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Structural Biology Collaboratory. Allow a team of researchers distributed anywhere in the world to perform a complete crystallographic experiment together. Enhance productivity by allowing remote collaborators to participate in experimental choices at the beam line. - PowerPoint PPT Presentation
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Goals
Structural Biology Collaboratory
• Allow a team of researchers distributed anywhere in the world to perform a complete crystallographic experiment together.
• Enhance productivity by allowing remote collaborators to participate in experimental choices at the beam line.
• Facilitate collaborative experiments in such areas as drug design and structural genomics.
• Fully utilize National resources for crystallographic experiments.
Remote access toexperimental facilities
24/7 access todata and computing
WWW Diffraction Image Viewer
Data Reductionand Structure Analysis
Synchrotron Research Resource
Data Collection
File Server and Compute Server
Crystal Mounting Robot
Structural Biology Collaboratory
• 6 live feeds per SMB-Crystallography beamline
• Currently available on 3 beamlines to increase to 6 over the coming 3 months
• Critical machine surveillance for remote monitoring
• Network limitations only allow low-quality feeds at present. Bottlenecks at SLAC and user’s institutions.
Benefits• Users can monitor sample
and beam line remotely• Staff can troubleshoot
and diagnose problems• Images served to automated
sample alignment software
General features• A web-base GUI• Secure access• Restricted access• Preset positions• Synchrotronization of clients• Camera enable/disable• Image control• Snapshot
Beamline Video System
Live Live video feeds to BLU-ICE/DCS• Full remote control of the experiment • Interactive crystal alignment• Automated loop alignment• Beam line alignment• Beam line diagnostics and user-support• Robot monitoring and sample tracking
Beamline Video System applications
Archive System
• Need driven: Two new CCD detectors operational, which generate
74MB images with a readout of 1 second. Current 24/7 average duty cycle is 1% limited by
manual sample mounting and low intensity of x-ray beam
Increase of duty cycle to 20% through Structural Genomics initiative to automate sample handling and Spear3 upgrade to provide 20x increase in beam intensity by 2004
Increase to at least 6 similar systems• Objectives:
Large-volume long term data storage system. A centralized data storage system to allow users to
share data easilywith their collaborators. Support for the large area and fast readout detectors. Meta-data catalog to allow searching of specific data
sets. Higher security and reliability than digital tapes.
• Current Status: A command-line based “Uploader” has been developed
and used by SMB staff rountinely. srbBrowser provided by SDSC is currently used for
downloading data from SRB. E-mail summaries to help book keeping. System requirements were gathered from users and
SMB staff.
Archive System Server
Blu-IceUnix “Uploader”
Archive System Database
SRB (Storage Res ourc e
Broker)
HPSS(High Performance
Storage System)
RAID System
WWW-GUI
SSRL or elsewhere
BLU-ICE• Automated backup during
data collection
WWW-GUI• Browse data at both SSRL
and SDSC computers.• Upload and download data.• Set access permission.• Define, monitor and prioritize
multiple arhicve jobs.• Searchable meta-data• E-mail summaries to help
book-keeping
Archive System Architecture
Automation Instrumentation
• A decade ago, interfaces were VT100-style• Modern interfaces are highly graphical and
intuitive but are typically instrument driven• Next generation interfaces are data driven
Data Driven Interfaces
High-throughput Structural Biology
• Next generation scientific challenges
Structural genomics and proteomics in the post genome sequencing era
High-throughput structural biology for drug discovery
• Global efforts Life sciences is moving
towards global collaborations in big-science efforts
Immense data generation and data mining at unprecedented rates
Structural Molecular Biology Macromolecular Crystallography Group at SSRL
• Peter Kuhn, Group Leader • Mike Soltis, Group Leader
• Collaboratory TeamJessica Chiu Thomas ErikssonKenneth Sharp
• SMB Scientific Group: Ana Gonzalez Irimpan Mathews Ashley Deacon Jeanette Hobbs
• StudentsJian Zhang Zepu Zhang Gilbert Martinez
• SMB Beamlines Group: Aina Cohen Paul Ellis Mitch Miller Dan Harrington Mike Hollenbeck Paul Phizackerley Russ Floyd John KovarikJohn Coller SMB Software-Development: Tim McPhillips Scott McPhillips, Gunter Wolf Henry v.d. Bedem Hillary Yu
• SMB Group: Linda Brinen Lisa Dunn Amanda Prado
• Funding Support from:NIH NCRR; DOE BER; NIH NIGMS; TSRI; Stanford Graduate Program