Team:Heidelberg/Notebook/Modeling

From 2010.igem.org

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__TOC__
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=Modeling Notebook=
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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
 +
[[Image:First_model_concept_iGEM_Heidelberg.JPG|center|alt=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
 +
* Telemeeting with Stephen Krämer
 +
** Advantages and limitations of fuzzy logic
 +
 
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<html>
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<div class="backtop">
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<a href="#top">&uarr;</a>
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</div>
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</html>
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==September==
 +
====First Week====
 +
* 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
 +
 
 +
====Second Week====
 +
* Presentation of miBEAT project-concept in official team meeting
 +
* mUTING subproject is started
 +
 
 +
====Third Week====
 +
* 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
 +
 
 +
====Fourth Week====
 +
* miBS designer is finished
 +
* 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==
 +
====First Week====
 +
* Further development of the scripts for miBEAT
 +
* mUTING is started
 +
 
 +
====Second Week====
 +
* Both models (neural network and fuzzy logic) are ready and waiting for data
 +
* Planning for normalization strategies
 +
 
 +
====Third Week====
 +
* Designs of Binding Sites to be tested in wet lab
 +
* miRockdown is finished
 +
 
 +
====Fourth Week====
 +
* Setting up the miBEAT GUI
 +
* Writing of documentation and introduction to the project
 +
* Fitting of models to the obtained data
 +
 
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<html>
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<div class="backtop">
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<a href="#top">&uarr;</a>
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</div>
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</html>
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{{:Team:Heidelberg/Single_Bottom}}

Latest revision as of 16:03, 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
  • Telemeeting with Stephen Krämer
    • Advantages and limitations of fuzzy logic

↑

September

First Week

  • 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

Second Week

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

Third Week

  • 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

Fourth Week

  • miBS designer is finished
  • 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

First Week

  • Further development of the scripts for miBEAT
  • mUTING is started

Second Week

  • Both models (neural network and fuzzy logic) are ready and waiting for data
  • Planning for normalization strategies

Third Week

  • Designs of Binding Sites to be tested in wet lab
  • miRockdown is finished

Fourth Week

  • Setting up the miBEAT GUI
  • Writing of documentation and introduction to the project
  • Fitting of models to the obtained data

↑

Retrieved from "http://2010.igem.org/Team:Heidelberg/Notebook/Modeling"