ReceptorLight

Description

Joint project of

• Computer Architecture and Advanced Computing, Prof. Dr.-Ing. M. Bücker
• Heinz-Nixdorf Chair for Distributed Information Systems, Prof. Dr. B. König Ries
• Central Service Provider for Information Technology, Andreas Henkel

In the newly established Collaborative Research Centre (CRC) "High-end light microscopy elucidates membrane receptor function (ReceptorLight)," scientists from Jena and Würzburg are analyzing the function of membrane receptors using the most modern light microscopy. The overall objective of this research initiative is to gain new insight into the underlying physical and biological phenomena and the advancement of high-performance light microscopy. The volume of the resulting data sets will be large. Currently, we expect to record multi-petabyte data. In addition to the sheer size, the research activities will also need to focus on the variety of data. The aim of project Z2 is to design, implement, and deploy a CRC-wide software platform to store, manage, share, and process data of all CRC projects. The platform will ensure reproducibility and sustainability of research results. It will also allow for an interactive access and will enable a systematic analysis of the large and heterogeneous data. Thus, this project will not only provide participating scientists with a tool to organize and analyze their data, but also foster the exchange of tools and the sharing of knowledge.

Collaborating Institutions

• Friedrich Schiller University Jena
• Julius Maximilian University of Würzburg
• Jena University Hospital
• Leibniz Institute of Photonic Technology
• Rudolf Virchow Center

Funding

German Research Foundation (DFG)

Links

• Project Page
• http://fusion.cs.uni-jena.de/receptorlight/
  
• Press releases
• www.uni-jena.de/Forschungsmeldungen/FM150522_SFB_Mikroskopie.html
  
• www.bionity.com/en/news/153153/high-performance-microscopy-for-membrane-receptors.html
• University-wide activities related to Computational and Data Science
• Master Degree Program Computational and Data Science
• Michael Stifel Center Jena for Data-Driven and Simulation Science

Publications

• Sheeba Samuel : Integrative data management for reproducibility of microscopy experiments. in E. Blomqvist, D. Maynard, A. Gangemi, R. Hoekstra, P. Hitzler, and O. Hartig, editors, The Semantic Web - 14th International Conference, ESWC 2017, Portorovz, Slovenia, May 28 - June 1, 2017, Proceedings, Part II, volume 10250 of Lecture Notes in Computer Science, pages 246-255. Springer, 2017. more ...

• Sheeba Samuel : A provenance-based semantic approach to support understandability, reproducibility, and reuse of scientific experiments. in Dissertation, Department of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, 2019. more ...

• F. Taubert : Automatic reproducibility and parallelism for biological image analysis workflows. in Dissertation, Department of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, 2019. more ...

• S. Samuel, B. König-Ries : Combining P-Plan and the REPRODUCE-ME ontology to achieve semantic enrichment of scientific experiments using interactive notebooks. in A. Gangemi, A. L. Gentile, A. G. Nuzzolese, S. Rudolph, M. Maleshkova, H. Paulheim, J. Z. Pan, and M. Alam, editors, The Semantic Web: ESWC 2018 Satellite Events, Heraklion, Crete, Greece, June 3-7, 2018, volume 11155 of Lecture Notes in Computer Science, pages 126-130. Springer, 2018. more ...

• F. Taubert, H. M. Bücker : On the reproducibility of biological image workflows by annotating computational results automatically. in X. Hu, Y. Gong, C.-R. Shyu, D. Korkin, Y. Bromberg, I. Yoo, J. Gao, and J. H. Zheng, editors, Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017), Kansas City, MO, USA, November 13-16, 2017, pages 1538-1545. IEEE, 2017. more ...

• S. Samuel, K. Groeneveld, F. Taubert, D. Walther, T. Kache, T. Langenstück, B. König-Ries, H. M. Bücker, C. Biskup : The story of an experiment: A provenance-based semantic approach towards research reproducibility. in A. Waagmeester, C. J. O. Baker, A. Splendiani, O. D. Beyan, and M. S. Marshall, editors, Proceedings of the 11th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2018), Antwerp, Belgium, December 3-6, 2018, volume 2275 of CEUR Workshop Proceedings. CEUR-WS.org, 2018. more ...

• S. Samuel, B. König-Ries : ProvBook: Provenance-based semantic enrichment of interactive notebooks for reproducibility. in M. van Erp, M. Atre, V. Lopez, K. Srinivas, and C. Fortuna, editors, Proceedings of the ISWC 2018 Posters & Demonstrations, Industry and Blue Sky Ideas Tracks co-located with 17th International Semantic Web Conference (ISWC 2018), Monterey, USA, October 8-12, 2018, volume 2180 of CEUR Workshop Proceedings. CEUR-WS.org, 2018. more ...

• S. Samuel, F. Taubert, D. Walther, B. König-Ries, H. M. Bücker : Towards reproducibility of microscopy experiments. in D-Lib Magazine, 23(1/2), 2017. more ...

• H. M. Bücker, D. Walther : Automatic differentiation of computer programs in the time and frequency domain. in Proceedings of the 2017 European Conference on Electrical Engineering and Computer Science EECS, Bern, Switzerland, November 17-19, 2017, pages 335-340, Los Alamitos, CA, USA, 2017. IEEE Computer Society. more ...

• S. Samuel, B. König-Ries : REPRODUCE-ME: ontology-based data access for reproducibility of microscopy experiments. in E. Blomqvist, K. Hose, H. Paulheim, A. Lawrynowicz, F. Ciravegna, and O. Hartig, editors, The Semantic Web: ESWC 2017 Satellite Events, Portorovz, Slovenia, May 28 - June 1, 2017, volume 10577 of Lecture Notes in Computer Science, pages 17-20. Springer, 2017. more ...

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