Data Analysis WorkbeNch (DAWN) Basham, Mark; Filik, Jacob; Wharmby, Michael T. ...
Journal of synchrotron radiation,
20/May , Volume:
22, Issue:
3
Journal Article
Peer reviewed
Open access
Synchrotron light source facilities worldwide generate terabytes of data in numerous incompatible data formats from a wide range of experiment types. The Data Analysis WorkbeNch (DAWN) was developed ...to address the challenge of providing a single visualization and analysis platform for data from any synchrotron experiment (including single‐crystal and powder diffraction, tomography and spectroscopy), whilst also being sufficiently extensible for new specific use case analysis environments to be incorporated (e.g. ARPES, PEEM). In this work, the history and current state of DAWN are presented, with two case studies to demonstrate specific functionality. The first is an example of a data processing and reduction problem using the generic tools, whilst the second shows how these tools can be targeted to a specific scientific area.
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EDNA is a framework for developing plugin‐based applications especially for online data analysis in the X‐ray experiments field. This article describes the features provided by the EDNA framework to ...ease the development of extensible scientific applications. This framework includes a plugins class hierarchy, configuration and application facilities, a mechanism to generate data classes and a testing framework. These utilities allow rapid development and integration in which robustness and quality play a fundamental role. A first prototype, designed for macromolecular crystallography experiments and tested at several synchrotrons, is presented.
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A novel raster‐scanning method combining continuous sample translation with the fast readout of a Pilatus P6M detector has been developed on microfocus beamline I24 at Diamond Light Source. This fast ...grid‐scan tool allows the rapid evaluation of large sample volumes without the need to increase the beam size at the sample through changes in beamline hardware. A slow version is available for slow‐readout detectors. Examples of grid‐scan use in centring optically invisible samples and in detecting and characterizing numerous microcrystals on a mesh‐like holder illustrate the most common applications of the grid scan now in routine use on I24.
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Motivation: Individual research groups now analyze thousands of samples per year at synchrotron macromolecular crystallography (MX) resources. The efficient management of experimental data is thus ...essential if the best possible experiments are to be performed and the best possible data used in downstream processes in structure determination pipelines. Information System for Protein crystallography Beamlines (ISPyB), a Laboratory Information Management System (LIMS) with an underlying data model allowing for the integration of analyses down-stream of the data collection experiment was developed to facilitate such data management.
Results: ISPyB is now a multisite, generic LIMS for synchrotron-based MX experiments. Its initial functionality has been enhanced to include improved sample tracking and reporting of experimental protocols, the direct ranking of the diffraction characteristics of individual samples and the archiving of raw data and results from ancillary experiments and post-experiment data processing protocols. This latter feature paves the way for ISPyB to play a central role in future macromolecular structure solution pipelines and validates the application of the approach used in ISPyB to other experimental techniques, such as biological solution Small Angle X-ray Scattering and spectroscopy, which have similar sample tracking and data handling requirements.
Contact:
leonard@esrf.fr; martin.walsh@diamond.ac.uk
Calcite and vaterite crystallisation is strongly influenced by the presence of additives during the reaction process, as demonstrated by organic molecules in biogenic calcium carbonate formation. The ...effect of additives on the lattice parameters of calcite and vaterite in syntheses are frequently reported, but only as discrete studies discussing a single polymorph. The intertwined nature of these polymorphs, due to their shared reaction pathway, is rarely discussed. In this work we report the results of a large scale citizen science project to explore the influence of amino acids and related additives on both polymorphs, highlighting their differences and commonalities in terms of the effect on the lattice parameters and polymorph selectivity.
Crystallisation pathways of calcium carbonate are strongly influenced by the presence of additives. Through X-ray diffraction, samples made by the Project M Scientists reveal the effect of amino acid and related additives on the crystal structures of calcite and vaterite.
SynchLink: an iOS app for ISPyB Ginn, Helen Mary; Mostefaoui, Ghita Kouadri; Levik, Karl Erik ...
Journal of applied crystallography,
October 2014, Volume:
47, Issue:
5
Journal Article
Peer reviewed
Open access
The macromolecular crystallography (MX) user experience at synchrotron radiation facilities continues to evolve, with the impact of developments in X‐ray detectors, computer hardware and automation ...methods making it possible for complete data sets to be collected on timescales of tens of seconds. Data can be reduced in a couple of minutes and in favourable cases structures solved and refined shortly after. The information‐rich database ISPyB, automatically populated by data acquisition software, data processing and structure solution pipelines at the Diamond Light Source beamlines, allows users to automatically track MX experiments in real time. In order to improve the synchrotron users' experience, efficient access to the data contained in ISPyB is now provided via an iOS 6.0+ app for iPhones and iPads. This provides users, both local and remote, with a succinct summary of data collection, visualization of diffraction images and crystals, and key metrics for data quality in real time.
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Diamond Light Source (DLS) provides a suite of world-leading beamlines for macromolecular crystallography (MX) experiments which are used by scientists from all over the world. Key to ...their success is an integrated approach to automating the hardware and software environments such that it is only necessary to enter the beamline hutch to change large batches of samples for the robotic sample changers. Alongside investing in automation, all beamlines are also equipped with Pilatus 6M-F detectors (25 – 100 Hz) resulting in fast data collections and high turnover of samples. Rapid downstream processing of the resulting data has been developed since this is essential to drive experimental decisions. The feedback from these pipelines needs to be made readily available to users in a timely manner and a number of tools are available for both local and remote visualization of results. Remote access to these facilities was a design requirement from the outset. Several tools have been integrated and developed to streamline the process of remote access yet give the same software environment remotely as would be experienced if the experimenter was present at the beamline. The advent of remote access for cryogenically frozen samples has led to the implementation of new shift patterns for the user programme, enabling frequent short shifts for the many groups who use DLS. Remote access to MX beamlines is also a prerequisite of many industrial clients of DLS. For the future we are moving forward with the development of remote access for in-situ data collection from crystallization plates following on from the success of this method for screening and collecting data by users at the beamlines. The implementation and impact of remote access at DLS will be presented here.
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