JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography

Structural Dynamics
Filip LeonarskiMeitian Wang

Abstract

In this paper, we present a data workflow developed to operate the adJUstiNg Gain detector FoR the Aramis User station (JUNGFRAU) adaptive gain charge integrating pixel-array detectors at macromolecular crystallography beamlines. We summarize current achievements for operating at 9 GB/s data-rate a JUNGFRAU with 4 Mpixel at 1.1 kHz frame-rate and preparations to operate at 46 GB/s data-rate a JUNGFRAU with 10 Mpixel at 2.2 kHz in the future. In this context, we highlight the challenges for computer architecture and how these challenges can be addressed with innovative hardware including IBM POWER9 servers and field-programmable gate arrays. We discuss also data science challenges, showing the effect of rounding and lossy compression schemes on the MX JUNGFRAU detector images.

References

Oct 26, 1999·Acta Crystallographica. Section D, Biological Crystallography·Z Dauter
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Wolfgang Kabsch
Feb 5, 2011·Nature·Henry N ChapmanJohn C H Spence
Dec 24, 2011·Acta Crystallographica. Section D, Biological Crystallography·Marcus MuellerClemens Schulze-Briese
Apr 6, 2012·Journal of Applied Crystallography·Andrea Thorn, George M Sheldrick
Apr 17, 2012·Acta Crystallographica. Section D, Biological Crystallography·Pavel V AfoninePaul D Adams
Sep 2, 2014·Journal of Synchrotron Radiation·Peter Denes, Bernd Schmitt
Dec 17, 2014·Nature Methods·Tobias WeinertMeitian Wang
May 2, 2015·Journal of Synchrotron Radiation·Gabriel BlajMatt Weaver
Jun 20, 2015·Journal of Applied Crystallography·Mark KönneckeJoachim Wuttke
Jul 26, 2015·Current Opinion in Structural Biology·P Andrew Karplus, Kay Diederichs
Sep 8, 2016·Acta Crystallographica. Section D, Structural Biology·Arnau CasanasMeitian Wang
Mar 1, 2018·Journal of Synchrotron Radiation·J KiefferT Vincent
Mar 14, 2018·Acta Crystallographica. Section D, Structural Biology·Graeme WinterGwyndaf Evans
Apr 6, 2019·Acta Crystallographica. Section D, Structural Biology·Graeme WinterDavid R Hall
Apr 30, 2019·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Andreas FörsterClemens Schulze-Briese
Sep 19, 2019·Nature Methods·Pedram MehrabiR J Dwayne Miller
Mar 11, 2020·Journal of Synchrotron Radiation·Isabelle MartielMeitian Wang

❮ Previous
Next ❯

Citations

Sep 18, 2020·IUCrJ·Herbert J BernsteinGraeme Winter

❮ Previous
Next ❯

Methods Mentioned

BETA
protein crystallography
chips
x-ray macromolecular crystallography

Software Mentioned

CAPI Storage , Network , and Analytics Programming ( SNAP )
HDF5
GPGPUs
DIALS
cctbx
ANODE
NUMA
pthreads
refine
NVMe

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.