ISPyB: an information management system for synchrotron macromolecular crystallography

Delageniere, S.; Brenchereau, Patrice; Launer, L.; Ashton, Alun; Leal, Ricardo M. F.; Veyrier, Stéphanie; Gabadinho, José; Gordón, E.; Jones, S.; Levik, Karl; McSweeney, Seán; Monaco, S.; Nanao, Max H.; Spruce, Darren; Svensson, Olof; Walsh, Martin A.; Leonard, Gordon A.

doi:10.1093/bioinformatics/btr535

Cited by 155 publications

(91 citation statements)

References 30 publications

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“…As the system is not subject to human weaknesses such as fatigue, emotional involvement with specific samples or the need to visualize samples, it is a powerful tool for the modern structural biologist. The scientist remains deeply involved through the ability to define specific experiment requirements via a database [66] and the availability of results in real time. Full automation also allows new data archiving policies to be implemented smoothly.…”

Section: Discussionmentioning

confidence: 99%

Fully automatic macromolecular crystallography: the impact of MASSIF-1 on the optimum acquisition and quality of data

Bowler

Svensson

Nurizzo

2016

Crystallography Reviews

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Automation is beginning to transform the way data are collected in almost all scientific disciplines. The combination of robotics and software now allows data to be collected consistently and reproducibly, eliminating human error and boredom. This approach has been applied to macromolecular crystallography at MASSIF-1, a fully automated beamline at the European Synchrotron Radiation Facility (ESRF). Considerable human effort is still dedicated to evaluating protein crystals in order to find the few crystals that diffract well or collecting hundreds of data sets to screen potential new drug candidates. The combination of ESRF-developed robotic sample handling and advanced software protocols now provides a new tool to structural biologists. Not only is the beamline used efficiently, running 24 h a day without getting tired, data collection is also performed consistently by an expert system, often better than with a human operator. In this review, we will focus on the impact this level of automation has had on the optimum acquisition of data from crystals of biological macromolecules.

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Section: Discussionmentioning

confidence: 99%

Fully automatic macromolecular crystallography: the impact of MASSIF-1 on the optimum acquisition and quality of data

Bowler

Svensson

Nurizzo

2016

Crystallography Reviews

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“…Multiple position/crystal experiments are selected either by specifying a number of positions in the diffraction plan for the sample or by requesting MXPressP or MXPressP_SAD (for Pseudo helical and Pseudo helical with SAD strategy) in the 'experiment type' field for the required samples in ISPyB (Delagenière et al, 2011). These new experiments operate in much the same way as the usual automated workflows on MASSIF-1 in that all the current features are retained, such as resolution selection, strategy input, diffraction volume calculation and smart beam sizing.…”

Section: Cc-by-nd 40 International License Peer-reviewed) Is the Autmentioning

confidence: 99%

“…Additionally, these measurements provided a distribution of crystal volumes allowing us to use a default beam diameter of 50 μ m, as this was the crystal dimension most frequently observed on the beamline. A specific beam diameter can be selected on a per sample basis in the diffraction plan in ISPyB (Delagenière et al, 2011), however, this option is usually used when users are sure that crystal volumes are significantly smaller than the default beam diameter (Figure 2). Using the information gathered during the mesh scan we can determine an optimised beam diameter.…”

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confidence: 99%

Recent improvements to the automatic characterization and data collection algorithms on MASSIF-1

Svensson

Gilski

Nurizzo

et al. 2017

Preprint

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SynopsisSignificant improvements in the sample location, characterisation and data collection algorithms on the autonomous ESRF beamline MASSIF-1 are described. The workflows now include dynamic beam diameter adjustment and multi-position and multi-crystal data collections.. CC-BY-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/236596 doi: bioRxiv preprint first posted online 2 Abstract Macromolecular crystallography (MX) is now a mature and widely used technique essential in the understanding of biology and medicine. Increases in computing power combined with robotics have enabled not only large numbers of samples to be screened and characterised but also for better decisions to be taken on data collection itself. This led to the development of MASSIF-1 at the ESRF, the world's first beamline to run fully automatically while making intelligent decisions taking user requirements into account. Since opening in late 2014 the beamline has now processed over 39,000 samples. Improvements have been made to the speed of the sample handling robotics and error management within the software routines.The workflows initially put in place, while highly innovative at the time, have been expanded to include increased complexity and additional intelligence using the information gathered during characterisation, this includes adapting the beam diameter dynamically to match the diffraction volume within the crystal. Complex multi-position and multi-crystal data collections are now also integrated into the selection of experiments available. This has led to increased data quality and throughput allowing even the most challenging samples to be treated automatically.Key words: X-ray centring; synchrotron instrumentation; macromolecular crystallography; automation; helical data collection; multiple crystal data collection . CC-BY-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/236596 doi: bioRxiv preprint first posted online 3 IntroductionAutomation is transforming the way scientific data are collected, allowing large amounts of high quality data to be gathered in a consistent manner (Quintana & Plätzer, 2015;Foster, 2005). Advances in robotics and software have been key in these developments and have had a particular impact on structural biology, allowing multiple constructs to be screened and purified (Camper & Viola, 2009;Hart & Waldo, 2013;Vijayachandran et al., 2011); huge numbers of crystallisation experiments to be performed (Elsliger et al., 2010;Ferrer et al., 2013;Heinemann et al., 2003;Joachimiak, 2009;Calero et al., 2014), samples to be mounted at synchrotrons (Cipriani et al., 2006; Cohen et al., 2002;Jacquamet et al., 2009;Papp et al., 2017;Snell et al., 2004), data to be analysed and processed (Bourenkov & Popov, 2010;Holton & Alber, 2004;Incardona et al., ...

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“…Many sites are beginning to offer flexible operation modes for PX experiments as remote access becomes more common. Full automation and sample information management systems such as ISPyB (Delagenière et al, 2011), allow the beam time allocated to individual groups to be broken down into shorter, more frequent sessions. Sites proposing high throughput screening will operate queuing systems with experimental slots assigned after the samples have been screened and ranked (Theveneau et al, 2013).…”

Section: New Directions Integrated Pipe-lines and Sample Characterisamentioning

confidence: 99%

Generation X-ray – A coming of age

Fox¹

2015

Arbor

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ABSTRACT:In 2014, the scientific community celebrated the impact crystallography has had on fundamental and applied science, and the ground-breaking discoveries that have gifted us with vision into the molecular and nano-worlds. UNESCO has declared 2015 as the International Year of Light, so now is perhaps a well timed moment to reflect on the role synchrotrons play in the field. Access to synchrotron radiation has revolutionized our ability to explore the properties, interactions and structure of materials, and broadened our understanding in diverse scientific arenas ranging from our cultural heritage, to nano-technology and new materials, to cellular systems and drug discovery. The range of potential synchrotron applications and fields of interest is enormous and beyond the scope of any single article, so my aim here, is simply to provide a snapshot filtered through the lens of biological crystallography. We will look back at how synchrotrons developed into the state-ofthe-art facilities we see today, how beamlines adapted to the quickening brought on by the introduction of high throughput techniques at the turn of the millennium, and forward to some of the new directions and technologies that are transforming modern light sources and crystallography.KEYWORDS: beamline; light sources; membrane protein; microfluidics; protein crystallography; serial crystallography; structural biology; synchrotron; XFEL. RESUMEN:La comunidad científica celebró en 2014 el impacto que la cristalografía ha tenido sobre la ciencia fundamental y aplicada, así como los de descubrimientos relevantes que nos han proporcionado una visión del mundo a escala molecular y nanométri-ca. La UNESCO ha declarado 2015 como el Año Internacional de la Luz por lo que quizás es un buen momento para reflexionar sobre el papel que han jugado y juegan los sincrotrones en esta ciencia. El acceso a la radiación sincrotrón ha revolucionado nuestra capacidad para explorar las propiedades, interacciones y estructura de materiales, así como ampliado nuestro conocimiento en distintos contextos científicos, desde el patrimonio cultural a la nanotecnología y nuevos materiales, hasta la exploración de sistemas celulares y búsqueda de fármacos. El rango de potenciales aplicaciones de los sincrotrones y sus campos de interés es vasto y queda fuera del alcance de un único artículo por lo que la intención del autor es la de proporcionar una imagen de los sincrotrones obtenida a través del filtro de la cristalografía macromolecular. Echaremos la vista atrás para ver cómo los sincrotrones han ido evolucionado hasta llegar a las actuales instalaciones en donde las líneas de trabajo asociadas a los mismos se están adaptado rápidamente a la introducción de las técnicas de alto rendimiento en el cambio del milenio; pero también miraremos hacia el futuro, hacia las nuevas tendencias y tecnologías que ya están transformando las actuales instalaciones y la misma cristalografía.PALABRAS CLAVE: biología estructural, cristalografía de proteínas, cristalografía en serie, línea, ...

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ISPyB: an information management system for synchrotron macromolecular crystallography

Cited by 155 publications

References 30 publications

Fully automatic macromolecular crystallography: the impact of MASSIF-1 on the optimum acquisition and quality of data

Fully automatic macromolecular crystallography: the impact of MASSIF-1 on the optimum acquisition and quality of data

Recent improvements to the automatic characterization and data collection algorithms on MASSIF-1

Generation X-ray – A coming of age

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