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
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