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

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