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4 Beamlines by Village Macromolecular Crystallography Soft Condensed Matter Spectroscopy Materials Engineering and Environment Surfaces and Interfaces

5 A National User Facility for Biological Electron Cryo-microscopy (ebic) Wellcome Trust Strategic Award/MRC/BBSRC, applicants: Helen Saibil, Kay Grünewald, David Stuart, Gerhard Materlik Funded initially by the Wellcome Trust, MRC and BBSRC at level of 15.6 M over 5 years, augmented to ~ 25 M by additional investment by the Trust in 2016 The facility currently includes: - 4 high-end 300kV automated cryo EMs (Titan Krios FEI) kev automated feeder instrument (Talos Arctica) - Cryo focussed ion beam instrument (SCIOS) - Sample prep incl. vitreous sectioning - Correlative fluorescence/em - FEI Oxford for CAT 3 samples

6 ebic 13 th May 2017

7 New ebic Facility Initially constructed with two large rooms for two Krios, remodel to house four - completed 9/16. Sample preparation, loading and general labs. + multiple rooms for smaller microscopes






13 Preparation Experiment Raw Data Processed Final Result

14 Scientific Computing User office Business IT STFC, CCPs, Universities, Collaborators Analysis Acquisition Controls


16 HPC / HTC Cluster (~3500 cores) X86, Nvidia GPU (K80, P100) High Performance Storage Lustre03, Lustre04, GPFS01, GPFS02 Network infrastructure 10Gb/s, 40Gb/s to some beamlines User Gateways, Visualisation, Data Transfer NX Service, Globus endpoint Support Predominantly Linux infrastructure, BUT also Windows support to beamlines/em/etc and VM platforms Relies on working with Corporate IT and other groups in Controls and Scientific Software

17 Target Available Used Performance XFS 50 TB 47 TB < 1GB/s Lustre TB 370 TB 6 GB/s Lustre TB 70 TB 2 GB/s GPFS01 1 PB 700 TB 15 GB/s GPFS PB 1.5 PB 40 GB/s STFC Archive n/a 9 PB 12 TB 50 TB per day ingest

18 Detector Computer 10 / 40Gbit/s Beamline Switch 10Gbit/s 1 Gbit/s Central Switch 1 Gbit/s 2 x 40 Gbit/s or 2x10 Gbit/s Storage GPFS Central computing 3500 CPU cores (between 4 GB and 12 GB RAM per core) 86 GPUs

19 x22 xn Beamline





24 Acquisition and Analysis in the Eclipse Framework ( Client server technology Experiment GUI Communication with EPICS and hardware Scan mechanism Acquisition Jython and Python Visualisation Communication with external analysis Analysis tools Data read, write, convert Metadata structure Workflows Analysis DAWN is a collection of generic and bespoke views collated into perspectives. The perspectives and views can be used in part or whole in either the GDA or DAWN. All core technologies open source

25 Interfaces

26 ~200GB Database, 2.5million connections/day


28 monitoring Standard Template? User Template files (GPFS) File discovery ( Job Queue (ActiveMQ)? SPP Pipeline (Scipion) session (ISPyB) logging Tomo Pipeline (IMOD)

29 Standard Template? User Template SPP Pipeline (Scipion) Tomo Pipeline (IMOD) Drift Correction MotionCor2 Combine Frames (Xmipp) Drift Correction MotionCor2 IMOD Image aberration (CTFFind) Particle Picker (e.g. Ethan) session (ISPyB)


31 Diamond s experiment data policy...users conducting Peer Reviewed Research will own the Experimental Data that they produce. Following the initial 30 day storage period, Diamond will create a single archive copy of the Experimental Data on tape. Users of Diamond Facilities are responsible for meeting any third-party data management obligations that may be applicable.

32 Data is archived and metadata captured from every stage of the process Session generation Time and users DLS User Office Database (UAS) 15 min ICAT Information catalogue Web Pages (TopCAT) ISPyB Processing DATA Data Registration TAPE DLS hosted STFC hosted



35 Data capture at full rate on both direct electron detectors (e.g. 17 fps for Falcon II or 40 fps for the K2). Falcon II data rate ~ movies/hr K2 data rate ~25-75 movies/hr All data are directly written to high speed central computing/storage facility. All data are archived to tape and stored for the lifetime of the media. Diamond cluster available to external users particularly during beamline shut downs.










45 Cryo-EM & Cryo-Tomo The resolution revolution Single particle analysis requires similar high quality samples to X-ray crystallography Massive advances in microscope, detectors (movies), software. Still much to come with improved sample presentation, automation, hardware/software. Already pretty efficient (data output> MX beamline, computional demands circa 1000-fold more).