Review biology case study

[iincer]

• The code should be clean.
• The problem should be well-motivated. Add as many references to the literature as needed.
• As this is user-facing, documentation, the notebook should look nice (add good figures).
• The contracts + operations used should be clear.
• The case-study owner should submit the case study as a PR that the reviewers gets to review.
• The PR is approved until the reviewer is satisfied with any requested changes.

[YuTaiwan]

Overall, the case study is interesting as it applies contract-based methodology in synthetic biology. One benefit of this case study is that it provides visualization of the contracts. However, as biology might be unfamiliar to some potential users of Pactis, an explanation of some terms and the high-level ideas of the systems are needed to make the case study self-contained.

1. The term "sensor" is somewhat confusing to me. From the content, it seems to be actively involved in the system and produces some output different from the input instead of just providing some values as the sensor behaves in the electronic system. It would be great if you could provide an analog of a genetic circuit to an actual circuit.

2. Each of the following terms needs at least one sentence to explain: Protein expression, express, inducer, plasmid, regulator, RPU, and fold-change.

3. The high-level description and goal of the system are missing. What is the application for the circuit behaving like a NAND gate to repress the RFP? What is the purpose of achieving the highest fold-change? Some background on the example would be great.

[ayush9pandey]

1. The term "sensor" is somewhat confusing to me. From the content, it seems to be actively involved in the system and produces some output different from the input instead of just providing some values as the sensor behaves in the electronic system. It would be great if you could provide an analog of a genetic circuit to an actual circuit.

I added some references for the reader to learn about synthetic biology and added more text to describe what a synthetic biological circuit is, including details about the subsystems in this case study.

2. Each of the following terms needs at least one sentence to explain:
   Protein expression, express, inducer, plasmid, regulator, RPU, and fold-change.

Done! Thanks for the suggestion!

3. The high-level description and goal of the system are missing.
   What is the application for the circuit behaving like a NAND gate to repress the RFP? What is the purpose of achieving the highest fold-change?
   Some background on the example would be great.

Done!

[ayush9pandey]

• The code should be clean.

  • The problem should be well-motivated. Add as many references to the literature as needed.

  • As this is user-facing, documentation, the notebook should look nice (add good figures).

  • The contracts + operations used should be clear.

  • The case-study owner should submit the case study as a PR that the reviewers gets to review.

  • The PR is approved until the reviewer is satisfied with any requested changes.

Fixed all of these. Added references, lots of comments throughout, documentation of functions, and beautified some plots.

All changes are in synbio branch. PR coming soon.