in-baltimore/) - Kai will give a talk at the Conference of the American Society for Mass Spectrometry in Baltimore, USA.
- [Postdoktoranden-Stipendium der Carl Zeiss Stiftung](https://bio.informatik.uni-jena.de/2014/06/postdoktoranden-stipendium-der-carl-zeiss-stiftung/) - Franziskas Antrag an die Carl Zeiss Stiftung im Rahmen des Nachwuchsförderprogramms 2014 wurde bewilligt. Zum Thema "Lücken im Kraftwerk der Zukunft" werden wir zukünftig zusammen mit Manja Marz den Hell/Dunkel-Zyklus bei Cyanobakterien mittels kombinierter Metabolom- und Transkriptomanalyse untersuchen.
- [Lehrveranstaltung von Sebastian an der Martin-Luther-Universität Halle](https://bio.informatik.uni-jena.de/2014/01/lehrveranstaltung-von-sebastian-an-der-martin-luther-universitat-halle/) - Sebastian hält am Donnerstag den 9. und 16. Januar zwei Vorlesungen an der Martin-Luther-Universität Halle zum Thema Genome Rearrangements und Gencluster. Vorlesungsunterlagen finden sich hier, hier und hier.
- [Lehrveranstaltungen von Ivo Große](https://bio.informatik.uni-jena.de/2013/11/lehrveranstaltungen-von-ivo-grose/) - Ivo Große von der Universität Halle wird uns am 9. und 16. Januar besuchen und zwei Vorlesungen zum Thema Motif Finding und EM-Algorithmus halten - klassische Themen der Bioinformatik, die in Jena leider nicht mehr gelehrt werden. Die erste Vorlesung findet am Donnerstag dem 9. Januar von 13:00 bis 16:00 Uhr im Seminarraum 113, Carl-Zeiss-Str.
- [JCB workshop starts today](https://bio.informatik.uni-jena.de/2013/09/jcb-workshop-starts-today/) - The Jena Centre for Bioinformatics Workshop “Bioinformatics meets Biodiversity” will be help Mon+Tue 23.-24.09.2013 in the Rosensäle in Jena. Most of our group will be there.
- [Meet Sebastian at GCB 2013](https://bio.informatik.uni-jena.de/2013/09/meet-sebastian-at-gcb-2013/) - Sebastian will attend the German Conference in Bioinformatics in Göttingen, Germany. Meet him there on Sep 12, 2013.
- [Meet Sebastian at WABI 2013](https://bio.informatik.uni-jena.de/2013/09/meet-sebastian-at-wabi-2013/) - Sebastian will attend the Workshop on Algorithms in Bioinformatics in Sophia Antipolis, France. He will present two papers on "The generalized Robinson-Foulds metric" and "Faster mass decomposition".
- [Meet us at ASMS 2013](https://bio.informatik.uni-jena.de/2013/06/meet-us-at-asms-2013/) - Martin and Kai will attend 61st ASMS Conference on Mass Spectrometry and Allied Topics in Minneapolis, Minnesota. We will present two posters (MP 734 and WP 231).
- [Meet Kerstin at Lipari Summer School](https://bio.informatik.uni-jena.de/2013/07/meet-kerstin-at-lipari-summer-school/) - Kerstin will attend Lipari School on Bioinformatics and Computational Biology - Computational Network Biology in Lipari, July 13-20, 2013.
- [Meet Sebastian at RECOMB CP 2012](https://bio.informatik.uni-jena.de/2012/02/meet-sebastian-at-recomb-cp-2012/) - Sebastian will attend the RECOMB Satellite Conference on Computational Proteomics 2012 in San Diego, April 6-8, 2012.
- [GCB 2012 is over](https://bio.informatik.uni-jena.de/2012/09/gcb-2012-is-over/) - We hope that everybody enjoyed the show -- we most certainly did! See you next year in Göttingen: 10. - 13. September 2013, see http://www.gcb2013.de/.
- [Änderung Vorlesung 'Bioinformatische Methoden in der Genomforschung'](https://bio.informatik.uni-jena.de/2011/11/anderung-vorlesung-bioinformatische-methoden-in-der-genomforschung/) - Die Vorlesung findet ab dem 28.11.2011 im SR 113 in der Carl-Zeiss-Str. 3 statt. Zeit: 12.30 - 14.00 Uhr
- [Congratulations to Konrad Grützmann](https://bio.informatik.uni-jena.de/2011/11/congratulations-to-konrad-grutzmann/) - Konrad Grützmann from the group of Prof. Stefan Schuster has received the "best poster award" at the German Conference for Bioinformatics (GCB 2011) for a poster presenting work from our joint publication, "Combinatorics of aliphatic amino acids". Congratulations!
- [Meet Malte at COCOON 2011](https://bio.informatik.uni-jena.de/2011/07/meet-malte-at-cocoon-2011/) - Malte will present a paper at the Computing and Combinatorics Conference (COCOON 2011) in Dallas, USA, August 14-16, 2011.
- [Meet Kerstin and Franziska at RECOMB 2011](https://bio.informatik.uni-jena.de/2011/02/meet-kerstin-and-franziska-at-recomb-2011/) - Kerstin will present a paper and Franziska will present a poster at the 15th Annual International Conference on Research in Computational Molecular Biology, Vancouver, Canada, on March 28-31, 2011.
- [Meet us at ASMS 2011](https://bio.informatik.uni-jena.de/2011/03/meet-us-at-asms-2011/) - Florian, Franziska, Kerstin, and Sebastian will attend 59th ASMS Conference on Mass Spectrometry and Allied Topics in Denver, Colorado. We will present a talk and three posters.
- [Bachelor theses](https://bio.informatik.uni-jena.de/2011/01/bachelor-theses/) - We have subjects for bachelor theses avaliable. See here.
- [We will present a paper at RECOMB 2011](https://bio.informatik.uni-jena.de/2010/12/we-will-present-a-paper-at-recomb-2011/) - Meet us in Vancouver, Canada.
- [Meet Sebastian in New Zealand Oct 2010 to Mar 2011](https://bio.informatik.uni-jena.de/2010/06/meet-sebastian-in-new-zealand-oct-2010-to-mar-2011/) - Sebastian will visit the University of Canterbury, Christchurch, New Zealand from October 2010 to March 2011. He will visit Mike Steel at the Biomathematics Research Centre.
- [We co-author a paper in Nature Methods](https://bio.informatik.uni-jena.de/2010/05/we-co-author-a-paper-in-nature-methods/) - The paper "Partitioning biological data with Transitivity Clustering" by Tobias Wittkop et al. has appeared in Nature Methods, see here. Abstract. Clustering objects according to given similarity or distance values is a ubiquitous problem in computational biology with diverse applications, e.g., in defining families of orthologous genes, or in the analysis of microarray experiments. While
- [Meet Sebastian at DGMS Jahrestagung 2010](https://bio.informatik.uni-jena.de/2010/02/meet-sebastian-at-dgms/) - Sebastian will give a tutorial on computational mass spectrometry at the DGMS Jahrestagung 2010 in Halle, March 7, 2010.
- [Meet Sebastian at RECOMB Satelite Conference on Computational Proteomics 2010](https://bio.informatik.uni-jena.de/2010/03/meet-sebastian-at-recomb-cp/) - Sebastian will attend the RECOMB Satelite Conference on Computational Proteomics 2010 in San Diego, March 27-28, 2010.
- [Meet Sylvain at TAMC 2010](https://bio.informatik.uni-jena.de/2010/04/meet-sylvain-at-tamc-2010/) - Sylvain will present a paper at the Theory and Applications of Models of Computation (TAMC) conference, Prague, Czech Republic, on June 7-11, 2010.
- [Hey du!](https://bio.informatik.uni-jena.de/2009/10/hey-du/) - Wir suchen noch Studentische Hilfskräfte - siehe Job offers!
- [We will present three papers at COCOON 2009](https://bio.informatik.uni-jena.de/2009/04/we-will-present-three-papers-at-cocoon-2009/) - Meet Anton, Bao, and our diploma student Birte Kehr in Niagara Falls, USA.
- [We will present a paper at WABI 2009](https://bio.informatik.uni-jena.de/2009/05/we-will-present-a-paper-at-wabi-2009/) - Meet our diploma student Tamara Steijger at Philadelphia, USA.

## Pages

- [Welcome to the Chair of Bioinformatics](https://bio.informatik.uni-jena.de/) - Homepage of Boecker lab Prof. Sebastian Böcker. Research interests are bioinformatics, algorithmics and machine learning for small molecule mass spectrometry.
- [Publications](https://bio.informatik.uni-jena.de/publications/) - For the textbook Algorithmic Mass Spectrometry: From molecules to masses and back again see here. 2026 J. A. Emmert, S. Böcker, and M. FleischauerProtocol for untargeted LC-MS/MS metabolomics annotation and differential abundance analysis using the SIRIUS Python clientSTAR Protoc 7(3):104771, 2026[DOI] E. van der Nol, Z. Luo, Q. Qing Gao, N. A. Haupt, S. Böcker,
- [Einführung in die Bioinformatik I-2](https://bio.informatik.uni-jena.de/lehre/alle-veranstaltungen/einfuhrung-in-die-bioinformatik-i-2/) - Veranstalter: Prof. Dr. Peter Dittrich Letztmalig/aktuell im SoSe 2026 Nächste Instanz geplant im SoSe 2027 Vorlesungstermin: 10:15-11:45 Uhr, SR 1086, Inselplatz 5; Beginn: 07.04.2026 Tutorium: 10:15-11:45 Uhr, SR 1085, Inselplatz 51. Termin: Donnerstag, 23.04.2026Übung (Start: 09.04.2026) Übungen werden im Moodle hochgeladen. Übungsleiter: Jonas Emmert; Roberto Herrero Perez Donnerstag, 14:15 -15:45h; SR 225 CZ3 Fragestunde: Klausur:
- [Proseminar Bioinformatik](https://bio.informatik.uni-jena.de/lehre/alle-veranstaltungen/proseminar-bioinformatik-2/) - Letztmalig/aktuell im SoSe 2026 Nächste Instanz geplant im SoSe 2027 Seminarleitung: Fleming Kretschmer Termin: Mittwoch, 08:30 - 10:00 Uhr Ort: SR 1086, CIP Beginn: 08.04.2026 Weitere Infos im Moodle
- [2-step](https://bio.informatik.uni-jena.de/software/2-step/) - 2-step allows transferable prediction of liquid chromatography retention times: predictions for new and known chromatographic setups (including new columns) across the space of biomolecules. A graph neural network-based architecture is used to first predict a Retention Order Index (ROI) based on compound structure and parameters of the chromatographic setup. The underlying model is trained on
- [Software](https://bio.informatik.uni-jena.de/software/) - SIRIUS+CSI:FingerID -- CANOPUS -- ZODIAC -- 2-step -- BCD Supertrees -- EPoS -- Gecko3 -- COCONUT Myopic MCES distance Computing the myopic MCES (Maximum Common Edge Subgraph) distance allows us to judge the (dis)similarity of molecular structures, arguably much better than using Tanimoto coefficients. The source code for computing myopic MCES distances is hosted by
- [SIRIUS workshops](https://bio.informatik.uni-jena.de/data/sirius-workshop/) - Here, you can find information for our SIRIUS workshops. Preparation To participate in the workshop, please do the following some days before the workshop: download and install/extract the version of SIRIUS 6 used in the workshop for your operating system, here . create a user account via the SIRIUS GUI, see below. In some cases
- [Data](https://bio.informatik.uni-jena.de/data/) - RepoRT The comprehensive repository for LC retention times is hosted on GitHub, a WebApp for easier submission is available here. MCES distance data All MCES distances are available here. CANOPUS evaluation data We evaluated CANOPUS on two MS/MS reference datasets: The SVM training dataset, which was also used for training CSI:FingerID (in 10-fold cross-validation), and
- [Beruf und Karriere](https://bio.informatik.uni-jena.de/lehre/alle-veranstaltungen/beruf-und-karriere/) - Veranstalter: Dr. Markus Fleischauer; Fleming Kretschmer Letztmalig/aktuell im SoSe 2026 Nächste Instanz geplant im SoSe 2027 Beginn: Montag, 13.04.2026; 14:15h - 15:45h Ort: SR 2009, CIP 13.04.2026 Einführung, Academia/Promotion 04.05.2026 Arbeit in der freien Wirtschaft, Startups 11.05.2026 Bewerbung, Lebenslauf, Stellenausschreibungen 22.06.2026 (?) Qualifikationen 29.06.2026 (?) Karriereanker
- [Members](https://bio.informatik.uni-jena.de/members/) - Chair Prof. Dr. Sebastian BöckerRoom 3011Phone +49-3641-9-46451sebastian.boecker@uni-jena.de Secretary Kathrin SchowtkaRoom 3012Phone +49-3641-9-46450kathrin.schowtka@uni-jena.de Postdocs Dr. Markus FleischauerDipl.-Bioinf.Room 3006Phone +49-3641-9-46455markus.fleischauer@uni-jena.de PhD Students Fleming KretschmerM.- Sc.Room 3008Phone +49-3641-9-46456fleming.kretschmer@uni-jena.de Nils HauptM.-Sc.Room 3007Phone +49-3641-9-46454nils.alexander.haupt@uni-jena.de Wei TangM.-Sc.Room 3005Phone +49-3641-9-46453wei.tang@uni-jena.de Jonas EmmertM.-Sc.Room 3007Phone +49-3641-9-46454jonas.emmert@uni-jena.de Roberto Herrero PérezM.-Sc.Room 3008Phone +49-3641-9-46456ro.he.perez@uni-jena.de Andrés Rogelio Martínez Bilesio M.-Sc.Room 3005Phone +49-3641-9-46455a.martinez@uni-jena.de Rayk KretzschmarM.-Sc.Room 3007Phone +49-3641-9-46454rayk.kretzschmar@uni-jena.de Alberto Dalla
- [Mitarbeiterin ERC BindingShadows [CLOSED]](https://bio.informatik.uni-jena.de/mitarbeiterin-erc-bindingshadows/) - UPDATE: This job posting is now closed. Thank you for your interest. Siehe unten für den Ausschreibungstext auf Deutsch. The Chair for Bioinformatics, Institute of Computer Science at the Friedrich-Schiller-University Jena offers the following positions: Multiple postdocs and PhD students as research associates (Wissenschaftliche Mitarbeiterin) These positions are part of the ERC advanced project BindingShadows,
- [Currents in Bioinformatics](https://bio.informatik.uni-jena.de/lehre/alle-veranstaltungen/currents-in-bioinformatics/) - Letztmalig/aktuell im SoSe 2026 Nächste Instanz geplant im WiSe 2026/2027 Seminarleitung: Andrés Rogelio Martínez Bilesio, Fleming Kretschmer Seminarort: Campus Inselplatz (CIP) SR 2009 Dienstag 16:15-17:45 Uhr Beginn: 07.04.26 Weitere Infos im Moodle 7.4.26 Organisatorisches, Wie liest man ein Paper? TBA Abgabe Deadline für Abstracts (siehe Template unten!) "Live" Paper Moodle Papers to present (choose one!)
- [Sequenzanalyse](https://bio.informatik.uni-jena.de/lehre/alle-veranstaltungen/sequenzanalyse/) - Veranstalter: Sebastian Böcker Letztmalig/aktuell im SoSe 2023 Nächste Instanz geplant im Achtung: im SoSe 2025 Algorithmische Phylogenetik statt Sequenzanalyse! Beginn: Donnerstag, 06.04.2023 Vorlesungstermine: Mo 12:30 - 14:00 Uhr (ca alle zwei Wochen) und Do 12:30 - 14:00 Uhr, SR 114 AB4 Übungsleiter: Fleming Kretschmer, Nils A. Haupt Übungstermine1. Übungsgruppe: Mo 10:15 - 11:45 Uhr, SR
- [Sommer 2026](https://bio.informatik.uni-jena.de/lehre/sommer-2026/) - Lehre im Sommersemester 2026 Grundsätzlich gilt: Termine für Vorlesungen und Tutorien sowie Folien zum Runterladen finden sich hier auf unseren Webseiten; Übungsblätter und alle weiteren Informationen zu unseren Übungen finden sich im Moodle. Sebastian Böcker hat ein Forschungsfreisemester im SS 2026 - folgende Veranstaltungen werden stattfinden: Vorlesung, Tutorium und Übung
- [SIRIUS Logos](https://bio.informatik.uni-jena.de/software/sirius/sirius-logos/) - SIRIUS word mark
- [Bioinformatische Methoden in der Genomforschung](https://bio.informatik.uni-jena.de/lehre/alle-veranstaltungen/bioinformatische-methoden-in-der-genomforschung/) - Veranstalter: Sebastian Böcker Letztmalig/aktuell im WiSe 2025/26 Nächste Instanz im WiSe 2027/28 Vorlesung: Donnerstag, 14:15 - 15:45h Ort: Carl-Zeiß-Straße 3, SR 131 Übung Aufgaben im Moodle Übungsleiter: Nils HauptMontag, 12:15 - 13:45h, Carl-Zeiß-Straße 3 SR 123Start: 30.10.2025 Tutorium: Montag 09:00-10:00, Campus Inselplatz (CIP) SR 2009 Start: 27.10.2025 Klausur: Montag, 02.03.2026 12:00 - 14:00h; HS 250
- [Einführung in die Bioinformatik I-1](https://bio.informatik.uni-jena.de/lehre/alle-veranstaltungen/einfuhrung-in-die-bioinformatik-i-1/) - Veranstalter: Peter Dittrich Letztmalig/aktuell im WiSe 2025/26 Nächste Instanz geplant im WiSe 2026/27 Vorlesung: Dienstag, 10:15 Uhr - 11:45 Uhr Tutorium: Übungen Aufgaben im Moodle Gruppe 1: Übungsleiter: Jonas Emmert Donnerstag 12:15 - 13:45, August-Bebel-Straße 4 SR 108 Start: 23.10.2025 Gruppe 2: Übungsleiter: Roberto Herrero Pérez Dienstag 08:15 - 9:45, Carl-Zeiß-Straße 3 SR131 Start: 21.10.2025 Vorläufiger
- [Impressum](https://bio.informatik.uni-jena.de/impressum/) - Kontaktadresse: Prof. Dr. Sebastian Böckersebastian.boecker@uni-jena.deTelefon: +49-3641-9-46451 Friedrich-Schiller-Universität JenaLehrstuhl für BioinformatikInselplatz 507743 Jena Haftungsausschluss (Disclaimer)
- [Sebastian Böcker](https://bio.informatik.uni-jena.de/sebastian-boecker/) - Postal Address Lehrstuhl für BioinformatikInstitut für InformatikInselplatz 507743 JenaPhone: +49-3641-9-46450Fax: +49-3641-9-46452 Selected publications See here for a complete and up-to-date list of publications. See here for my Google Scholar page. R. Schmid, S. Heuckeroth, A. Korf, [... including S. Böcker], D. Petras, X. Du, and T. Pluskal. Integrative analysis of multimodal mass spectrometry data in
- [Datamining und Sequenzanalyse](https://bio.informatik.uni-jena.de/lehre/alle-veranstaltungen/datamining-und-sequenzanalyse/) - Veranstalter: Markus Fleischauer Letztmalig/aktuell im WiSe 2024/25 Nächste Instanz geplant im WiSe 2025/26 Termine: Die erste Veranstaltung findet am Freitag, den 17.10., statt! Mo 10:15-11:45h, Carl-Zeiß-Straße 3 - SR 217 (PC-Pool) (VORÜBERGEHEND) Fr 12:30-14:00h, August-Bebel-Straße 4 - SR 102 (Seminarraum) (VORÜBERGEHEND) Weitere infos zur Vorlesung im Moodle
- [Job offers](https://bio.informatik.uni-jena.de/jobs/) - We are looking for multiple PhD students and PostDocs (wissenschaftliche Mitarbeiter:innen) n the context of our ERC project BindingShadows! Everybody with a solid background in bioinformatics, algorithmics and/or machine learning is welcome. Interest or knowledge in mass spectrometry is a plus but not required. Please see here for more information. In addition, in case you
- [Algorithmische Phylogenetik](https://bio.informatik.uni-jena.de/lehre/alle-veranstaltungen/algorithmische-phylogenetik/) - Veranstalter: Sebastian Böcker Letztmalig/aktuell im SoSe 2025 Nächste Instanz geplant im SoSe 2027 Achtung: im SoSe 2025 Algorithmische Phylogenetik statt Sequenzanalyse! Vorlesungstermin (Beginn: 07.04.2025) die Videos zur Vorlesung werden an den festgelegten Termine im Ablaufplan freigeschaltet Tutorium am Do, von 12.30h -14.00h im SR 3423 EAP2 15.05. | 22.05. | 05.06. | 12.06. | 19.06.
- [Winter 25/26](https://bio.informatik.uni-jena.de/lehre/winter-25-26/) - Lehre im Wintersemester 2025/26 Grundsätzlich gilt: Termine für Vorlesungen und Tutorien sowie Folien zum Runterladen finden sich hier auf unseren Webseiten; Übungsblätter und alle weiteren Informationen zu unseren Übungen finden sich im Moodle. Vorlesung, Tutorium und Übung Einf. 1 Datamining Vorlesung und Übung Bioinformatische Methoden der Genomforschung Currents
- [Bachelor- und Masterarbeitsthemen](https://bio.informatik.uni-jena.de/masterarbeiten/) - Wir betreuen am Lehrstuhl natürlich gern Bachelorarbeiten, Studienarbeiten und Masterarbeiten. Allerdings hat es sich als nicht sinnvoll herausgestellt, Listen mit Themen auf dieser Seite zu veröffentlichen: Schon nach wenigen Wochen sind diese Listen in der Regel nicht mehr aktuell. Forschung ist ein äußerst dynamisches Feld, und wenn uns ein Thema auf den Fingern brennt, dann
- [Was ist eigentlich Bioinformatik?](https://bio.informatik.uni-jena.de/schueler/was-ist-eigentlich-bioinformatik/) - Es gibt Grenzbereiche, in denen sich die Informatik mit einer oder mehrerer weiteren Wissenschaften verbunden, und vielleicht etwas Neues gebildet hat -- so wie sich um das Jahr 1960 die Informatik an der Schnittstelle zwischen Mathematik und Elektrotechnik bildete. Anfangs wird dabei Informatik nur als Hilfsmittel und Werkzeug (Datenbanken, Visualisierung) verwendet, um Fragen der anderen
- [Methoden der Metabolomik](https://bio.informatik.uni-jena.de/lehre/alle-veranstaltungen/lehre-sommer-2023-methoden-der-metabolomik/) - Seminarleitung: Markus Fleischauer Termin: Blockveranstaltung, 25.09.23 bis 29.09.23 Ort: TBA Beginn: 25.09.23
- [Alle Veranstaltungen](https://bio.informatik.uni-jena.de/lehre/alle-veranstaltungen/) - Grundsätzlich gilt: Termine für Vorlesungen und Tutorien sowie Folien zum Runterladen finden sich hier auf unseren Webseiten; Übungsblätter und alle weiteren Informationen zu unseren Übungen finden sich im Moodle. Bachelor Vorlesung, Tutorium und Übung Einf. 1 Vorlesung, Tutorium und Übung Einf. 2 Datamining Proseminar Wahlpflicht Vorlesung, Tutorium und Übung Genomforschung Vorlesung und Übung alg. phylo
- [Lehre](https://bio.informatik.uni-jena.de/lehre/)
- [Algorithmische Massenspektrometrie](https://bio.informatik.uni-jena.de/lehre/alle-veranstaltungen/algorithmische-massenspektrometrie/) - Veranstalter: Sebastian Böcker Letztmalig/aktuell im WiSe 2024/25 Nächste Instanz geplant im WiSe 2026/27 Vorlesung: Montag, 12:30 -14:00h; SR 130 CZ3 Übungsleiter: Fleming Kretschmer Übungstermin: Dienstag, 12:30 -14:00; SR 123 CZ3 Tutorium: Montag, 14:15 -15:45h; R3423 im EAP2 (14 tägl.)(21.10.24 / 11.11.24 / 18.11.24 / 02.12.24 / 16.12.24 / 13.01.25 / 27.01.25) Vorläufiger Ablauf Literatur Lehrbuch
- [Currents in Bioinformatics](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2018/currents-on-bioinformatics/) - Seminarleiter: Thomas Köhler Termin: Di 16-18h, SR 3423 EAP Beginn: 10.04.2018 Im Journal Club wird wöchentlich ein aktueller Artikel aus der bioinformatischen Forschung vorgestellt und diskutiert. Details werden in der ersten Veranstaltung besprochen. Vorläufiger Ablaufplan Date Paper Presenter and Backup 10.04. Organisatorisches, Besprechen der Themen Martin 17.04. How to read a scientific paper? Sebastian 24.04. Bayesian
- [Sequenzanalyse](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2017/sequenzanalyse/) - Veranstalter: Sebastian Böcker Vorlesungstermine: Mo 12.30-14.00h, SR 123 CZ3 Vorlesungstermine: Do 08.30-10.00h (14tgl.), SR 123 CZ3 Übungsleiter: Kai Dührkop, Markus Fleischauer Übungstermine: Mo 8:30 -10:00, SR 3423 EAP Vorläufiger Ablauf Termin Themen Folien Übungsblatt Übungsabgabe Mo 03.04. (V) Einführung, Formalitäten, biologischer Hintergrund Mo 10.04. (V) Metriken auf Strings Do 20.04. (V) Alignment-Problem Folien Fr 21.04. (Ü) Besprechung Übungsblatt
- [Gecko3](https://bio.informatik.uni-jena.de/software/gecko3/) - Gecko3 is an open-source software for finding gene clusters in 500 and more genomes on a laptop computer. The underlying gene cluster model can cope with low degrees of conservation and misannotations, and is complemented by a sound statistical evaluation. Gecko3 does not assume monophylecity or collinearity of gene clusters. Gecko3 offers an easy-to-use graphical
- [COCONUT](https://bio.informatik.uni-jena.de/software/coconut/) - The "COpolymer COmposition NUmbering Tool" is a tool for estimating the composition distribution from mass spectra of synthetic copolymers. It is based on Linear Programming and is capable of automatically resolving overlapping isotopes and isobaric ions. It also features spectral pre-processing methods: baseline correction, spectral smoothing and peak picking (centroiding). COCONUT provides an easy-to-use graphical user interface. Installation Download
- [COSMIC](https://bio.informatik.uni-jena.de/software/cosmic/) - COSMIC is a workflow that allows you to assign confidence to structure annotations. For every structure annotated by CSI:FingerID, COSMIC provides a confidence score (a number between 0 and 1) that tells you how likely it is that this annotation is correct. This is similar in spirit to what is done in spectral library search:
- [Links](https://bio.informatik.uni-jena.de/links/) - Informationen zum Studium der Bioinformatik in Jena finden sich hier. Our chair participates in the EU International Graduate School HUMAN, Harmonising and Unifying Blood Metabolomic Analysis Networks Our chair participates in an ongoing project supported by the Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft (TMWWDG) with funds from the European Union (ERDF, 2023 VFE
- [Winter 24/25](https://bio.informatik.uni-jena.de/lehre/winter-24-25/) - Lehre im Wintersemester 2024/25 Grundsätzlich gilt: Termine für Vorlesungen und Tutorien sowie Folien zum Runterladen finden sich hier auf unseren Webseiten; Übungsblätter und alle weiteren Informationen zu unseren Übungen finden sich im Moodle. [include-page id="8934" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Tutorium und Übung) " more="mehr»"] Einf. 1 [include-page id="8951" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter="
- [Annotating small molecules from massive affinity selection libraries](https://bio.informatik.uni-jena.de/annotating-small-molecules-from-massive-affinity-selection-libraries/) - The discovery of pharmacologically active molecules that effectively target specific drug receptors necessitates the screening of millions of compounds. In contrast to traditional high-throughput methods, affinity selection-based strategies enable the rapid screening of entire compound libraries in a single experiment. This technique involves incubating a compound library with the drug target of interest, followed by
- [Sommer 2023](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2023/) - Lehre im Sommersemester 2023 [include-page id="9537" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Tutorium und Übung) " more="mehr»"] [include-page id="9547" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" " more="mehr»"] [include-page id="7641" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" " more="mehr»"] [include-page id="10308" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" " more="mehr»"] [include-page id="9414" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" " more="mehr»"] [include-page id="10835"
- [Sommer 2018](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2018/) - Lehre im Sommersemester 2018 [include-page id="7080" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="7070" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="7107" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Proseminar) " more="mehr»"] [include-page id="7098" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (ASQ) " more="mehr»"] [include-page id="7113" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter="
- [Sommer 2019](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2019/) - Lehre im Sommersemester 2019 [include-page id="7597" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="7641" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="7609" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Proseminar) " more="mehr»"] [include-page id="7615" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (ASQ) " more="mehr»"] [include-page id="7612" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter="
- [Sommer 2020](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2020/) - Lehre im Sommersemester 2020 [include-page id="8228" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="8243" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="8278" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" " more="mehr»"] [include-page id="8743" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" " more="mehr»"]
- [Sommer 2021](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2021/) - Lehre im Sommersemester 2021 [include-page id="9537" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="9547" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" " more="mehr»"] [include-page id="9559" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" " more="mehr»"]
- [Sommer 2022](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2022/) - Lehre im Sommersemester 2022 [include-page id="9537" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Tutorium und Übung) " more="mehr»"] [include-page id="8243" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="9547" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" " more="mehr»"] [include-page id="9414" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (ASQ- Modul) " more="mehr»"] [include-page id="10308" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" "
- [Winter 16/17](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1617/) - Lehre im Wintersemester 2016/2017 [include-page id="6200" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Übung und Tutorium) " more="mehr»"] [include-page id="6215" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Praktikum) " more="mehr»"] [include-page id="6222" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Übung und Tutorium) " more="mehr»"] [include-page id="6226" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Übung und Tutorium) " more="mehr»"] [include-page id="6194"
- [Winter 17/18](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1718/) - Lehre im Wintersemester 2017/2018 [include-page id="6833" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Übung und Tutorium) " more="mehr»"] [include-page id="6847" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Praktikum) " more="mehr»"] [include-page id="6851" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Übung und Tutorium) " more="mehr»"] [include-page id="6842" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Seminar) " more="mehr»"]
- [Winter 18/19](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1819/) - Lehre im Wintersemester 2018/2019 [include-page id="7373" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="7378" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Praktikum) " more="mehr»"] [include-page id="7381" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung; auch für BachelorStudenten) " more="mehr»"] [include-page id="7387" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Seminar) " more="mehr»"]
- [Winter 19/20](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1920/) - Lehre im Wintersemester 2019/2020 [include-page id="7909" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="7918" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Praktikum) " more="mehr»"] [include-page id="7902" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung; auch für BachelorStudenten) " more="mehr»"] [include-page id="7915" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Seminar) " more="mehr»"]
- [Winter 20/21](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-20-21/) - Lehre im Wintersemester 2020/2021 Sticky Note mit Informationen zur Lehre im Wintersemester. [include-page id="8934" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="8943" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Praktikum) " more="mehr»"] [include-page id="8951" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Übung und Tutorium; auch für Bachelor-Studies) " more="mehr»"] [include-page id="8960" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore="
- [Winter 21/22](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-21-22/) - Lehre im Wintersemester 2021/2022 [include-page id="8934" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Tutorium und Übung) " more="mehr»"] [include-page id="8943" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Praktikum) " more="mehr»"] [include-page id="7641" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="7902" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Tutorium und Übung) " more="mehr»"] [include-page id="8960" displayTitle="true"
- [Winter 22/23](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-22-23/) - Lehre im Wintersemester 2022/2023 [include-page id="8934" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Tutorium und Übung) " more="mehr»"] [include-page id="6215" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Praktikum) " more="mehr»"] [include-page id="8951" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung, Tutorium und Übung) " more="mehr»"] [include-page id="8960" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Seminar) " more="mehr»"]
- [Sommer 2016](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2016/) - Lehre im Sommersemester 2016 [include-page id="5911" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="5922" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (ASQ) " more="mehr»"] [include-page id="5934" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (ASQ) " more="mehr»"] [include-page id="5947" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Proseminar) " more="mehr»"] [include-page id="5918" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Seminar) "
- [Currents in Bioinformatics](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-21-22/currents-in-bioinformatics/) - Letztmalig/aktuell im WiSe 2023/24 Nächste Instanz geplant im SoSe 2024 Dienstag 16:15 - 17:45 Uhr; SR 3423 EAP2 Beginn: 17.10.2023 Seminarleitung: Sebastian Böcker Vorläufige Paper-Liste [1] G. McCallum and C. Tropini, “The gut microbiota and its biogeography,” Nat Rev Microbiol, pp. 1–14, Sep. 2023, doi: 10.1038/s41579-023-00969-0. [2] A. Sharma, D. Czégel, M. Lachmann, C. P.
- [Workshop: Summer School on Non-Targeted Metabolomics Data Mining for Biomedical Research 21-25 August 2023](https://bio.informatik.uni-jena.de/workshops/2023-non-targeted-metabolomics-data-mining-for-biomedical-research/) - Preparation for SIRIUS+CSI:FingerID Download the GUI and CLI version for your operating system from https://bio.informatik.uni-jena.de/software/sirius/ Install SIRIUS following the installation instructions on https://bio.informatik.uni-jena.de/software/sirius/ Open SIRIUS (in case of problems, have a look at the online documentation or contact us). [OPTIONAL] Create personal User Account using your academic email address and verify your email address using
- [Workshops](https://bio.informatik.uni-jena.de/workshops/) - Coming soon!
- [Retention time repository](https://github.com/michaelwitting/RepoRT)
- [Mitarbeiter Harvester](https://bio.informatik.uni-jena.de/jobs/mitarbeiter-harvester/) - Join the team! The Chair for Bioinformatics, Institute of Computer Science at the Friedrich-Schiller-University Jena offers the following position: PostDoc/PhD students as a research associate (Wissenschaftliche Mitarbeiter) The position is part of the project Harvester, funded by the Deutsche Forschungsgemeinschaft. Topic of research: Metabolomics complements investigation of the genome, transcriptome, and proteome of an organism.
- [PhD Position for EU HUMAN Doctoral Network](https://bio.informatik.uni-jena.de/jobs/phd-position-for-eu-human-dorctoral-network/) - The Chair for Bioinformatics, Institute of Computer Science at the Friedrich-Schiller-University Jena offers the following position: PhD Student for EU HUMAN Doctoral Network (Wissenschaftliche Mitarbeiterin) The doctoral network HUMAN (Harmonising and Unifying Blood Metabolomic Analysis Networks) is a multidisciplinary consortium that focuses on topics such as cross-laboratory comparisons, integration, co-evaluation, and proofing of liquid chromatography
- [Plums](https://bio.informatik.uni-jena.de/software/plums/) - PLUMS is a software that analyses tandem mass spectra of synthetic polymers. It helps to identify fragmentation series of homopolymers by determining the end groups of the fragments. Therefor no further knowledge of the polymer class or the fragmentation mechanism is required. The user only needs a peak list of the matrix–assisted laser desorption/ionization tandem
- [Für Schüler](https://bio.informatik.uni-jena.de/schueler/) - Wir haben eine Seite eingerichtet, die hoffentlich alles beinhaltet was ihr zum Bioinformatik-Studium in Jena wissen wollt und auf die wichtigsten Seiten der Uni verlinkt! Außerdem gibt es hier ein Einführungsvideo als Appetithappen. Du willst wissen was Bioinformatik ist? Wie der Job eines Bioinformatikers aussieht? Erfahre mehr über die vielfältigen Forschungsfelder, aktuelle Forschungsarbeiten und die verschiedene
- [Lecture notes on Algorithmic Mass Spectrometry](https://bio.informatik.uni-jena.de/textbook-algoms/) - Textbook for computational mass spectrometry (algorithms, combinatorics, a little statistics and machine learning) by Sebastian Böcker
- [Datamining und Sequenzanalyse](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-21-22/datamining-und-sequenzanalyse/) - Veranstalter: Markus Fleischauer Termine: Mo 10:15-11:45h ab 10.11.21 -> Mi 16:30-18:00h , Fr 12:30-14:00h Wo: EAP2; LinuxPool 1 Vorläufiger Ablauf Termin Thema Folien Aufgaben Daten Material 18.10. • Organisatorisches• Wiederholung Java/OOP• Systemkonfiguration Einführung Leitfaden Projektpräsentation .gitignore . • git git • gradle• Beginn Exakte Suche gradleexactSearch Aufgaben ExactSearch datenExactSearch
- [Lehre in früheren Semestern](https://bio.informatik.uni-jena.de/lehre/lehre-history/) - Lehre im Sommersemester 2015 Lehre im Wintersemester 2014/2015 Lehre im Sommersemester 2014 Lehre im Wintersemester 2013/2014 Lehre im Sommersemester 2013 Lehre im Wintersemester 2012/2013 Lehre im Sommersemester 2012 Bachelor Bioinformatik [include-page id="2203" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="2215" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page
- [Data Mining und Sequenzanalyse](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1718/data-mining-und-sequenzanalyse/) - Veranstalter: Markus Fleischauer, Martin Hoffmann Termine: Mo 10:15-11:45h, Fr 12:15-13:45h, Linux-Pool I EAP2 Vorläufiger Ablauf Termin Thema Folien Aufgaben Daten 16.10. • Organisatorisches • Wiederholung Linux/Java/OOP Einfuehrung Leitfaden Projektpraesentation 20.10. • git • Gradle git und gradle 23.10. • Beginn Exakte Suche aufgabenExakteSuche dataExactSearch 27.10. Projektarbeit 30.10. • Exakte Suche • Collections slidesExactSearch collections 03.11. •
- [Data Mining und Sequenzanalyse](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1819/data-mining-und-sequenzanalyse/) - Veranstalter: Kai Dührkop, Markus Fleischauer Termine: Mo 10:15-11:45h, Fr 12:15-13:45h, Linux-Pool I EAP2 Vorläufiger Ablauf Termin Thema Folien Aufgaben Daten 15.10. • Organisatorisches • Wiederholung Linux/Java/OOP Einfuehrung Leitfaden Projektpraesentation 19.10. • git git 22.10. • gradle gradle 26.10. • Collection • Beginn Exakte Suche collections aufgabenExakteSuche dataExactSearch 29.10. Projektarbeit 02.11. Projektarbeit 05.11. Projektarbeit 09.11. • Unit
- [Privacy Policy](https://bio.informatik.uni-jena.de/privacy-policy-fsu-csi-2021-07-05/) - Last updated: July 5, 2021 We collect personal data such as email addresses when you provide it to us through registration or emails. We use those data to provide you the requested services and for other purposes for which you have given your consent. Furthermore, when querying our services your computer provides us with its
- [Terms of Service](https://bio.informatik.uni-jena.de/terms-of-service-fsu-csi-2021-07-05/) - Terms of use Last updated: July 5, 2021 1. Definitions "Academic use" is defined as the non-profit usage of the SIRIUS web services for teaching and research within an academic institution or research institute. For-profit use, usage for consultancy or service, and usage within collaborative projects funded by non‐academic institutions is excluded. "SIRIUS web services"
- [Sommer 2017](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2017/) - Lehre im Sommersemester 2017 [include-page id="6563" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="6594" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Vorlesung und Übung) " more="mehr»"] [include-page id="6583" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (Proseminar) " more="mehr»"] [include-page id="6588" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter=" (ASQ) " more="mehr»"] [include-page id="6575" displayTitle="true" displayStyle="DT_TEASER_MORE" titleBefore=" " titleAfter="
- [CANOPUS](https://bio.informatik.uni-jena.de/software/canopus/) - CANOPUS is a tool for predicting compound classes directly from MS/MS. Because it does not depend on any database, CANOPUS is suitable for the classification of unknowns. CANOPUS runs as a webservice and is integrated in SIRIUS from version 4.4. Installation Please, download the appropriate SIRIUS version for your operating system, here. You need version
- [Currents in Bioinformatics](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2021/currents-in-bioinformatics/) - Onlineveranstaltung; Zoom-Meeting Dienstag 16:15-17:45 Uhr Beginn: 13.04.2021 Seminarleitung: Fleming Kretschmer Diese Veranstaltung findet dieses Semester online statt. Teilnehmer erhalten den Einladungslink per E-mail über Friedolin. Vorläufiger Ablaufplan Date Paper Presenter and Backup 13.04 Organisatorisches, Besprechen der Themen 20.04. - 27.04. [1] 04.05. [10] 11.05. [15] 18.05. Schnelldurchlauf "Bioinformatics" Papers 25.05.
- [passatutto](https://bio.informatik.uni-jena.de/passatutto/)
- [SIRIUS](https://bio.informatik.uni-jena.de/software/sirius/)
- [ZODIAC](https://bio.informatik.uni-jena.de/software/zodiac/) - ZODIAC performs de novo molecular formula annotation on complete biological datasets (high-resolution, high mass accuracy LC-MS/MS runs). In order to use ZODIAC, please download SIRIUS 4.4; ZODIAC is integrated. SIRIUS ranks molecular formulas for each compound individually using fragmentation trees and isotope pattern analysis. ZODIAC takes the fragmentation trees as input and reranks the molecular
- [MoLE](https://bio.informatik.uni-jena.de/software/mole/) - The “Molecule Labeling Estimator” is a tool for estimating heavy isotope incorporations of molecules based on mass spectrometry data. The basic concept of the underlying method is to simulate the isotope pattern of the sample molecule for different incorporations and to match those with the isotope pattern of the measured sample. Both peak intensities and
- [PEACE](https://bio.informatik.uni-jena.de/software/peace/) - PEACE (Parameterized and Exact Algorithms for Cluster Editing) is a project for clustering experimental data using a weighted graph derived from pairwise similarity information. The underlying mathematical model is the NP-complete Cluster Editing problem. Similar models are used in the clustering algorithms CLICK and CAST. Advantages are that you do not have to specify cluster
- [Algorithmische Massenspektrometrie](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1617/algorithmische-massenspektrometrie/) - Veranstalter: Sebastian Böcker Vorlesung: Freitag (beginnend: 21.10.2016), 08:30 Uhr - 10.00 Uhr; SR 120 CZ3 Übungsleiter: Kai Dührkop Übungstermin: Dienstag (beginnend: 01.11.2016); 12.15 Uhr - 13.45 Uhr; SR 125 CZ3 Tutorium: Montag, 10:15 - 11:45; 14 tägl. (Beginn: 24.10.2016); SR 3423 EAP2 Vorläufige Ablauf Termin Themen Folien Übung Skript 21.10.2016 Themenüberblick, Organisatorisches Folien 28.10.2016 Einführung
- [Algorithmische Massenspektrometrie](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1819/algorithmische-massenspektrometrie/) - Veranstalter: Sebastian Böcker Vorlesung: Donnerstag, 12:30 Uhr - 14.00 Uhr; SR 385 SR 114 CZ3 Übungsleiter: Kai Dührkop, Martin Hoffmann Übungstermin: Dienstag (beginnend: 23.10.2018); 12.15 Uhr - 13.45 Uhr; SR 114 AB4 Tutorium: Montag, 12:30 - 14:00; 14 tägl. (Beginn: 29.10.2018); SR 131 CZ3 SR 3423, EAP2 Vorläufiger Ablauf Termin Themen Folien Übung 18.10.2018 Themenüberblick, Organisatorisches
- [Einführung in die Bioinformatik I-2](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2020/einfuhrung-in-die-bioinformatik-i-2/) - Vorlesungstermin: Di 10:15-11:45 Uhr, SR 131 CZ 3 (Beginn: 05.05.2020) Veranstalter: apl. Prof. Dr. Peter Dittrich Übung (Beginn: 07.05.2020) Do 14:15 - 15:45 Uhr, CZ3 SR 131 Übungsleiter: Marcus Ludwig Tutorium: Klausur: Donnerstag, 13.08.2020; 10:00 - 12:00 Uhr; SR 306 CZ3 Vorläufiger Vorlesungsplan
- [Currents in Bioinformatics](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2020/currents-in-bioinformatics/) - Beginn: 05.05.2020 16:15-17:45Seminarleitung: Martin Hoffmann Dieses Semester online über Zoom, den Einladungslink erhaltet ihr jede Woche per Email. Die Liste der zu besprechenden paper findet ihr hier: jc2020_sommer
- [Proseminar Bioinformatik](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2020/proseminar-bioinformatik/) - Seminarleitung: Martin Hoffmann Termin: Fr 10:15 - 11:45 h Ort: (SR 3423 EAP2) Dieses Seminar wird bis auf weiteres online stattfinden, genauere Informationen werden zeitnah versendet Beginn: 08.05.2020
- [BioinfoWelten (redirect)](http://bioinfowelten.uni-jena.de/#new_tab)
- [Bioinformatik in Jena (redirect)](http://bioinformatik.uni-jena.de/#new_tab)
- [sirius2 (redirect)](https://bio.informatik.uni-jena.de/sirius2/)
- [Datamining und Sequenzanalyse](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1920/data-mining-und-sequenzanalyse/) - Veranstalter: Markus Fleischauer Termine: Mo 10:15-11:45h, Fr 12:30-14:00h, Linux-Pool I EAP2 Vorläufiger Ablauf Termin Thema Folien Aufgaben Daten 14.10. • Organisatorisches• Wiederholung Linux/Java/OOP Einfuehrung Leitfaden Projektpraesentation .gitignore 18.10. • git• gradle gitgradle 21.10. • Collection• Beginn Exakte Suche exactSearchcollections aufgabenExakteSuche dataExactSearch 25.10. Projektarbeit 28.10. Projektarbeit 01.11. Projektarbeit
- [Bond Order](https://bio.informatik.uni-jena.de/software/bond-order-assignment/) - Bond order is essential for several applications in chemistry. Unfortunately, this information is omitted in many data formats of molecule graphs. We have developed a Java-based program that computes bond order assignments of molecule graphs using a penalty function as suggested by Wang et al. 2006. This program implements our tree decomposition-based dynamic programming algorithm
- [Einführung in die Bioinformatik I-2](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2019/einfuhrung-in-die-bioinformatik-i-2/) - Vorlesungstermin: Di 10:15-11:45h, SR 225 CZ 3 (Beginn: 09.04.2019) Veranstalter: Sebastian BöckerÜbung: Gruppe 1: Do 14:15 - 15:45h, CZ3 SR 131 Übungsleiter: Marcus Ludwig Gruppe 2: Do 14:15 - 15:45h, CZ3 SR 125Übungsleiter: Emanuel Barth, Maximilian Collatz Tutorium: Donnerstag, 10:15 - 11:45 Uhr am 18.04.19 / 25.04.19 / 16.05.19 / 23.05.19 / 06.06.19 / 20.06.19 / 04.07.19;
- [Einführung in die Bioinformatik I-1](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1920/einfuhrung-in-die-bioinformatik-i-1/) - Veranstalter: Peter Dittrich Vorlesungstermin: Di 10:15-11:45h, SR 384 CZ3 Übung: beginnt in der 2. Vorlesungswoche - 23.10.2019 Gruppe 1: Übungsleiter: Marcus Ludwig Mi 14:15-15:45h, SR 130 CZ3 Gruppe 2: Übungsleiter: Emanuel Barth Mi 14:15-15:45h, SR 131 CZ3 Tutorium: wird noch festgelegt Vorläufiger Vorlesungsplan Datum Thema Folien Übungsblatt Abgabe am 15.10. Formales, Ablauf
- [Einführung in die Bioinformatik I-2](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2016/einfuhrung-in-die-bioinformatik-i-2/) - Veranstalter: Peter Dittrich Vorlesungstermin: Di 10:15-11:45h, SR 225 CZ 3 Übungstermin: Do 14:15-15:45 Übung Übungsleiter: Marcus Ludwig Raum: SR 1 (TO, 113), Lessingstrasse 8 Tutorium: Fr 14:15 - 15:45 Uhr (14- tägl.), SR 125 CZ3 Klausur: 03.08.2016 10-12 s.t. (also punkt 10 Uhr!) SR025 AB 4 Hinweis: nicht-programmierfähigen Taschenrechner und Thoska nicht vergessen! Vorläufiger Vorlesungsplan Datum Thema Folien
- [Einführung in die Bioinformatik I-1](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1617/einfuhrung-in-die-bioinformatik-i-1/) - Veranstalter: Sebastian Böcker Vorlesungstermin: Di 10:15-11:45h, SR 225 CZ3 Übungsgruppe 1: Mi 14:15 - 15:45h, SR 108 AB4 Übungsleiter: Marcus Ludwig Übungsgruppe 2: Mi 14:15 - 15:45h, SR 206 CZ3 Übungsleiter: Emanuel Barth, Maximilian Collatz Tutorium: Di 08:30 - 10:00h, SR 3423 EAP2 (14 tägl., beginnend am 25.10.2016) Vorläufiger Vorlesungsplan Datum Thema Folien Übungsblatt Abgabe am 18.10. Formales, Ablauf Übung
- [Einführung in die Bioinformatik I-2](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2017/6563-2/) - Vorlesungstermin: Di 10:15-11:45h, SR 225 CZ 3 Veranstalter: Sebastian Böcker Übungstermin: Gruppe 1: Do 14:15 - 15:45h, SR 314, CZ3 Gruppe 2: Do 14:15 - 15:45h, SR 131, CZ3 Übungsleiter: Marcus Ludwig, E. Barth Tutorium: (14- tägl.; Beginn: 20.04.): Do 12:30 - 14:00h, SR 3423 EAP2 Klausurtermin (schriftlich): am Dienstag, den 01.08.2017 von 10 - 12 Uhr, SR
- [Einführung in die Bioinformatik I-1](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1718/einfuhrung-in-die-bioinformatik-i-1/) - Veranstalter: Peter Dittrich Vorlesungstermin: Di 10:15-11:45h, SR 1 TO Lessingstrasse 8 Übung: Gruppe 1: Mi 14:15 - 15:45h, CZ3 SR130 Übungsleiter: Marcus Ludwig Gruppe 2: Mi 14:15 - 15:45h, CZ3 SR131 Übungsleiter: Emanuel Barth, Maximilian Collatz Tutorium: Termin wird in der 1. Vorlesung festgelegt Vorläufiger Vorlesungsplan Datum Thema Folien Übungsblatt Abgabe am 17.10. Formales, Ablauf Übung 0
- [Einführung in die Bioinformatik I-2](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2018/einfuhrung-in-die-bioinformatik-i-2/) - Vorlesungstermin: Di 10:15-11:45h, SR 225 CZ 3 Veranstalter: Peter Dittrich Übung: erster Termin am 19.04. Gruppe 1: Do 14:15 - 15:45h, SR 3423 EAP Übungsleiter: Marcus Ludwig Gruppe 2: Do 14:15 - 15:45h, CZ3 SR131 Übungsleiter: Emanuel Barth, Maximilian Collatz Tutorium: (14- tägl.): voraussichtlich Mo 14.15 - 16.15 Klausur: Donnerstag, 09.08.2018; 10.00 - 12.00 Uhr; August-Bebel-Str. 4 - HS (Domaschk-Hörsaal)
- [Einführung in die Bioinformatik I-1](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1819/einfuhrung-in-die-bioinformtik-i-1/) - Veranstalter: Sebastian Böcker Vorlesungstermin: Di 10:15-11:45h, SR 348 CZ3 Übung: beginnt am 24.10.2018 Gruppe 1: Mi 14:15 - 15:45h, CZ3 SR130 Übungsleiter: Marcus Ludwig Gruppe 2: Mi 14:15 - 15:45h, CZ3 SR131 Übungsleiter: Emanuel Barth, Maximilian Collatz Tutorium: 08:30 Uhr - 10:00 Uhr, 14-tägl. (Beginn: 24.10.2018); SR 3423 EAP2 Vorläufiger Vorlesungsplan Datum Thema Folien Übungsblatt Abgabe am
- [SIRIUS 4.4 (Beta)](https://bio.informatik.uni-jena.de/sirius-4-4/) - Changelog
- [SIRIUS 4.0.1](https://bio.informatik.uni-jena.de/software/sirius-4-0-1/)
- [Beruf und Karriere](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2020/beruf-und-karriere/) - Veranstalter: Sebastian Böcker Termin: Ort: SR 3423 EAP2 Beginn: Ablaufplan
- [Currents in Bioinformatics](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1920/currents-in-bioinformatics/) - Seminarleiter: Sebastian Böcker Termin: Di 16-18h, SR 3423 EAP2 Beginn: 15.10.2019 Im Journal Club wird wöchentlich ein aktueller Artikel aus der bioinformatischen Forschung vorgestellt und diskutiert.Details werden in der ersten Veranstaltung besprochen. Vorläufiger Ablaufplan Date Paper Presenter and Backup 15.10. Organisatorisches, Besprechen der Themen 22.10. 29.10. 05.11. 12.11.
- [Datenschutz](https://bio.informatik.uni-jena.de/datenschutz/) - Datenschutzerklärung Diese Datenschutzerklärung klärt Sie über die Art, den Umfang und Zweck der Verarbeitung von personenbezogenen Daten (nachfolgend kurz „Daten“) innerhalb unseres Onlineangebotes und der mit ihm verbundenen Webseiten, Funktionen und Inhalte sowie externen Onlinepräsenzen, wie z.B. unser Social Media Profile auf (nachfolgend gemeinsam bezeichnet als „Onlineangebot“). Im Hinblick auf die verwendeten Begrifflichkeiten, wie z.B.
- [Disclaimer](https://bio.informatik.uni-jena.de/disclaimer/) - Inhalt des Onlineangebotes Die Inhalte der Webseiten der Friedrich-Schiller-Universität Jena werden mit größter Sorgfalt recherchiert und implementiert. Fehler im Bearbeitungsvorgang sind dennoch nicht ausgeschlossen. Die Friedrich-Schiller-Universität Jena übernimmt keine Gewähr für die Aktualität, Korrektheit und Vollständigkeit der bereitgestellten Informationen. Haftungsansprüche gegen die Friedrich-Schiller-Universität Jena, welche sich auf Schäden materieller oder ideeller Art beziehen, die durch die
- [Currents on Bioinformatics](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2019/currents-on-bioinformatics/) - Seminarleiter: Sebastian BöckerTermin: Di 16-18 h, SR 3423 EAP2Beginn: 09.04.2019 Im Journal Club wird wöchentlich ein aktueller Artikel aus der bioinformatischen Forschung vorgestellt und diskutiert.Details werden in der ersten Veranstaltung besprochen. Vorläufiger Ablaufplan DatePaperPresenter and Backup09.04.Organisatorisches, Besprechen der ThemenMartin List of papers: list Template:https://bio.informatik.uni-jena.de/wp-content/uploads/2018/11/Abstract_Template_21.doc
- [Beruf und Karriere](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2019/beruf-und-karriere/) - Veranstalter: Sebastian BöckerTermin: Einführungsveranstaltung am 08.04.2019 Mittwoch, 24.04.2019, 15:00 - 17:30 UhrMittwoch, 15.05.2019, 15:00 - 17:30 UhrMittwoch, 05.06.2019, 15:00 - 17:30 UhrMittwoch, 03.07.2019, 15:00 - 17:30 UhrOrt: SR 3423 EAP2Beginn: 08.04.2019 Ablaufplan DatumThema08.04.2019Einführung24.04.2019Lebensläufe15.05.2019Stellenausschreibung 05.06.2019Karriereanker 03.07.2019Qualifikation
- [Script Algorithmic Mass Spectrometry (redirect)](https://bio.informatik.uni-jena.de/script-algoms/)
- [Proseminar Bioinformatik](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2019/proseminar-bioinformatik/) - Seminarleitung: Martin HoffmannTermin: Mi 08:15 - 09:45 h Ort: SR 3423 EAP2 Vorläufiger Terminplan TerminThemaVortragende(r)10.04.19Vorbesprechung 17.04.19Einführung: Wissenschaftliche Paper lesen, Vorträge halten 24.04.19Einführung: Wissenschaftliche Poster gestalten 08.05.19 15.05.1922.05.1929.05.1905.06.1912.06.1919.06.1926.06.1903.07.1910.07.19
- [Currents in Bioinformatics](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1819/currents-in-bioinformatics/) - Seminarleiter: Martin Hoffmann Termin: Di 16-18h, SR 3423 EAP2 Beginn: 16.10.2018 Im Journal Club wird wöchentlich ein aktueller Artikel aus der bioinformatischen Forschung vorgestellt und diskutiert. Details werden in der ersten Veranstaltung besprochen. Vorläufiger Ablaufplan Date Paper Presenter and Backup 16.10. Organisatorisches, Besprechen der Themen 23.10. How to read a paper 30.10. 06.11. 13.11. 20.11. 27.11.
- [Algorithmische Phylogenetik](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2018/algorithmische-phylogenetik/) - Veranstalter: Sebastian Böcker Vorlesungstermin: Montag, 12.30 - 14.00 Uhr; SR 128 CZ3 + Donnerstag, 08.30 - 10.00 Uhr; SR 130 CZ3 (14-tägl.) Übungsleiter: Markus Fleischauer Donnerstag, 12.30 - 14.00 Uhr; SR 123 CZ3 mündliche Prüfung: 02.08.2018 & 09.08.2018 - Liste liegt im Sekretariat Vorläufige Ablauf Termin Themen Folien Übung (Abgabe) Mo 09.04. V Einführung, Formalitäten
- [MSICorrect](https://bio.informatik.uni-jena.de/software/msicorrect/)
- [Proseminar Bioinformatik](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2018/proseminar-bioinformatik/) - Seminarleitung: Martin Hoffmann Termin: Mi 08:15-09:45h Do 16:00 - 17:30 Uhr SR 3423, EAP2 SR 128 CZ3 Vorläufiger Terminplan Termin Thema Vortragende(r) 11.04. Vorbesprechung 18.04. verschoben 26.04. Einführung: Wissenschaftliche Paper lesen, Vorträge halten 03.05. Einführung: Wissenschaftliche Poster gestalten 09.05. Journal Club
- [Beruf und Karriere](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2018/beruf-und-karriere/) - Veranstalter: Sebastian Böcker Termin: Mo 14:30 - 17:15, Ort: SR 3423 EAP2 Termin: 16.04.2018; 07.05.2018; 28.05.2018; 11.06.2018 Ablaufplan Datum Thema 16.04.2018 Einführung 07.05.2018 Lebensläufe, Stellenausschreibung 28.05.2018 Karriereanker, Qualifikation 11.06.2018
- [Bioinformatische Methoden in der Genomforschung](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1718/bioinformatische-methoden-in-der-genomforschung/) - Veranstalter: Sebastian Böcker Vorlesungstermin: Do 12.30-14.00h, SR 122 CZ3 Tutorium: Beginn: 01.11.17, Mi 10.15-11.45h, SR 3423 EAP2, 14-tägl. Übungstermin: Mo 12.30-14.00h, SR 131 CZ3 Übungsleiter: Martin Hoffmann Vorläufiger Ablaufplan Termin Themen Folien Übungsausgabe Übungsabgabe 19.10. Vorlesung: Einführung 23.10. Übung entfällt 26.10. Vorlesung: BACs sortieren Vorlesung1_Folien uebung1 02.11.2017 30.10. Übung 01.11. Tutorium 02.11. Vorlesung: Microarrays 1 Vorlesung2_folien
- [Currents in Bioinformatics](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1718/currents-in-bioinformatics/) - Seminarleiter: Martin Hoffmann Termin: Di 16-18h, SR 3423 EAP Beginn: 17.10.2017 Im Journal Club wird wöchentlich ein aktueller Artikel aus der bioinformatischen Forschung vorgestellt und diskutiert. Details werden in der ersten Veranstaltung besprochen. Vorläufiger Ablaufplan Date Paper Presenter and Backup 17.10. Organisatorisches, Besprechen der Themen 24.10. 31.10. 07.11. Open Molecule Generator Martin 14.11. 21.11. 28.11. 05.12.
- [Greedy Strict Consensus Merger](https://bio.informatik.uni-jena.de/software/gscm/)
- [BCD Supertrees](https://bio.informatik.uni-jena.de/software/bcd/)
- [CSI:FingerID](https://bio.informatik.uni-jena.de/software/csi-fingerid/) - CSI:FingerId is a search engine for searching molecular structures in PubChem using tandem mass spectra.
- [Praktikum Strukturvorhersage](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2017/praktikum-strukturvorhersage/) - Daten von der CASMI 2017 challange 1-45: casmi2017 Aufgaben: struktAufklaerung_Aufgaben
- [Proseminar Bioinformatik](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2017/proseminar-bioinformatik/) - Seminarleitung: Franziska Hufsky, Martin Hoffmann Termin: Mi 08:15-09:45h SR 3423, EAP2 Vorläufiger Terminplan Termin Thema Vortragende(r) 05.04. verschoben 12.04. Vorbesprechung 19.04. Einführung: Wissenschaftliche Paper lesen 26.04. Einführung: Wissenschaftliche Vorträge halten 03.05. Einführung: Wissenschaftliche Poster gestalten
- [LaTeX Grundlagen für Naturwissenschaftler](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2017/latex-grundlagen-fur-naturwissenschaftler/) - Seminarleiter: Martin Hölzer (Marz-Gruppe) Termin Einführungsveranstaltung: 21.04.2017; 09.00 - 10.00 Uhr; SR 3423 EAP2 Termin Blockveranstaltung: wird noch bekannt gegeben! Vorläufiger Ablaufplan Was ist LaTeX? Warum LaTeX? Basics: Syntax Erzeugen des Dokuments Dokumentaufbau, Seitenlayout und Prämbel Dokumentstruktur Crossreferencing Text Formatierung: Encoding Schriften White Space Listen Boxen Fußnoten, Randnotizen etc. Silbentrennung Farben Abbildungen und Tabellen: Bilder importieren Floats Tabellen
- [Currents on Bioinformatics](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2017/currents-on-bioinformatics/) - Seminarleiter: Martin Hoffmann Termin: Di 16-18h, SR 3423 EAP Beginn: 04.04.2017 Im Journal Club wird wöchentlich ein aktueller Artikel aus der bioinformatischen Forschung vorgestellt und diskutiert. Details werden in der ersten Veranstaltung besprochen. Vorläufiger Ablaufplan Date Paper Presenter and Backup 04.04. Organisatorisches, Besprechen der Themen Martin List of papers:
- [Scriptsprachen in der Bioinformatik](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2017/scriptsprachen-in-der-bioinformatik/) - Seminarleiter: Emanuel Barth, Kai Dührkop Termin Vorlesung: Freitag, 10 - 12 Uhr, SR 3423 EAP2 Termin Praktikum: Freitag, 12 - 14 Uhr, LinuxPool 1 EAP2 Slides und Übungen: Python Grundlagen (Übung 1) Funktionale Programmierung (Übung 2) Datenstrukturen und Web-APIS (Übung 3) numpy und matplotlib (Übung 4)
- [Algorithmische Phylogenetik](https://bio.informatik.uni-jena.de/lehre/lehre-history/winter-1617/algorithmische-phylogenetik/) - Veranstalter: Sebastian Böcker Vorlesungstermin: Montag, 12.30 - 14.00 Uhr; SR 131 CZ3 + Donnerstag, 12.30 - 14.00 Uhr; SR 123 CZ3 Übungsleiter: Markus Fleischauer Mittwoch, 10.00 - 11.30 Uhr; SR 119 AB4 Vorläufige Ablauf Termin Themen Folien Übung Mo 17.10. V Einführung, Formalitäten Do 20.10. V verschoben Mo 24.10. V Kurze Einführung Graphentheorie Folien 1
- [LATEX Grundlagen für Naturwissenschaftler](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2016/latex-grundlagen-fur-naturwissenschaftler/) - Seminarleiter: Franziska Hufsky, Markus Fleischauer, Marcus Ludwig Termin Einführungsveranstaltung: 11.04.2016; 16:00 - 18:00 Uhr im SR 3423 EAP2 Termin Blockveranstaltung: 08.08.2016 bis 14.08.2016, 10:00 – 16:00 Uhr im LinuxPool II (Raum 3413, EAP2) Vorläufiger Ablaufplan Was ist LaTeX? Warum LaTeX? Basics: Handout, Aufgaben Syntax Erzeugen des Dokuments Dokumentaufbau, Seitenlayout und Prämbel Dokumentstruktur Crossreferencing Text Formatierung: Handout, Aufgaben Encoding Schriften White
- [Proseminar Bioinformatik](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2016/proseminar-bioinformatik/) - Seminarleitung: Franziska Hufsky Termin: Mi 12:30-14h SR 3423 EAP2 Vorläufiger Terminplan Termin Thema Vortragende(r) 06.04. Vorbesprechung 13.04. Einführung: Wissenschaftliche Paper lesen 20.04. Einführung: Wissenschaftliche Vorträge halten 27.04. Journal Club: Wolf et al. In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics, 11:148, 2010. 04.05. Einführung: Wissenschaftliche Poster gestalten 11.05. Algorithms
- [Scriptsprachen in der Bioinformatik](https://bio.informatik.uni-jena.de/lehre/lehre-history/sommer-2016/scriptsprachen-in-der-bioinformatik/) - Seminarleiter: Emanuel Barth, Kai Dührkop Termin Vorlesung: Freitag, 10 - 12 Uhr, SR 3423 EAP2 Termin Praktikum: Freitag, 12 - 14 Uhr, LinuxPool 1 EAP2 Slides und Übungen: Python Grundlagen (Übung 1) Funktionale Programmierung (Übung 2) Datenstrukturen und Web-APIS (Übung 3) numpy und matplotlib (Übung 4)
- [Decomp](https://bio.informatik.uni-jena.de/software/decomp/)
- [EPoS](https://bio.informatik.uni-jena.de/epos/)
- [Theses](https://bio.informatik.uni-jena.de/publications/theses/)

## Categories

- [News](https://bio.informatik.uni-jena.de/category/news/)
- [Sirius News](https://bio.informatik.uni-jena.de/category/sirius-news/) - This is the category for siriues and fingerid news
- [Pearls from the swines](https://bio.informatik.uni-jena.de/category/pearls-from-the-swines/)

## Tags

- [epos](https://bio.informatik.uni-jena.de/tag/epos/)
- [sirius](https://bio.informatik.uni-jena.de/tag/sirius/)
- [fingerid](https://bio.informatik.uni-jena.de/tag/fingerid/)
- [bioinfojena](https://bio.informatik.uni-jena.de/tag/bioinfojena/)
- [CSI:FingerID](https://bio.informatik.uni-jena.de/tag/csifingerid/)
- [UniJena](https://bio.informatik.uni-jena.de/tag/unijena/)
- [user meeting](https://bio.informatik.uni-jena.de/tag/user-meeting/)
- [SIRIUS; SIRIUS 4; CSI:FingerID](https://bio.informatik.uni-jena.de/tag/sirius-sirius-4-csifingerid/)
- [SIRIUS 4](https://bio.informatik.uni-jena.de/tag/sirius-4/)
- [ASMS2019](https://bio.informatik.uni-jena.de/tag/asms2019/)
- [ASMSATL](https://bio.informatik.uni-jena.de/tag/asmsatl/)
- [ISMB](https://bio.informatik.uni-jena.de/tag/ismb/)
- [ECCB](https://bio.informatik.uni-jena.de/tag/eccb/)
- [SIRIUS 4.4](https://bio.informatik.uni-jena.de/tag/sirius-4-4/)
- [MacOS](https://bio.informatik.uni-jena.de/tag/macos/)
- [GNPS](https://bio.informatik.uni-jena.de/tag/gnps/)
- [FBMN](https://bio.informatik.uni-jena.de/tag/fbmn/)
- [ZODIAC](https://bio.informatik.uni-jena.de/tag/zodiac/)
- [CANOPUS](https://bio.informatik.uni-jena.de/tag/canopus/)
- [MZmine](https://bio.informatik.uni-jena.de/tag/mzmine/)
- [software](https://bio.informatik.uni-jena.de/tag/software/)
- [release](https://bio.informatik.uni-jena.de/tag/release/)
- [conference visit](https://bio.informatik.uni-jena.de/tag/conference-visit/)