Team:Heidelberg/Notebook/Modeling

From 2010.igem.org

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Welcome to the notebook of the modeling project.
Welcome to the notebook of the modeling project.
This notebook includes the work in four different tracks: miBEAT, miRockdown, miBS Designer and the model training set.
This notebook includes the work in four different tracks: miBEAT, miRockdown, miBS Designer and the model training set.
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Have fun!
 
==April==
==April==
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* Telemeeting with Stephen Krämer
* Telemeeting with Stephen Krämer
** Advantages and limitations of fuzzy logic
** Advantages and limitations of fuzzy logic
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==September==
==September==
====07.09.2010====
====07.09.2010====
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* Planning for normalization strategies
* Planning for normalization strategies
* Designs of Binding Sites to be tested in wet lab
* Designs of Binding Sites to be tested in wet lab
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Revision as of 09:20, 27 October 2010

Modeling Notebook

Welcome to the notebook of the modeling project. This notebook includes the work in four different tracks: miBEAT, miRockdown, miBS Designer and the model training set.

April

29.04.2010

  • Meeting with Nao
    • Discuss about last year's modeling approach
    • Problems to be avoided

July

13.07.2010

  • Discussion about first model idea
The first model concept


30.07.2010

  • Discussion about programming languages
    • Advantages of R, Perl and MatLab
    • Decision to use Perl and Matlab
    • Request for Matlab license

August

First week

  • Activation of MatLab-Accounts
  • Start working on several tutorials

Second week

  • Meeting with Dr. König
    • Advantages and disadvantages of different modeling approaches
    • Possibility to use Neuronal Networks and Support Vector Machines

Third week

  • Activation of MatLab fuzzy logic toolbox

Fourth week

  • Meeting with Tim and Nao
    • Options to optimize a fuzzy logic model
  • Start of subproject miBSdesigner

22.08.2010

  • Telemeeting with Stephen Krämer
    • Advantages and limitations of fuzzy logic

↑

September

07.09.2010

  • Project miBEAT starts
    • decision to create an interactive GUI on the wiki
    • creation of test GUI using javascript
  • Activation of MatLab neural net toolbox
    • Start of Neural Network model

08.09.2010

  • Presentation of miBEAT project-concept in official team meeting
  • miBS designer is finished
  • mUTING subproject is started

16-17.09.2010

  • 6th Workshop on Computation of Biochemical Pathways and Genetic Networks
    • Parameter estimation in fuzzy/noisy systems
    • Global sensitivity analysis
    • New approaches to spatial modeling
    • Computation of microRNA regulatory network
  • Discussion with Professor Sanghamitra Bandyopadhyay from the Machine Intelligence Unit of the Indian Statistical Institute in Kolkata
    • Advise to use a Rough set modeling approach

28.09.2010

  • Project miRockdown Starts
    • Development of an modified miBS designer to be part of miBEAT
    • Development of miRockdown concept
    • Decision on the use of the modified targetscan_50_context_scores–Algorithm for binding site evaluation

October

  • Both models (neural network and fuzzy logic) are ready and waiting for data
  • Planning for normalization strategies
  • Designs of Binding Sites to be tested in wet lab

↑

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