Team:Heidelberg/Notebook/Modeling

From 2010.igem.org

(Difference between revisions)
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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.
Have fun!
Have fun!
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====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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==Juli==
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==July==
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====13.06.2010====
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* Work starts full time
 +
====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====
+
====21.07.2010====
* Discussion about programming languages
* Discussion about programming languages
** Advantages of R, Perl and MatLab
** Advantages of R, Perl and MatLab
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* 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====
====11.08.2010====
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====22.08.2010====
====22.08.2010====
* 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
==September==
==September==
====07.09.2010====
====07.09.2010====
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* Projectstart miBEAT
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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
====08.09.2010====
====08.09.2010====
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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
====16-17.09.2010====
====16-17.09.2010====
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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
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*** http://en.wikipedia.org/wiki/Rough_set
 
====28.09.2010====
====28.09.2010====
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* Project Start miRockdown
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* Project miRockdown Starts
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** Developement of miRockdown concept
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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
{{:Team:Heidelberg/Single_Bottom}}
{{:Team:Heidelberg/Single_Bottom}}

Revision as of 07:56, 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. Have fun!

April

29.04.2010

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

July

  • Work starts full time

13.07.2010

  • Discussion about first model idea
The first model concept


21.07.2010

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

August

05.08.2010

  • Activation of MatLab-Accounts

09.08.2010

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

11.08.2010

  • Activation of MatLab fuzzy logic toolbox

18.08.2010

  • Meeting with Tim and Nao
    • Options to optimize a fuzzy logic model

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

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 miRockdown concept
    • Decision on the use of the modified targetscan_50_context_scores–Algorithm for binding site evaluation

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