leonarski_fandClaude Opus 5.5
f81c0c7f0f
- docs/PUBLICATIONS.md: how to cite (Rugnux: bioRxiv 2026 preprint; Jungfraujoch: J. Synchrotron
Rad. 2023 stays primary, J. Appl. Cryst. 2026 for real-time serial / live indexing) and the
paper list (IUCrJ 2023 MAX IV, Struct. Dyn. 2020, TORO J. Appl. Cryst. 2024); linked from the
toctree, ACKNOWLEDGEMENT, README, RUGNUX and JUNGFRAUJOCH pages. All DOIs checked on Crossref.
- Landing page: a Publications band with two typeset title-page cards (Rugnux preprint and the
J. Appl. Cryst. paper, with the 2023 primary reference), nav and footer links; HTML/CSS only, no
logos or images.
- rugnux prints a one-line citation in its startup banner (fits the 78-column console) and the
full reference ("If you find rugnux useful, please cite ...") at the head of _report.txt.
- Files jfjoch_writer writes from Rugnux live mode name both programs: the MTZ files get a
"From Jungfraujoch <version>, data collection" HISTORY record after Rugnux's (and a Rugnux
record where the map tables carry none), the placed/refined model mmCIF get Rugnux
(phasing/refinement) and Jungfraujoch (data collection) in _software. The round-trip tests
expect those additions.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HVeDQqrMy3Kh9NQw823gEb
4.0 KiB
Publications
How to cite
Rugnux — if you find Rugnux useful, please cite:
F. Leonarski and M. Wang, "Rugnux: from diffraction images to structure at synchrotrons and XFELs in one program" (2026), bioRxiv doi:10.64898/2026.10.24.761522.
Jungfraujoch — the primary citation is:
F. Leonarski, M. Brückner, C. Lopez-Cuenca, A. Mozzanica, H.-C. Stadler, Z. Matěj, A. Castellane, B. Mesnet, J. Wojdyla, B. Schmitt and M. Wang, "Jungfraujoch: hardware-accelerated data-acquisition system for kilohertz pixel-array X-ray detectors" (2023), J. Synchrotron Rad. 30, 227-234 doi:10.1107/S1600577522010268.
Work that relies on real-time serial crystallography, live indexing feedback or the system's full data rate should also cite:
J. Duan, H.-C. Stadler, J. Nan, Z. Matěj, G. Gotthard, F. Dworkowski, M. Bjelčić, O. Aurelius, A. Mozzanica, S. Grimm, M. Burian, T. Ursby, M. Wang and F. Leonarski, "Jungfraujoch: 38 GB s⁻¹ real-time serial crystallography – data acquisition and live indexing feedback" (2026), J. Appl. Cryst. 59, 1668-1677 doi:10.1107/S1600576726008083.
Data collected with Jungfraujoch and processed with Rugnux in the broker (Rugnux live mode) come out
of both programs, and the files jfjoch_writer writes from them name both: please cite both.
Rugnux
- F. Leonarski and M. Wang, "Rugnux: from diffraction images to structure at synchrotrons and XFELs in one program" (2026), bioRxiv doi:10.64898/2026.10.24.761522.
Jungfraujoch
- J. Duan, H.-C. Stadler, J. Nan, Z. Matěj, G. Gotthard, F. Dworkowski, M. Bjelčić, O. Aurelius, A. Mozzanica, S. Grimm, M. Burian, T. Ursby, M. Wang and F. Leonarski, "Jungfraujoch: 38 GB s⁻¹ real-time serial crystallography – data acquisition and live indexing feedback" (2026), J. Appl. Cryst. 59, 1668-1677 doi:10.1107/S1600576726008083 — the system at its full data rate, with live indexing feedback during serial data collection.
- P. Gasparotto, L. Barba, H.-C. Stadler, G. Assmann, H. Mendonça, A. W. Ashton, M. Janousch, F. Leonarski and B. Béjar, "TORO Indexer: a PyTorch-based indexing algorithm for kilohertz serial crystallography" (2024), J. Appl. Cryst. 57, 931-944 doi:10.1107/S1600576724003182 — the GPU indexing algorithm behind Jungfraujoch's real-time indexing.
- F. Leonarski, J. Nan, Z. Matěj, Q. Bertrand, A. Furrer, I. Gorgisyan, M. Bjelčić, M. Kepa, H. Glover, V. Hinger, T. Eriksson, A. Cehovin, M. Eguiraun, P. Gasparotto, A. Mozzanica, T. Weinert, A. Gonzalez, J. Standfuss, M. Wang, T. Ursby and F. Dworkowski, "Kilohertz serial crystallography with the JUNGFRAU detector at a fourth-generation synchrotron source" (2023), IUCrJ 10, 729-737 doi:10.1107/S2052252523008618 — serial crystallography at 2 kHz with a JUNGFRAU 4M and Jungfraujoch at the BioMAX beamline of MAX IV.
- F. Leonarski, M. Brückner, C. Lopez-Cuenca, A. Mozzanica, H.-C. Stadler, Z. Matěj, A. Castellane, B. Mesnet, J. Wojdyla, B. Schmitt and M. Wang, "Jungfraujoch: hardware-accelerated data-acquisition system for kilohertz pixel-array X-ray detectors" (2023), J. Synchrotron Rad. 30, 227-234 doi:10.1107/S1600577522010268 — the primary citation: the FPGA-accelerated acquisition system.
- F. Leonarski, A. Mozzanica, M. Brückner, C. Lopez-Cuenca, S. Redford, L. Sala, A. Babic, H. Billich, O. Bunk, B. Schmitt and M. Wang, "JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography" (2020), Struct. Dyn. 7, 014305 doi:10.1063/1.5143480 — the data handling problem of the JUNGFRAU detector that Jungfraujoch was designed to solve.