Team:ETHZ Basel/Internal

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(Difference between revisions)
(→Mathematical Modeling)
(→Mathematical Modeling)
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Christoph:
Christoph:
* first box: E. lemming, these aren't the devices we used for modeling, that is what we model, anchor not necessarily the plasmid
* first box: E. lemming, these aren't the devices we used for modeling, that is what we model, anchor not necessarily the plasmid
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 +
* 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
* 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
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* Combined mathematical models: shouldn't light-switch-chemo-movement be the complete?  
* Combined mathematical models: shouldn't light-switch-chemo-movement be the complete?  
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* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Combined#Light_switch_-_Chemotaxis : interfaces had to be defined, show that the individual models are without restrictons combinable by user wish
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* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Combined#Light_switch_-_Chemotaxis : 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/Light_Switch
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Light_Switch
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* "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
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* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Chemotaxis: first proofreading '''Simona DONE'''
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Chemotaxis: first proofreading '''Simona DONE'''
C: give an idea about the complexity, e.g. high number of proteins and interactions;  
C: give an idea about the complexity, e.g. high number of proteins and interactions;  
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please gibe a clearer description of the plots, for an external person it's almost not understandable
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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* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Combined
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* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Combined C: see above
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* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Experimental_Design
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* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Experimental_Design C: OK
===Information Processing===
===Information Processing===

Revision as of 15:24, 24 October 2010

Internal

This section will be removed before wiki-freeze!

Acknowledged problems/incomplete pages


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.

Suggestions

  • We need to be consistent in the use of formal/informal language. what do you decide upon this?

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.

Teaser & Motivation

Images

Simona: Achievements image: increase resolution; Same for first image. (Response from George: resolution was decreased to match to LowRes Lemmings screenshot. It looks incoherent, if only E. lemming is HighRes. See this version.)

Thanuja: a better picture to suggest what we have done? any creative ideas to make a better first impression? (Response from George: Yes, please make suggestions! I ran out of ideas. ;-))

Simona: pictures look very cool; if possible, change the one from 'Information processing' (Response from George: Do you have a suggestion, what we could take?)

Text

Motivation & Project Idea

Simona: E. lemming is the 2010 iGEM project of ETH Zurich! We are controlling the movement of any E. coli cell by hijacking chemotaxis, monitoring its spatial behavior by image processing techniques and directing it towards an user - define target by smart control algorithms! Find out more about our motivation and project idea!

E. lemming - The movie

Simona: Watch a short animation of E. lemming! Find out the core concepts behind our project and how we combined biology, mathematical modeling and image processing techniques to create E. lemming!

Biology & Wet Laboratory

Simona: How is it implemented? By coupling the Che proteins of the chemotaxis pathway to a synthetic light - sensitive spatial localization system, their activity can be reversibly controlled. To find out more about E. lemming on the molecular level and to find information regarding the wet laboratory experiments, visit our Biology & Wet Laboratory section.

Mathematical Modeling

SimonaMathematical Modeling How does modeling help? To find out how the mathematical models we developed not only supported wet lab experiments by optimizing the biological network structure to be used, but also provided a test bench for our information processing system, visit the Mathematical Modeling section!

Information Processing

Simona How is it controlled? Implementation of a comprehensive information processing workflow for controlling E. lemming was achieved by combining microscopy, image analysis and processing and controlling algorithms. Find out more about how the information processing part of our project not completed E. lemming, but also created a brand new synthetic biology game: E.lemming!

Achievements

Simona: OK


Motivation

General

  • Movies: George & Luzi Almost done, but needs speech! Elsa
  • Matlab Toolboxes: Moritz & George

Proofreading

Introduction

Biology & Wet Laboratory

Mathematical Modeling

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

Information Processing

Achievements

Pick-a-task

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