Realizing New Horizons in X-ray Crystallography Data Processing
实现 X 射线晶体学数据处理的新视野
基本信息
- 批准号:8269804
- 负责人:
- 金额:$ 34.67万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2011
- 资助国家:美国
- 起止时间:2011-06-01 至 2015-05-31
- 项目状态:已结题
- 来源:
- 关键词:AccelerationAccountingAddressAdherenceAgingAlgorithmsArchitectureBackBenchmarkingBiologicalBiologyCodeCollaborationsCollectionCommunicable DiseasesCommunitiesComplexComputer softwareControlled EnvironmentDNADNA-Directed RNA PolymeraseDataData AnalysesData QualityData SetDefectDevelopmentDiamondDiseaseDrug InteractionsFeedsGenerationsGoalsImageIndividualLaboratoriesLightLiteratureMapsMeasurementMeasuresMethodsModelingModificationMolecularMolecular StructureMonitorNIH Program AnnouncementsNamesNational Institute of General Medical SciencesOutcomePatternProcessProtein Structure InitiativeProteinsProteomeProtocols documentationPublished CommentRadiationRelianceReportingResearchResearch InfrastructureRibosomesRoentgen RaysRoleSamplingScientistServicesShapesSignal TransductionSourceSource CodeSpecimenSpeedSpottingsStructureSynchrotronsSystemTechnologyTestingTimeTwin Multiple BirthUnited States National Institutes of HealthVirusVisualWorkX ray diffraction analysisX-Ray CrystallographyX-Ray Diffractionbasebeamlinechaperonincomputerized data processingdata acquisitiondata reductiondesigndetectordrug discoveryexperienceimaging detectorimprovedinsightinstrumentmacromoleculeopen sourceoperationphysical propertyportabilityprocessing speedprogramsresearch studysmall moleculesoftware developmentsoftware systemsstructural biologystructural genomicssuccesssynchrotron radiationtechnology developmenttool
项目摘要
DESCRIPTION (provided by applicant): This project responds to NIH/NIGMS Program Announcement PAR-10-073, Technology Development for High-Throughput Structural Biology. The atomic structure of macromolecules as determined by X-ray crystallography has led to key biological insights in the last 60 years, and remains a prime focus of both academic and industrial research today. X-ray diffraction experiments are largely performed at synchrotron radiation facilities in the U.S. and abroad. The success of the experiment is dependent on the collection of large amounts of diffraction data, often from numerous crystalline samples. The best outcome is achieved if the diffraction datasets can be processed immediately, allowing real-time experimental adjustments and/or the examination of alternate crystal specimens. Aging software used to process the diffraction images is rapidly becoming obsolete for two reasons. First, the diversity of diffraction results is not well-modeled, and secondly, a new generation of X-ray detectors using pixel-array technology will far outpace the ability to process the data. These challenges will be addressed in this proposal by a team of scientists working at two synchrotron facilities (the Advanced Light Source at Lawrence Berkeley National Laboratory and the Stanford Synchrotron Radiation Laboratory). A new software system, New Horizons, will be designed for high-throughput operation at synchrotron beamlines, where it can be incorporated into existing software environments that control the experiment. Rapid measurements of crystal quality will be reported to the experimenter, so that protocol adjustments can be made. The new system will be benchmarked against existing data processing programs such as MOSFLM, to assure adherence to standard practice. Orders-of-magnitude advances in speed will be obtained by implementing the software on general purpose graphics processing units (GPGPUs), while at the same time adhering to standards such as OpenCL to assure portability. GPU acceleration will permit the implementation of superior models based on small-molecule work, extending both the data processing accuracy and range of applicability; in particular it will be possible to analyze a wider variety of crystals containing lattice defects. An open-source model will be used to assure that New Horizons can be utilized and adapted by synchrotron facilities worldwide.
描述(由申请人提供):本项目响应NIH/NIGMS计划公告PAR-10-073,高通量结构生物学技术开发。在过去的60年里,由X射线晶体学确定的大分子的原子结构导致了关键的生物学见解,并且仍然是当今学术和工业研究的主要焦点。X射线衍射实验主要在美国和国外的同步辐射设施中进行。实验的成功取决于大量衍射数据的收集,这些数据通常来自许多晶体样品。如果衍射数据集可以立即处理,允许实时实验调整和/或检查替代晶体样品,则可以实现最佳结果。用于处理衍射图像的老化软件由于两个原因正在迅速过时。首先,衍射结果的多样性没有得到很好的模拟,其次,使用像素阵列技术的新一代X射线探测器将远远超过处理数据的能力。这些挑战将由在两个同步加速器设施(劳伦斯伯克利国家实验室的先进光源和斯坦福大学同步辐射实验室)工作的一组科学家在本提案中解决。一个新的软件系统,新视野,将被设计为高通量操作在同步加速器光束线,在那里它可以被纳入现有的软件环境,控制实验。晶体质量的快速测量将报告给实验者,以便进行协议调整。新系统将以现有的数据处理程序(如数据库管理系统)为基准,以确保遵守标准做法。通过在通用图形处理器(GPGPU)上实现软件,同时遵守OpenCL等标准以确保可移植性,将获得速度的数量级提升。GPU加速将允许实施基于小分子工作的上级模型,扩展数据处理精度和适用范围;特别是可以分析更广泛的含有晶格缺陷的晶体。将使用一个开放源模型,以确保世界各地的同步加速器设施可以利用和改造新视野号。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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NICHOLAS K SAUTER其他文献
NICHOLAS K SAUTER的其他文献
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{{ truncateString('NICHOLAS K SAUTER', 18)}}的其他基金
DIALS: New Computational Methods to Enable Challenging Crystallographic Experiments
DIALS:新的计算方法可实现具有挑战性的晶体学实验
- 批准号:
9234571 - 财政年份:2016
- 资助金额:
$ 34.67万 - 项目类别:
DIALS: New Computational Methods to Enable Challenging Crystallographic Experiments
DIALS:新的计算方法可实现具有挑战性的晶体学实验
- 批准号:
9008859 - 财政年份:2016
- 资助金额:
$ 34.67万 - 项目类别:
DIALS: New Computational Methods to Enable Challenging Crystallographic Experiments
DIALS:新的计算方法可实现具有挑战性的晶体学实验
- 批准号:
9242823 - 财政年份:2016
- 资助金额:
$ 34.67万 - 项目类别:
DIALS / CCTBX: Serial crystallography computational methods aimed at biomolecular function
DIALS / CCTBX:针对生物分子功能的串行晶体学计算方法
- 批准号:
9886005 - 财政年份:2016
- 资助金额:
$ 34.67万 - 项目类别:
DIALS / CCTBX: Serial crystallography computational methods aimed at biomolecular function
DIALS / CCTBX:针对生物分子功能的串行晶体学计算方法
- 批准号:
10576330 - 财政年份:2016
- 资助金额:
$ 34.67万 - 项目类别:
DIALS / CCTBX: Serial crystallography computational methods aimed at biomolecular function
DIALS / CCTBX:针对生物分子功能的串行晶体学计算方法
- 批准号:
10359776 - 财政年份:2016
- 资助金额:
$ 34.67万 - 项目类别:
Towards real-time XFEL data reduction with CCTBX
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8350339 - 财政年份:2012
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Towards real-time XFEL data reduction with CCTBX
通过 CCTBX 实现实时 XFEL 数据缩减
- 批准号:
8551674 - 财政年份:2012
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$ 34.67万 - 项目类别:
Towards real-time XFEL data reduction with CCTBX
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8704958 - 财政年份:2012
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$ 34.67万 - 项目类别:
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- 批准号:
8897402 - 财政年份:2012
- 资助金额:
$ 34.67万 - 项目类别:
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