@article{PfeufferBielowWeinetal.2024, author = {Pfeuffer, Julianus and Bielow, Chris and Wein, Samuel and Jeong, Kyowon and Netz, Eugen and Walter, Axel and Alka, Oliver and Nilse, Lars and Colaianni, Pasquale Domenico and McCloskey, Douglas and Kim, Jihyung and Rosenberger, George and Bichmann, Leon and Walzer, Mathias and Veit, Johannes and Boudaud, Bertrand and Bernt, Matthias and Patikas, Nikolaos and Pilz, Matteo and Startek, Michał Piotr and Kutuzova, Svetlana and Heumos, Lukas and Charkow, Joshua and Sing, Justin Cyril and Feroz, Ayesha and Siraj, Arslan and Weisser, Hendrik and Dijkstra, Tjeerd M. H. and Perez-Riverol, Yasset and R{\"o}st, Hannes and Kohlbacher, Oliver and Sachsenberg, Timo}, title = {OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data}, volume = {21}, journal = {Nature Methods}, number = {3}, publisher = {Springer Science and Business Media LLC}, issn = {1548-7091}, doi = {10.1038/s41592-024-02197-7}, pages = {365 -- 367}, year = {2024}, language = {en} } @article{KontouWalterAlkaetal.2023, author = {Kontou, Eftychia E. and Walter, Axel and Alka, Oliver and Pfeuffer, Julianus and Sachsenberg, Timo and Mohite, Omkar and Nuhamunanda, Matin and Kohlbacher, Oliver and Weber, Tilmann}, title = {UmetaFlow: An untargeted metabolomics workflow for high-throughput data processing and analysis}, volume = {15}, journal = {Journal of Cheminformatics}, doi = {10.1186/s13321-023-00724-w}, year = {2023}, abstract = {Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for untargeted metabolomics that combines algorithms for data pre-processing, spectral matching, molecular formula and structural predictions, and an integration to the GNPS workflows Feature-Based Molecular Networking and Ion Identity Molecular Networking for downstream analysis. UmetaFlow is implemented as a Snakemake workflow, making it easy to use, scalable, and reproducible. For more interactive computing, visualization, as well as development, the workflow is also implemented in Jupyter notebooks using the Python programming language and a set of Python bindings to the OpenMS algorithms (pyOpenMS). Finally, UmetaFlow is also offered as a web-based Graphical User Interface for parameter optimization and processing of smaller-sized datasets. UmetaFlow was validated with in-house LC-MS/MS datasets of actinomycetes producing known secondary metabolites, as well as commercial standards, and it detected all expected features and accurately annotated 76\% of the molecular formulas and 65\% of the structures. As a more generic validation, the publicly available MTBLS733 and MTBLS736 datasets were used for benchmarking, and UmetaFlow detected more than 90\% of all ground truth features and performed exceptionally well in quantification and discriminating marker selection.}, language = {en} } @inproceedings{GesingGrunzkeBalaskoetal.2011, author = {Gesing, Sandra and Grunzke, Richard and Balasko, Akos and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and Fels, Gregor and Herres-Pawlis, Sonja and Kacsuk, Peter and Kozlovszky, Miklos and Kr{\"u}ger, Jens and Packschies, Lars and Sch{\"a}fer, Patrick and Schuller, Bernd and Schuster, Johannes and Steinke, Thomas and Szikszay Fabri, Anna and Wewior, Martin and M{\"u}ller-Pfefferkorn, Ralph and Kohlbacher, Oliver}, title = {Granular Security for a Science Gateway in Structural Bioinformatics}, booktitle = {Proc. IWSG-Life 2011}, year = {2011}, language = {en} } @inproceedings{BirkenheuerBlunkBreuersetal.2011, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schuster, Johannes and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {MoSGrid: Progress of Workflow driven Chemical Simulations}, volume = {826}, booktitle = {Proc. of Grid Workflow Workshop 2011, Cologne, Germany}, publisher = {CEUR Workshop Proceedings}, year = {2011}, language = {en} } @inproceedings{GesingHerresPawlisBirkenheueretal.2012, author = {Gesing, Sandra and Herres-Pawlis, Sonja and Birkenheuer, Georg and Brinkmann, Andre and Grunzke, Richard and Kacsuk, Peter and Kohlbacher, Oliver and Kozlovszky, Miklos and Kr{\"u}ger, Jens and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Steinke, Thomas}, title = {The MoSGrid Community - From National to International Scale}, booktitle = {EGI Community Forum 2012}, year = {2012}, language = {en} } @article{BirkenheuerBlunkBreuersetal.2011, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and dos Santos Vieira, Ines and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schmalz, Hans-G{\"u}nther and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {A Molecular Simulation Grid as new tool for Computational Chemistry, Biology and Material Science}, volume = {3}, journal = {Journal of Cheminformatics 2011}, number = {Suppl 1}, doi = {10.1186/1758-2946-3-S1-P14}, year = {2011}, language = {en} } @inproceedings{GesingKacsukKozlovszkyetal.2011, author = {Gesing, Sandra and Kacsuk, Peter and Kozlovszky, Miklos and Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and Fels, Gregor and Grunzke, Richard and Herres-Pawlis, Sonja and Kr{\"u}ger, Jens and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Steinke, Thomas and Szikszay Fabri, Anna and Warzecha, Klaus Dieter and Wewior, Martin and Kohlbacher, Oliver}, title = {A Science Gateway for Molecular Simulations}, booktitle = {EGI (European Grid Infrastructure) User Forum 2011, Book of Abstracts}, pages = {94 -- 95}, year = {2011}, language = {en} } @article{GesingHerresPawlisBirkenheueretal.2012, author = {Gesing, Sandra and Herres-Pawlis, Sonja and Birkenheuer, Georg and Brinkmann, Andr{\´e} and Grunzke, Richard and Kacsuk, Peter and Kohlbacher, Oliver and Kozlovszky, Miklos and Kr{\"u}ger, Jens and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Steinke, Thomas}, title = {A Science Gateway Getting Ready for Serving the International Molecular Simulation Community}, volume = {PoS(EGICF12-EMITC2)050}, journal = {Proceedings of Science}, year = {2012}, language = {en} } @article{BirkenheuerBlunkBreuersetal.2012, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and dos Santos Vieira, Ines and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment}, volume = {4}, journal = {Journal of Cheminformatics}, number = {Suppl 1}, doi = {10.1186/1758-2946-4-S1-P21}, pages = {21}, year = {2012}, language = {en} } @article{GesingGrunzkeKruegeretal.2012, author = {Gesing, Sandra and Grunzke, Richard and Kr{\"u}ger, Jens and Birkenheuer, Georg and Wewior, Martin and Sch{\"a}fer, Patrick and Schuller, Bernd and Schuster, Johannes and Herres-Pawlis, Sonja and Breuers, Sebastian and Balasko, Akos and Kozlovszky, Miklos and Szikszay Fabri, Anna and Packschies, Lars and Kacsuk, Peter and Blunk, Dirk and Steinke, Thomas and Brinkmann, Andr{\´e} and Fels, Gregor and M{\"u}ller-Pfefferkorn, Ralph and J{\"a}kel, Ren{\´e} and Kohlbacher, Oliver}, title = {A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics}, journal = {Journal of Grid Computing}, year = {2012}, language = {en} }