EMEN2 Steve Ludtke NCMI Baylor College of Medicine NCRR

Current EMEN Database Diverse data requirements: purification  data collection  reconstruction OODB (Zope based) Direct equipment interface 290 users from dozens of labs ~7 Tb image data 2-3 Tb/year of image data 385,000 total records

LIMS Centralized databases (PDB, EBI, etc.) vs. in-house archives with detailed information Scientific Database vs. Electronic Notebook

Film/Frame Id DefocusMag Total Dose ExpTime ccd_ #1 0.8 um138.44k s ccd_ #2 2.5 um138.44k s ccd_ #1 0.8 um138.44k s ccd_ #2 2.5 um138.44k s ccd_ #1 0.8 um138.44k s ccd_ #2 2.5 um138.44k s ccd_ #1 0.8 um138.44k s ccd_ #2 2.5 um138.44k s ccd_search1 #1 0.8 um138.44k s ccd_search2 #2 2.5 um138.44k s ccd_search3 #1 0.8 um138.44k s ccd_search4 #2 2.5 um138.44k s ccd_search5 #1 0.8 um138.44k s ccd_search6 #2 2.5 um138.44k s Excellent mineability Limited flexibility Good for centralized databases (standards)

Excellent flexibility Rich information content Limited mineability

Goals BOTH flexibility and mineability KISS Database should think like the scientist, not the other way around Archive detailed experimental protocols Association of databases

New Concepts Object Oriented Databases (OODB) Web Ontologies (semantic web) Evolving collaborative environment (wikipedia) XML Peer to Peer Networking Blogging

Experimental Protocol Experimental Parameter Record Descriptive Text Experimental Parameter

Temperature Parameter Ontology Ambient_Conditions Ambient_TemperatureAmbient_Pressure Ambient_Relative Humidity Specimen_Temperature Grid_Temperature Grid_Temperature_ Imaging Grid_Temperature_ Previtrification

grid negative_stain_gridvitrified_grid manually_vitrified_gridvitrobot_vitrified_grid manually_vitrified_grid_ flash_photolysis TEM_specimen holey_carbon_grid quantifoil_grid Protocol Ontology

manually_vitrified_grid A preprepared #grid was placed in a pair of forceps and loaded into the plunger. $cryogen was preprepared below the plunger (ethane and other cryogens which may become solid are reliquefied using a room temperature copper rod immediately prior to plunging). $grid_volume of specimen was deposited on the front of the grid using a pipette. The grid was then blotted on $grid_blot_side using $filter_paper_type and the plunger was triggered after a $grid_plunge_delay to rapidly submerse the grid in the cryogen. The forceps were then released from the guillotine and the grid was placed in $grid_storage_id in $grid_storage_slot. The grid storage button was then placed in $cryofreezer_id for storage until imaging.

EMEN2 Ease of use (new protocols without DBA) Protocol archival Protocol and Parameter Ontologies (P2P) ‘Blogging’ Traceability Workflow Dissemination (mirroring) Data Mining

plot bfactor vs truedefocus where truedefocus is between 0.1 and 5.0 and bfactor is between 1 and 1000

Microscopy Session CCD FrameMicrograph Scan Particles Project Microscope Particles

plot bfactor vs truedefocus where truedefocus is between 0.1 and 5.0 and bfactor is between 1 and 1000 split by protocol

plot bfactor vs truedefocus where truedefocus is between 0.1 and 5.0 and bfactor is between 1 and 1000 split by creator

plot bfactor vs truedefocus where truedefocus is between 0.1 and 5.0 and bfactor is between 1 and 1000 split by microscope

Microscopy Session CCD FrameMicrograph Scan Particles Project Microscope Particles

EMEN2 Status Core library functional –BerkeleyDB + Python All EMEN data  EMEN2 Begun work on Web-based front-end –Apache + Cheetah P2P incorporated into design, but implementation incomplete Formal XML interfaces (OWL for exchange incomplete)

Acknowledgements Thanks to: National Center for Research Resources Agouron Institute Haili Tu Runsun Pan

Relational vs. OODB Tables Tabular Storage Fixed Records No Table-mixing Classes Hierarchical Storage Flexible Records Mixed Class Reports

EMEN Goals Project Management Data Archival Data Mining Automation Flexibility Communication with Collaborators Dissemination Portability

plot intendeddefocus vs truedefocus where truedefocus>0 and intendeddefocus>0

Group Address Affiliations City Contact Contact Name Fax # Group Name Institution Phone # State Support Sources Website URL Zip Code Microscope CCD Camera Type CCD Model # CCD Serial # CCD Size X CCD Size Y C C C S Microscope Serial # Pole Piece Sensitivity Title Voltage Project Axis Codes Bio-hazard Codes Biomedical Properties Biophysical Properties Biochemical Properties Genetic Characterization Goals of Project Height (of specimen) Keywords for Project Length (of specimen) Mass (of specimen) Particle Diameter Project Description Project Title Sequence Specimen Storage Location (Data) Symmetry (of specimen) User Address Degrees Department First Name Institution Last Name Login Name Phone Aliquot Buffer Concentration Date Received Identifiers Received By Storage Loc. Volume Freezing Session Aliquots Used Apparatus Blotting Concentration Frozen By Grid Batch Grids Used Grid Type Hole Size Mesh Size Number of Grids Post Freezing Pre-Treatment Storage Loc. Substrate Substrate Prep. Freezing Tech. Vitrobot Parm. Purification Buffer Concentration Description Purification Meth. Spec. Stability Storage Condn. Labnotebook Links (web) Notebook Text Structure Factor From Whom Processed Source Reference Comments CCD Anti Blooming Astigmatism Parm. Beam Diameter B Factor Binning Camera Camera Length Camera Units Dose Drift Parm. Energy Filter Exposure # Exposure Time Frame ID Ice Comments Ice Thickness Identifier Intended Defocus Lens Current Magnification Peak S/N Ratio Screen Current Screen Magnification Tilt Angle True Defocus True Magnification (X,Y) Coordinates Zoom Factor Micrograph Amplitude Cont. Astig. Parm. Beam Diameter B Factor Camera Length Camera Units Contamination Dos e Drift Parm. Energy Filter Exposure # Exposure Time Film ID Ice Comments Ice Thickness Illum. Angle Intended Defocus Lens Current Magnification Maximum Res. Micrograph Qual. Peak S/N Ratio Screen Current Screen Mag. Tilt Angle True Defocus True Mag. (X,Y) Coordinates Microscopy Sess. Apertures Camera Length Camera Units Condenser C S Develop Time Film Type Freezing Session Magnification Microscope Room Humidity Room Temp. Specimen Temp. Spot Size Voltage Scan Averaging Fac. Brightness Contrast Exposure Time Parameters Scanned By Scanner Used Scan Step