Team:ETHZ Basel/Internal

From 2010.igem.org

(Difference between revisions)
(→Responsibilities, Tasks & Suggestions)
(→Responsibilities, Tasks & Suggestions)
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** ToDo:
** ToDo:
** Suggestions:
** Suggestions:
 +
*** Someone: first paragraph, define 'anchor' and 'tumbling' and 'directed movement' before using the terms, second paragraph: quite unclear, if possible, add more details & explain more
 +
*** Someone: add a few sentences (and link them) regarding ARL & Safety
* https://2010.igem.org/Team:ETHZ_Basel/Biology/Molecular_Mechanism
* https://2010.igem.org/Team:ETHZ_Basel/Biology/Molecular_Mechanism
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** ToDo:
** ToDo:
** Suggestions:
** Suggestions:
 +
*** Someone: added reference [2]. would be good if a biologist can check if it's the right one. Looks like the page ends abruptly. something like a conclusion perhaps?
* https://2010.igem.org/Team:ETHZ_Basel/Biology/Archeal_Light_Receptor
* https://2010.igem.org/Team:ETHZ_Basel/Biology/Archeal_Light_Receptor
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** ToDo:
** ToDo:
** Suggestions:
** Suggestions:
-
*** Someone: improve language
+
*** Christoph: improve language
 +
*** Christoph: first box: E. lemming, these aren't the devices we used for modeling, that is what we model, anchor not necessarily the plasmid
 +
*** Christoph: please rearrange: 1. WHAT complex model set up, consisting of chemotaxis, light, move, implemented and coupled 2. WHY explain support a little bit more
 +
*** Christoph: Model implementation: tab and text order should be equal; implementation and adaption of literature described ones, movement by our own!
 +
*** Christoph: Combined mathematical models: shouldn't light-switch-chemo-movement be the complete?
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Light_Switch
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Light_Switch
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** ToDo:
** ToDo:
** Suggestions:
** Suggestions:
 +
*** Christoph: To model the relocation, we decided to adapt a model recently published by Sorokina et al [1]. As a first step we reimplemented the model as published in the paper." make one good sentence
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Chemotaxis
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Chemotaxis
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*** Moritz: state that models are based on published models and adapted by us.
*** Moritz: state that models are based on published models and adapted by us.
*** Someone: add picture from chemotaxis pathway
*** Someone: add picture from chemotaxis pathway
 +
*** Christoph: give an idea about the complexity, e.g. high number of proteins and interactions;
 +
*** Christoph: why did we use only Spiro and Mello?;
 +
*** Christoph: models: text first as it explains the plots;
 +
*** Christoph: please gibe a clearer description of the plots, for an external person it's almost not understandable
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Movement
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Movement
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** ToDo:
** ToDo:
** Suggestions:
** Suggestions:
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*** Christoph: make clear we did this completely on our own, not implemented but created!
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Combined
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Combined
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** ToDo:
** ToDo:
** Suggestions:
** Suggestions:
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*** Christoph: interfaces had to be defined, show that the individual models are without restrictons combinable by user wish, number of combinations
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Experimental_Design
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Experimental_Design
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** ToDo:
** ToDo:
** Suggestions:
** Suggestions:
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*** Someone: 50 μm (?) high flow channel; remove question mark
* https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Microscope
* https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Microscope
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** ToDo:
** ToDo:
** Suggestions:
** Suggestions:
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*** Someone: in second part of the page, 'cells with highest score'; define the score
 +
*** Someone: clearly define the reference used: [1] Stuurman et al. 2007; could not uniquely identify it
* https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/CellDetection
* https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/CellDetection
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** ToDo:
** ToDo:
** Suggestions:
** Suggestions:
 +
*** Someone: Corrected minor spelling mistakes. Gave names to the 2 steps of the cell detection algorithm. Added subheadings to make it more readable & structured. Revert if necessary.
* https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Visualization
* https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Visualization
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** Suggestions:
** Suggestions:
*** Jörg: add explanation (legend) to the movie.
*** Jörg: add explanation (legend) to the movie.
 +
*** Someone: spacing, subheadings & some bullet points); suggesting more images for the user experience part
* https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Controller
* https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Controller

Revision as of 21:20, 25 October 2010

Internal

This section will be removed before wiki-freeze!

DO NOT EDIT NOW!!!

General remarks

  • Protein names: normally written
  • gene names: italic
  • Directed movement NOT running, please correct!
  • chemotaxis pathway NOT Chemotaxis nor chemotactic
  • E. lemming with space
    • E. lemming vs THE E. lemming: E. lemming: Project name (whole assay), The E. lemming: One single genetically modified E. coli
  • far-red light, not far red light, please correct!
  • internal links - we should refer to other internal pages (hyperlinks) where appropriate, inside the paragraphs.
  • in silico & in vivo, not in-silico & in-vivo

Teaser & Animations

  • Drafts of teaser & animation text

Responsibilities, Tasks & Suggestions

Introduction

  • https://2010.igem.org/Team:ETHZ_Basel/Introduction/Movie
    • Responsibility: George
    • Proofreading: Elsa
    • Status: 50%
    • ToDo: improve text, add speech
    • Suggestions:
      • Elsa: change background to other color
      • Jörg: add automated microscope image
      • Vincent: make chapters, different effect for highlighting of parts

Biology & Wet Laboratory

  • https://2010.igem.org/Team:ETHZ_Basel/Biology
    • Responsibility: Elsa
    • Proofreading: Katharina
    • Status:
    • ToDo:
    • Suggestions:
      • Someone: first paragraph, define 'anchor' and 'tumbling' and 'directed movement' before using the terms, second paragraph: quite unclear, if possible, add more details & explain more
      • Someone: add a few sentences (and link them) regarding ARL & Safety

Mathematical Modeling

  • https://2010.igem.org/Team:ETHZ_Basel/Modeling
    • Responsibility: Moritz
    • Proofreading: Christoph
    • Status:
    • ToDo:
    • Suggestions:
      • Christoph: improve language
      • Christoph: first box: E. lemming, these aren't the devices we used for modeling, that is what we model, anchor not necessarily the plasmid
      • Christoph: please rearrange: 1. WHAT complex model set up, consisting of chemotaxis, light, move, implemented and coupled 2. WHY explain support a little bit more
      • Christoph: Model implementation: tab and text order should be equal; implementation and adaption of literature described ones, movement by our own!
      • Christoph: Combined mathematical models: shouldn't light-switch-chemo-movement be the complete?
  • https://2010.igem.org/Team:ETHZ_Basel/Modeling/Light_Switch
    • Responsibility: Moritz
    • Proofreading: Luzi
    • Status:
    • ToDo:
    • Suggestions:
      • Christoph: To model the relocation, we decided to adapt a model recently published by Sorokina et al [1]. As a first step we reimplemented the model as published in the paper." make one good sentence
  • https://2010.igem.org/Team:ETHZ_Basel/Modeling/Chemotaxis
    • Responsibility: George
    • Proofreading: Simona
    • Status:
    • ToDo:
    • Suggestions:
      • Elsa: link to chemotaxis
      • Moritz: state that models are based on published models and adapted by us.
      • Someone: add picture from chemotaxis pathway
      • Christoph: give an idea about the complexity, e.g. high number of proteins and interactions;
      • Christoph: why did we use only Spiro and Mello?;
      • Christoph: models: text first as it explains the plots;
      • Christoph: please gibe a clearer description of the plots, for an external person it's almost not understandable

Information Processing

Achievements

Team

Suggestions

first paragraph, define 'anchor' and 'tumbling' and 'directed movement' before using the terms
second paragraph: quite unclear, if possible, add more details & explain more
add a few sentences (and link them) regarding ARL & Safety

50 μm (?) high flow channel; remove question mark

in second part of the page, 'cells with highest score'; define the score
clearly define the reference used: [1] Stuurman et al. 2007; could not uniquely identify it

Original sentence 'It should be noticed that this signal changes with time constant in the range of hours' rephrased to:'It should be noticed that this signal constantly changes with time in the range of hours.' Revert if meaning changed.

added reference [2]. would be good if a biologist can check if it's the right one. Looks like the page ends abruptly. something like a conclusion perhaps?

spacing, subheadings & some bullet points); suggesting more images for the user experience part

Corrected minor spelling mistakes. Gave names to the 2 steps of the cell detection algorithm. Added subheadings to make it more readable & structured. Revert if necessary.

check with biology to keep it updated (check list)

Add link to Biozentrum Unibas.

Christoph will do this by Sunday

Christoph:

  • first box: E. lemming, these aren't the devices we used for modeling, that is what we model, anchor not necessarily the plasmid
  • too many "in order to"
  • mathematical modeling overview: please rearrange: 1. WHAT complex model set up, consisting of chemotaxis, light, move, implemented and coupled 2. WHY explain support a little bit more
  • Model implementation: tab and text order should be equal; implementation and adaption of literature described ones, movement by our own!

C: give an idea about the complexity, e.g. high number of proteins and interactions; why did we use only Spiro and Mello?; models: text first as it explains the plots; please gibe a clearer description of the plots, for an external person it's almost not understandable

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