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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Where is crystallography going? Grimes, Jonathan M.; Hall, David R.; Ashton, Alun W. ...
Acta crystallographica. Section D, Structural biology,
February 2018, Volume:
74, Issue:
2
Journal Article
Peer reviewed
Open access
Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and ...cryo‐crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments. In addition, X‐ray free‐electron lasers offer to capture fragments of reciprocal space without radiation damage, and open up the subpicosecond regime of protein dynamics and activity. But electrons have recently stolen the limelight: so is X‐ray crystallography in rude health, or will imaging methods, especially single‐particle electron microscopy, render it obsolete for the most interesting biology, whilst electron diffraction enables structure determination from even the smallest crystals? We will lay out some information to help you decide.
Macromolecular crystallography has provided results that underpin much biological discovery and there is still scope for further development; however, a revolution in electron imaging now means that it can also routinely provide detailed atomic‐level descriptions. This article attempts to tease out where crystallography is going and consider what its place might be in the new landscape.
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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
SuRVoS: Super-Region Volume Segmentation workbench Luengo, Imanol; Darrow, Michele C.; Spink, Matthew C. ...
Journal of structural biology,
April 2017, 2017-04-00, 20170401, Volume:
198, Issue:
1
Journal Article
Peer reviewed
Open access
Segmentation of biological volumes is a crucial step needed to fully analyse their scientific content. Not having access to convenient tools with which to segment or annotate the data means many ...biological volumes remain under-utilised. Automatic segmentation of biological volumes is still a very challenging research field, and current methods usually require a large amount of manually-produced training data to deliver a high-quality segmentation. However, the complex appearance of cellular features and the high variance from one sample to another, along with the time-consuming work of manually labelling complete volumes, makes the required training data very scarce or non-existent. Thus, fully automatic approaches are often infeasible for many practical applications. With the aim of unifying the segmentation power of automatic approaches with the user expertise and ability to manually annotate biological samples, we present a new workbench named SuRVoS (Super-Region Volume Segmentation). Within this software, a volume to be segmented is first partitioned into hierarchical segmentation layers (named Super-Regions) and is then interactively segmented with the user's knowledge input in the form of training annotations. SuRVoS first learns from and then extends user inputs to the rest of the volume, while using Super-Regions for quicker and easier segmentation than when using a voxel grid. These benefits are especially noticeable on noisy, low-dose, biological datasets.
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The web‐based IceBear software is a versatile tool to monitor the results of crystallization experiments and is designed to facilitate supervisor and student communications. It also records and ...tracks all relevant information from crystallization setup to PDB deposition in protein crystallography projects. Fully automated data collection is now possible at several synchrotrons, which means that the number of samples tested at the synchrotron is currently increasing rapidly. Therefore, the protein crystallography research communities at the University of Oulu, Weizmann Institute of Science and Diamond Light Source have joined forces to automate the uploading of sample metadata to the synchrotron. In IceBear, each crystal selected for data collection is given a unique sample name and a crystal page is generated. Subsequently, the metadata required for data collection are uploaded directly to the ISPyB synchrotron database by a shipment module, and for each sample a link to the relevant ISPyB page is stored. IceBear allows notes to be made for each sample during cryocooling treatment and during data collection, as well as in later steps of the structure determination. Protocols are also available to aid the recycling of pins, pucks and dewars when the dewar returns from the synchrotron. The IceBear database is organized around projects, and project members can easily access the crystallization and diffraction metadata for each sample, as well as any additional information that has been provided via the notes. The crystal page for each sample connects the crystallization, diffraction and structural information by providing links to the IceBear drop‐viewer page and to the ISPyB data‐collection page, as well as to the structure deposited in the Protein Data Bank.
The IceBear web application for monitoring and recording the results of crystallization experiments is introduced. This software includes tools for interacting directly with the ISPyB synchrotron database: metadata from shipped crystals can be uploaded directly to ISPyB, and for each sample a link to the synchrotron ISPyB diffraction information becomes available in IceBear.
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7.
How best to use photons Winter, Graeme; Gildea, Richard J.; Paterson, Neil G. ...
Acta crystallographica. Section D, Structural biology,
March 2019, Volume:
75, Issue:
3
Journal Article
Peer reviewed
Open access
Strategies for collecting X‐ray diffraction data have evolved alongside beamline hardware and detector developments. The traditional approaches for diffraction data collection have emphasised ...collecting data from noisy integrating detectors (i.e. film, image plates and CCD detectors). With fast pixel array detectors on stable beamlines, the limiting factor becomes the sample lifetime, and the question becomes one of how to expend the photons that your sample can diffract, i.e. as a smaller number of stronger measurements or a larger number of weaker data. This parameter space is explored via experiment and synthetic data treatment and advice is derived on how best to use the equipment on a modern beamline. Suggestions are also made on how to acquire data in a conservative manner if very little is known about the sample lifetime.
Different modes of data collection are explored, and the effect of flux and multiplicity on the resulting quality of the data set is discussed. Advice is offered on how to collect data in the absence of prior knowledge of the sample.
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The recent resolution revolution in cryo‐EM has led to a massive increase in demand for both time on high‐end cryo‐electron microscopes and access to cryo‐electron microscopy expertise. In ...anticipation of this demand, eBIC was set up at Diamond Light Source in collaboration with Birkbeck College London and the University of Oxford, and funded by the Wellcome Trust, the UK Medical Research Council (MRC) and the Biotechnology and Biological Sciences Research Council (BBSRC) to provide access to high‐end equipment through peer review. eBIC is currently in its start‐up phase and began by offering time on a single FEI Titan Krios microscope equipped with the latest generation of direct electron detectors from two manufacturers. Here, the current status and modes of access for potential users of eBIC are outlined. In the first year of operation, 222 d of microscope time were delivered to external research groups, with 95 visits in total, of which 53 were from unique groups. The data collected have generated multiple high‐ to intermediate‐resolution structures (2.8–8 Å), ten of which have been published. A second Krios microscope is now in operation, with two more due to come online in 2017. In the next phase of growth of eBIC, in addition to more microscope time, new data‐collection strategies and sample‐preparation techniques will be made available to external user groups. Finally, all raw data are archived, and a metadata catalogue and automated pipelines for data analysis are being developed.
This paper provides an introduction to the Electron Bio‐Imaging Centre (eBIC) at Diamond Light Source: an external user facility established in the UK for high‐end cryo‐electron microscopy. Details are given of the first year of operation along with highlights and future challenges.
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dxtbx: the diffraction experiment toolbox Parkhurst, James M.; Brewster, Aaron S.; Fuentes-Montero, Luis ...
Journal of applied crystallography,
August 2014, Volume:
47, Issue:
4
Journal Article
Peer reviewed
Open access
Data formats for recording X‐ray diffraction data continue to evolve rapidly to accommodate new detector technologies developed in response to more intense light sources. Processing the data from ...single‐crystal X‐ray diffraction experiments therefore requires the ability to read, and correctly interpret, image data and metadata from a variety of instruments employing different experimental representations. Tools that have previously been developed to address this problem have been limited either by a lack of extensibility or by inconsistent treatment of image metadata. The dxtbx software package provides a consistent interface to both image data and experimental models, while supporting a completely generic user‐extensible approach to reading the data files. The library is written in a mixture of C++ and Python and is distributed as part of the cctbx under an open‐source licence at http://cctbx.sourceforge.net.
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Best practices for managing large CryoEM facilities Alewijnse, Bart; Ashton, Alun W.; Chambers, Melissa G. ...
Journal of structural biology,
09/2017, Volume:
199, Issue:
3
Journal Article, Conference Proceeding
Peer reviewed
Open access
This paper provides an overview of the discussion and presentations from the Workshop on the Management of Large CryoEM Facilities held at the New York Structural Biology Center, New York, NY on ...February 6–7, 2017. A major objective of the workshop was to discuss best practices for managing cryoEM facilities. The discussions were largely focused on supporting single-particle methods for cryoEM and topics included: user access, assessing projects, workflow, sample handling, microscopy, data management and processing, and user training.
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