Advanced Instrumentation for the New Millenium -- Biological ...

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  • 1. U. Washington Cell System Initiative System: DC-TC Interaction (immunological synapse) Closed Loop (experimentation & modeling) Education Interdisciplinary - Applied Math, Signal Processing (UW-CSI, UW-EE) - Experiment (UW-CSI) - Instrumentation (Amnis, PNNL-EMSL) - Reagents (Isis, Immunex, etc) - Informatics (CSI, CSE)
  • 2. Key Concepts from Monday
    • Knowledge tomography
      • How do we know what we know?
    • Publish the raw data
      • Even if we are willing, how can it be understandable
      • One scientist’s junk is another scientist’s treasure
      • True in sequencing, more true in function
    • Need to process and understand exponentially increasing amount of data
    • Interdisciplinary research depends on ability to communicate. People skills, yes, but languages too
    • Need new forms of education, starting early
    • modeling
  • 3. Design of Complex Systems Abstraction, Languages, Tools + physics PDE Logic RTL HDL always fork control(); datapath(); join design/ synthesis verification spice models binary , fixed speeds & sizes synchronous functional blocks layout rules Moore’s law  density & productivity
  • 4. Applicability to Biology
    • Engineers pay a huge price to maintain the independence of each level
    • Evolution isn’t so kind. Ever seen a synchronous mouse?
    • Applicable concepts:
      • The power of formal languages to enable group thought and to bring computers into the game
      • The power of models to coalesce knowledge and (glaringly) illuminate inconsistencies
      • The power of abstraction, when properly applied
  • 5. Labscape To discover languages and tools for biology that scientists will find indispensable for their own work , and which will also directly support communication and collaboration.
  • 6. Approach: Focus on Procedure
    • Language can be simple, agreement may be possible (as opposed to interpretation…)
    • Tools based on a language for procedure might be useful for lab workers…
    • Its coming anyway. Automation and integration  biologist as programmer (sorry). So let’s turn this fact into an advantage.
    • It is also essential for modeling and simulation
  • 7. Language 73 74 Trial 10/25/01 Abstraction, Language Abstraction is useful (and used) for describing procedure. And it is not limiting! Combine Separate Dispense Incubate Irradiate Measure Store/Retrieve
  • 8. First Tool: Ubiquitous Laboratory Assistant
    • Ostensible Objective: Simplify laboratory work
      • Preparation
      • Execution
      • Documentation
    • Ulterior Motive
      • Produce a formal (web accessible) representation of the procedure as a consequence of doing the work.
    • Characteristics
      • Always available
      • Presents useful information
      • Gathers and organizes data
    • It is not an electronic laboratory notebook!
  • 9. Science Fiction But, Roddenberry had it right… Human attention does not scale with Moore’s law
  • 10. Science Fact
    • There is much that we can do to help the experimenter in the lab
      • Simpler interaction (paper is not the best at everything!)
      • Provide task appropriate information
      • Simplify the documentation phase
      • Support freeform annotation
      • Provide access to related information at the lab bench
      • Goes anywhere, even in restricted environments
  • 11. Implementation
    • Scope: activities of CSI and collaborator’s labs
    • Not dependent on sketchy technologies
    • Adds value at every step
  • 12. Preliminary Result
  • 13. Applications (new tools!)
    • Collaboration
      • Individual efficiency
      • Teamwork
      • Oversight
      • Education
      • Flexible standardization
      • Variation  data instead of noise
    • Automation/Integration
    • Computation
      • Data analysis
      • Modeling and Simulation
    Acknowledgements Bob Franza Gaetano Borriello Joeseph Duncan Chia-Yang Hung Jing Su Gary Look Jong Hee Kang Miryung Kim Stefan Sigurdsson Sunny Consolvo Anthony LaMarca NSF REC DARPA Intel Immunex