Team:Heidelberg/Notebook/Modeling

From 2010.igem.org

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=Modeling Notebook=
=Modeling Notebook=
Welcome to the notebook of the modeling project.
Welcome to the notebook of the modeling project.
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This notebook comprises the work on four sublanes: miBEAT, miRockdown, miBS designer and the model training set.
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This notebook includes the work in four different tracks: miBEAT, miRockdown, miBS Designer and the model training set.
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Have fun!
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==Notebook==
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===<u>April</u>===
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==April==
====29.04.2010====
====29.04.2010====
* Meeting with Nao
* Meeting with Nao
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** Discuss about last years modeling approach
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** Discuss about last year's modeling approach
** Problems to be avoided
** Problems to be avoided
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===<u>Juli</u>===
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==July==
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====13.06.2010====
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====13.07.2010====
* Discussion about first model idea
* Discussion about first model idea
[[Image:First_model_concept_iGEM_Heidelberg.JPG|center|alt=The first model concept]]
[[Image:First_model_concept_iGEM_Heidelberg.JPG|center|alt=The first model concept]]
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====21.06.2010====
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====30.07.2010====
* Discussion about programming languages
* Discussion about programming languages
** Advantages of R, Perl and MatLab
** Advantages of R, Perl and MatLab
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** Request for Matlab license
** Request for Matlab license
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===<u>August</u>===
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==August==
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====05.08.2010====
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====First Week====
* Activation of MatLab-Accounts
* Activation of MatLab-Accounts
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* Start working on several tutorials
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====09.08.2010====
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====Second Week====
* Meeting with Dr. König
* Meeting with Dr. König
** Advantages and disadvantages of different modeling approaches
** Advantages and disadvantages of different modeling approaches
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** Possibility to use Neuronal Networks and Support Vektor Machines
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** Possibility to use Neuronal Networks and Support Vector Machines
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*** http://en.wikipedia.org/wiki/Support_vector_machine
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====11.08.2010====
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====Third Week====
* Activation of MatLab fuzzy logic toolbox
* Activation of MatLab fuzzy logic toolbox
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====18.08.2010====
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====Fourth Week====
* Meeting with Tim and Nao
* Meeting with Tim and Nao
** Options to optimize a fuzzy logic model
** Options to optimize a fuzzy logic model
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* Start of subproject miBSdesigner
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====22.08.2010====
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* Telemeeting with Stephen Krämer
* Telemeeting with Stephen Krämer
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** Advantages and limitations of a fuzzy logic
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** Advantages and limitations of fuzzy logic
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===<u>September</u>===
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<html>
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====07.09.2010====
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<div class="backtop">
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* Projectstart miBEAT
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<a href="#top">&uarr;</a>
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</div>
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</html>
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==September==
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====First Week====
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* Project miBEAT starts
** decision to create an interactive GUI on the wiki
** decision to create an interactive GUI on the wiki
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** creation of test model using javascript
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** creation of test GUI using javascript
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* Activation of MatLab neuro net toolbox  
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* Activation of MatLab neural net toolbox  
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** Projectstart Neuronal Network model
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** Start of Neural Network model
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====08.09.2010====
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====Second Week====
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* Presentation of miBEAT project-concept on official team meeting
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* Presentation of miBEAT project-concept in official team meeting
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* mUTING subproject is started
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====16-17.09.2010====
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====Third Week====
* 6th Workshop on Computation of Biochemical Pathways and Genetic Networks
* 6th Workshop on Computation of Biochemical Pathways and Genetic Networks
** Parameter estimation in fuzzy/noisy systems
** Parameter estimation in fuzzy/noisy systems
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* Discussion with Professor Sanghamitra Bandyopadhyay from the Machine Intelligence Unit of the Indian Statistical Institute in Kolkata
* 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
** Advise to use a Rough set modeling approach
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*** http://en.wikipedia.org/wiki/Rough_set
 
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====28.09.2010====
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====Fourth Week====
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* Project Start miRockdown
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* miBS designer is finished
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** Developement of miRockdown concept
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* Project miRockdown Starts
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** Development of an modified miBS designer to be part of miBEAT
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** Development of miRockdown concept
** Decision on the use of the modified targetscan_50_context_scores–Algorithm for binding site evaluation
** Decision on the use of the modified targetscan_50_context_scores–Algorithm for binding site evaluation
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{{:Team:Heidelberg/Pagemiddle}}
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==October==
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__TOC__
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====First Week====
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{{:Team:Heidelberg/Bottom}}
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* Further development of the scripts for miBEAT
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* mUTING is started
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====Second Week====
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* Both models (neural network and fuzzy logic) are ready and waiting for data
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* Planning for normalization strategies
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====Third Week====
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* Designs of Binding Sites to be tested in wet lab
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* miRockdown is finished
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====Fourth Week====
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* Setting up the miBEAT GUI
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* Writing of documentation and introduction to the project
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* 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"