Documentation ToDo's


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Here you can find and extend a list of things that need to be done in the Project Documentation section. In brackets there is a suggestion of who could perform the change or addition, or find someone else to do it.


Global Tasks

  • Review/extend Christophe's introduction (talk about background of Synthetic Biology, our motivation, mention the variants we have developed, conclude with our decision to implement the counter).
  • (Robin) Make an illustration of the state machine, possibly including a chart with all subsequent transitions and states???.
  • (Robin, Dominic) Include/redesign the concept section, include/redesign contents of Introduction draft page.
  • (Alex) Make an new illustration of the block diagram of the system and write more text on the system architecture.
  • (Alex or Zlatko?) Make an illustration of the parts diagram according to Randy's conventions.
  • Check for consistency / update all registry parts online.
  • Someone write results, later discussion and conclusion - those we have and those we have not.


  • The output needs to be clearly labeled (-> state 3)


  • (Dominic, others?) Make an illustration of the qualitative input-output dependence of EPD
  • (Dominic, others?) Make an illustration of the qualitative input-output dependence of EPD, including internal mechanisms
  • (Dominic) Extend the experimental section.
  • (Dominic) In the purpose of the input module, you write about the Signal 'S'. But this signal is neighter in the picture, nor explained anywhere in the text.
  • (Dominic) In the schematic of the input module: The names in the legend do not correspond to the names in the picture.


  • (Robin?) Fit the content of the Chapter to the following structure: Purpose, Schematic, Strategies & Evaluation, Actual Implementation
  • (???) In the purpose section we should describe in detail how the NOR module fits into the counter system.
  • (???) Revise the introduction of the NOR Module on the Main Page
  • (???) Describe the words 'Zinc Hand' 'Zinc Finger' in the glossary
  • (Alex) Design -> Repressors: What do you want to write about RNA Polymerase?
  • (Alex) Design -> Repressors -> Zinc Finger Proteins: You write that we use several different designs. Is this still up to date?
  • (Alex, ???) Design -> Repressors -> Zinc finger Protein Binding Sites: I think it would be nice to have some pictures there.
  • (Alex) Design -> Interconnected NOR System -> Repression: This section is not up to date (As far as I understand, we decided not to use any repressor connectet to the ZF)
  • (Alex) Design -> Interconnected NOR System -> Additional Comments: Maybe not up to date.
  • (Alex) Syntesis and Assembly: Section has to be completed.


  • (Tamara, Kris) Adapt the current model and account for different max/mins of Pr and Prm. Check consistency of illustrations with new (upcoming) illustrations and definitions
  • Adapt text, insert subtitles, keep main page minimal.
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