Documentation ToDo's

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Here you can find 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.
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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.
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== Big Tasks ==
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== Global Tasks ==
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* 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).
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* (Robin) Make an '''illustration of the state machine''', possibly including a chart with all subsequent transitions and states???.
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* (Robin, Dominic) Include/redesign the '''concept section''', include/redesign contents of [[Introduction]] draft page.
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* (Alex) Make an new illustration of the '''block diagram''' of the system and write more text on the system architecture.
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* (Alex or Zlatko?) Make an illustration of the '''parts diagram''' according to Randy's conventions.
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* Check for consistency / update all '''registry parts''' online.
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* Someone write results, later discussion and conclusion - those we have and those we have not.
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* (Dominic) '''Input Module''': There should be a good '''introduction''' on the Main Page. Now there are sort of two introductions that I just copied there but don't really fit in...
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== Concept ==
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* (???) Write an '''introduction for the documentation''', don't forget to say that there are some previous ideas in the Appendix.
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* The output needs to be clearly labeled (-> state 3)
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* (Jonas) There is no '''section about the modularity of our counter system''' (how to connect multiple systems to count to 2^n). I think this is a very important aspect and should be well documented. This, I think, will be part of the concept.
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* (Robin) Wikify The '''Concept'''-Presentation of Zlatko and Jonas.
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== Small Tasks ==
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== EPD ==
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=== Input Module ===
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* (Dominic, others?) Make an illustration of the '''qualitative input-output dependence of EPD'''
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* (Dominic, others?) Make an illustration of the '''qualitative input-output dependence of EPD, including internal mechanisms'''
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* (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 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.
* (Dominic) In the schematic of the input module: The names in the legend do not correspond to the names in the picture.
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* (Dominic) In the 'suitable strategies' section of the input module, you name two remaining possible solutions. The lambda system is explained afterwards and this should be mentioned here. For the Lux system there should be a short description.
 
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* (Dominic) In the 'selected system' section of the input module, you say '... (which is crucial as modeling has shown).' I think this should have some reference to the modeling section.
 
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* (Dominic, Biologists..) You often use the words 'clone' and 'synthesize' in the context of connecting DNA Parts. Are these the correct technical terms? Maybe we could put something in the glossary.
 
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* (Dominic) In the legend of the 'cloning steps and debugging'-Picture you write in point four, that there will be three cloning sessions (with two to for individual steps). Later in the cloning schedule you talk about four cloning sessions.
 
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=== NOR Module ===
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== 4SD ==
* (Robin?) Fit the content of the Chapter to the following structure: Purpose, Schematic, Strategies & Evaluation, Actual Implementation
* (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.
* (???) In the purpose section we should describe in detail how the NOR module fits into the counter system.
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* (Alex) Design -> Interconnected NOR System -> Additional Comments: Maybe not up to date.
* (Alex) Design -> Interconnected NOR System -> Additional Comments: Maybe not up to date.
* (Alex) Syntesis and Assembly: Section has to be completed.
* (Alex) Syntesis and Assembly: Section has to be completed.
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== Modeling ==
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* (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
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* Adapt text, insert subtitles, keep main page minimal.

Latest revision as of 17:27, 1 November 2005

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.

Contents

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.

Concept

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

EPD

  • (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.

4SD

  • (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.

Modeling

  • (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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