From 2010.igem.org

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Revision as of 08:51, 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

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

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
miBS designer is finished
mUTING subproject is started

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 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

Both models (neural network and fuzzy logic) are ready and waiting for data
Planning for normalization strategies
Designs of Binding Sites to be tested in wet lab

@@ Line 19: / Line 19: @@
 ==July==
-* Work starts full time
 ====13.07.2010====
 * Discussion about first model idea
@@ Line 25: / Line 25: @@
-====21.07.2010====
+====30.07.2010====
 * Discussion about programming languages
 ** Advantages of R, Perl and MatLab
@@ Line 32: / Line 32: @@
 ==August==
-====05.08.2010====
+====First week====
 * Activation of MatLab-Accounts
+* Start working on several tutorials
-====09.08.2010====
+====Second week====
 * Meeting with Dr. König
 ** Advantages and disadvantages of different modeling approaches
 ** Possibility to use Neuronal Networks and Support Vector Machines
-====11.08.2010====
+====Third week====
 * Activation of MatLab fuzzy logic toolbox
-====18.08.2010====
+====Fourth week====
 * Meeting with Tim and Nao
 ** Options to optimize a fuzzy logic model
+* Start of subproject miBSdesigner
 ====22.08.2010====
@@ Line 61: / Line 63: @@
 ====08.09.2010====
 * Presentation of miBEAT project-concept in official team meeting
+* miBS designer is finished
+* mUTING subproject is started
 ====16-17.09.2010====
@@ Line 74: / Line 78: @@
 ====28.09.2010====
 * 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==
+* Both models (neural network and fuzzy logic) are ready and waiting for data
+* Planning for normalization strategies
+* Designs of Binding Sites to be tested in wet lab
 {{:Team:Heidelberg/Single_Bottom}}

Team:Heidelberg/Notebook/Modeling