User:Yeem/BE.180 notes/Semester review

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Programming in BE

Abstract concepts

  • Abstraction hierarchy: high to low
  • Decouling: breaking a complex system down

Comparison of Python and Biology


  • Functions
  • Classes
  • Inheritance
    • Instances
    • Passing data


  • DNA
    • TAATA, etc.
  • Parts
    • Basic biological function encoded in DNA
  • Devices
    • One or more parts that encode a human-defined function
  • Systems
  • One or more devices that perform a human-defined function

Recall that for an example of a genetic device, we spent a bunch of time making genetically encoded inverters, where one protein controls the operator of another protein. (see figure)

PoPS-based inverter

Protein kinases

Kinase cascade

(figure) Protein kinase B phosphorylates protein kinase C to prevent it from phosphorylating something else. Is this a good device?

  • No. Signal is specific. PEpS not interchangeable. Need common signal carrier.

How can you fix it?

  • ???

Goal: can you describe a biological function that you can use without worrying about the details?


DNA to RNA to Protein

  • ATCG to AUCG (one to one mapping for DNA to RNA)
  • Mapping via a triplet code (RNA to protein)
  • Looking at a piece of DNA, since there's 20 amino acids and 64 possible combinations of 3 nucleotides, there's redundancy
  • Redundancy means flexibility in the specific DNA sequence

If you had the coding region of a particular open reading frame, and you found that there was a restriction site in the middle of it, you could remove it by specifying the same amino acid with a different nucleotide sequence.

Programming in time & space

See other notes for more info

Explored two examples of early languages

  • Growing point language ("GPL") developed by Coore
  • "Crop circle language" language
  1. With "structured computer programming", you can
    • Reuse functions
      • Call function more than once
    • Nest functions
  2. Even with differences, we've been able to map to biology
    • We've made genetic devices that can respond to intermediate levels of an input signal


sender-receiver diagram

Band detectors: detect intermediate concentration

  • i.e., AHL low, PoPS low
  • AHL high, PoPs low
  • AHL juuuuuust right, PoPS high