900612 ESP -- SURF Center : Meeting with Chris, June 11, 2007
This page last changed on Dec 02, 2014 by kgomes.

Minutes

  1. Phases: HAB, BAC, LARV
  2. Phases run protocols
  3. Phase is a series of operations (could be one protocol, but more likely more). Can be one puck, but more likely more.
  4. Phase is a standard set of operations
  5. Each protocol needs a puck (with filter)
  6. Filter may or may not have probes, whole cell has no probes, just brings home sample
  7. All pucks have serial numbers.
  8. pucks outer diameter is the same.
  9. there are different pucks for different
  10. SH = standard hybridization, detect molecules of interest. Heat it up and liquify. Filter and then apply to SH2. SH1 pucks can be used lysate.
  11. Why do we want to keep track of serial numbers on pucks
  12. Once puck is closed, not sure what is in there.
  13. Serial numbers help keep track of what they intend to use it for after build.
  14. Some have physical specimen and they need to figure out which puck has the specimen
  15. After filteration, put on another filter, then more chemistry, then image.
  16. Final PUCK is WCR (whole cell archival) is then sample is then preserved and brought home for shore side analysis
  17. Associated with probes is spot map (array map) ".Gal File" (what probe in what X,Y location). Often listed as "Spot 23" then lookup with tell you X,Y
  18. Image is analyzed and you get intensities.
  19. Device can do "auto exposure" to figure out where it needs to be to get image in linear range of CCD chip.
  20. Also ask for constant exposure (do more than one constant exposure).
  21. Use standard curves and control spots on map.
  22. Standard curve is number of bugs/intensity
  23. Run exposure that you have standard curve for and then get intensity which then you lookup on the spot map.
  24. Low res images come across the wire (high res is 1MB).
  25. Phases can change the protocols (should we force users to use unique names- Chris thinks this would be good)
  26. Array map evolves.
  27. Protocols use same reagants, same amount
  28. Phase-protocol combination (Phase tells you what the amounts are in the different protocols)
  29. Volumes filtered varies (tell it "Collect a liter", instrument decides how much until to filter until clogged)
  30. Print info comes from "gal file". Old print is excel file.
  31. Some filters are thrown away, some are archived.
  32. Comments also need to be captured.
  33. Events are "when we sample"
  34. User specifies start of phase
    1. Then delay (7 minutes let's say), then sample is taken (that is the actual "start"). The rest of the protocols depend on the environmental characteristics.
  35. There will be maximum time for each phase (can be shorter, never longer).
  36. Instrument capacities:
    1. Pucks:
    2. Reagants: 20
    3. Waste: fixed in current machine
  37. Configuration file tells what reagents are at what valve.
  38. There is a waste 1 and waste 2 (NOTE this is dependent on the reagent. specify which waste reagent goes to)
  39. Power budget.
  40. Instrument run
    1. Take series of protocol, to build phases
    2. write high level script
    3. derive max volumes.
  41. Number of pucks is usual limitation
  42. sometimes waste can be limiter.
Attendees
  1. Chris Scholin
  2. Rich Schramm
  3. Brian Schlining
  4. Karen Salamy
  5. Kevin Gomes
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