Team:Heidelberg/Notebook/Modeling

From 2010.igem.org

(Difference between revisions)
 
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==August==
==August==
-
====First week====
+
====First Week====
* Activation of MatLab-Accounts
* Activation of MatLab-Accounts
* Start working on several tutorials
* Start working on several tutorials
-
====Second week====
+
====Second Week====
* Meeting with Dr. König
* Meeting with Dr. König
** Advantages and disadvantages of different modeling approaches
** Advantages and disadvantages of different modeling approaches
** Possibility to use Neuronal Networks and Support Vector Machines
** Possibility to use Neuronal Networks and Support Vector Machines
-
====Third week====
+
====Third Week====
* Activation of MatLab fuzzy logic toolbox
* Activation of MatLab fuzzy logic toolbox
-
====Fourth week====
+
====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
* Start of subproject miBSdesigner
* Start of subproject miBSdesigner
-
 
-
====22.08.2010====
 
* 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====
+
====First Week====
* Project miBEAT starts  
* 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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** Start of Neural Network model
** Start of Neural Network model
-
====08.09.2010====
+
====Second Week====
* Presentation of miBEAT project-concept in official team meeting
* Presentation of miBEAT project-concept in official team meeting
-
* miBS designer is finished
 
* mUTING subproject is started
* mUTING subproject is started
-
====16-17.09.2010====
+
====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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** New approaches to spatial modeling
** New approaches to spatial modeling
** Computation of microRNA regulatory network
** Computation of microRNA regulatory network
-
 
* 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
-
====28.09.2010====
+
====Fourth Week====
 +
* miBS designer is finished
* Project miRockdown Starts
* Project miRockdown Starts
** Development of an modified miBS designer to be part of miBEAT
** Development of an modified miBS designer to be part of miBEAT
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==October==
==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
* Both models (neural network and fuzzy logic) are ready and waiting for data
* Planning for normalization strategies
* Planning for normalization strategies
 +
 +
====Third Week====
* Designs of Binding Sites to be tested in wet lab
* 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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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

↑

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