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Willkommen zum Wiki des Praxisseminars:
Rechnergestützte Systembiologie SS 2017

Aktuelles

Vorbesprechung findet am 19.04. um 10:15 in 017/A6 statt.

Allgemeine Informationen

SWS: 4, ECTS: 5
Dozentin: Heike Siebert
Tutorin:
Sprache: Deutsch/Englisch

Termine

Praxisseminar Mi 10-14 h Arnimallee 6 SR 017 (Bioinformatik-Pool)

Content:

The course focuses on the modeling of molecular networks using discrete/logical approaches. The theoretical framework will be introduced and software tools presented. On the basis of suitable research articles, the participants will conduct their own modeling project in small groups.

Final presentation

Each group should prepare a 30-minutes talk presenting the key findings of their modeling project, touching on biological background, model construction and analysis, results and conclusions. Each group member should do about half of the presentation. The talk will be followed by a discussion.

Additionally a rough documentation of the modeling project should be handed in, including bullet points on reasoning and references for model construction, list of validation and analysis steps and an overview of the respective results.

Zeitplan

Datum Thema Todo
19.04. Vorbesprechung  
26.04. Intro Systembiologie Karlebach/Shamir paper
03.05. Structural Analysis Network Software - short presentation
10.05. Network Software, Boolean modeling I  
17.05. Boolean modeling II  
24.05. Perturbation analysis, multi-valued modeling, project  
31.05. Software Tutorial BoolNet, Model checking  
07.06. Software Tutorial GINsim, experimental data starting point network
14.06. Softare Tutorial PyBoolNet, experimental data data questions
21.06. Software Tutorial EpiLog informal status report
28.06. Uncertainty analysis, Project  
05.07. Project informal status report
12.07. Synthetic Biology, Project  
19.07. Final presentations documentation

Material

Modeling Project

Cell fate decisions
Laslo et al., 2008

Apoptosis regulation
Igney, Krammer, 2002
Zou et al., 2002

Segmentation clock
Aulehla et al., 2003
Rida et al., 2004

C. elegans endoderm development
Maduro et al., 2002

p53 Mdm2 network
Shi et al., 2012
Wade et al., 2010

Software tutorials

GINsim
Website with tutorials and models
Papers:background, application

BoolNet
Website
Papers: background, application

PyBoolNet
Website with tutorial and models
Papers:background, application

EpiLog
Website with tutorial and models
Papers: Cellular Automata, application

Deliverables

  • Presentation modeling project
  • Documentation modeling project
  • Softwaretutorial
Topic revision: r21 - 12 Jul 2017, HeikeSiebert
 
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