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EMEN2

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

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EMEN2

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  1. EMEN2 Steve Ludtke NCMI Baylor College of Medicine NCRR

  2. 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

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

  4. Excellent mineability • Limited flexibility • Good for centralized databases (standards)

  5. Excellent flexibility Rich information content Limited mineability

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

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

  8. Experimental Protocol Record Descriptive Text Experimental Parameter Experimental Parameter Experimental Parameter Experimental Parameter Experimental Parameter Experimental Parameter

  9. Parameter Ontology Temperature Ambient_Conditions Specimen_Temperature Ambient_Temperature Ambient_Pressure Ambient_RelativeHumidity Grid_Temperature Grid_Temperature_Previtrification Grid_Temperature_Imaging

  10. Protocol Ontology TEM_specimen grid vitrified_grid negative_stain_grid holey_carbon_grid manually_vitrified_grid vitrobot_vitrified_grid quantifoil_grid manually_vitrified_grid_ flash_photolysis

  11. 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.

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

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

  14. Microscope Project Microscopy Session Micrograph CCD Frame Scan Particles Particles

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

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

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

  18. Microscope Project Microscopy Session Micrograph CCD Frame Scan Particles Particles

  19. 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)

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

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

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

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

  24. Group      Address      Affiliations      City      Contact Email      Contact Name      Fax #      Group Name      Institution     Phone #      State      Support Sources      Website URL      Zip Code 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) Purification      Buffer      Concentration      Description      Purification Meth.      Spec. Stability      Storage Condn. 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. Micrograph      Amplitude Cont.      Astig. Parm.     Beam Diameter      B Factor      Camera Length      Camera Units      Contamination      Dose      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      CS     Develop Time      Film Type      Freezing Session      Magnification      Microscope      Room Humidity      Room Temp.      Specimen Temp.      Spot Size      Voltage 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 Microscope      CCD Camera Type      CCD Model #      CCD Serial #      CCD Size X      CCD Size Y      CC     CS     Microscope Serial #      Pole Piece      Sensitivity      Title      Voltage Scan      Averaging Fac.      Brightness      Contrast      Exposure Time      Parameters      Scanned By      Scanner Used      Scan Step Reference      Comments User      Address      Degrees      Department      Email      First Name      Institution      Last Name      Login Name      Phone Labnotebook      Links (web)      Notebook Text Structure Factor      From Whom      Processed      Source

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