Imperial College/Courses/Spring2008/Synthetic Biology/Computer Modelling Practicals

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(New page: __NOTOC__ {{Template:ImperialCollege Spring2008 SyntheticBiologyCourse ComputerModellingPractical}} <div style="padding: 10px; width: 720px; border: 5px solid #B3CD4E;"> '''Spring 2008''...)
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'''Spring 2008'''
'''Spring 2008'''
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'''Instructor:''' [[User:Vincent Rouilly| Vincent Rouilly]]
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'''Instructor:''' [[User:Vincent Rouilly| Vincent Rouilly]].
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'''TAs:'''
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'''Room:'''      Biochemistry building, 310.
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'''Room:'''      to be defined
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'''Welcome!'''  
'''Welcome!'''  
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==Announcements==
==Announcements==
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*You can find the latest changes to the 20.109 wiki at [[Special:Recentchanges/Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals | Recent changes for 20.109]]
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*'''[[User:Vincent Rouilly|Vincent]] 08:43, 5 February 2008 (CST)''': Practical 2 has been rescheduled, and will run this thurs (7th Feb) from 9-12 in room 311 Biochem.
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*'''[[User:Johnsy|Johnsy]] 04:57, 31 January 2008 (CST)''':  Practical 2 Postponed until further notice.
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*'''[[User:Vincent Rouilly|Vincent]] 11:08, 18 January 2008 (CST)''': First practical report due on '''Monday 21st January, before 5pm'''. You can submit by emailing to me (PDF or Word format).
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*'''[[User:Vincent Rouilly|Vincent]] 06:43, 18 January 2008 (CST)''': Practical-2 re-run planned on January 31st. Practical-2 report not due before February 7th, 5pm. 
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*'''[[User:Vincent Rouilly|Vincent]] 04:06, 15 January 2008 (CST)''': Computer Lab, planned on Tuesday 15th Jan <font color=red> POSTPONED </font>. Computer Lab on Thursday 17th Jan (9-12), <font color=green> CONFIRMED </font>
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* Registration to OpenWetWare required ([[Join|Join OWW]])
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*You can find the latest changes to the course wiki at [[Special:Recentchanges/Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals | Recent changes for the course]]
   
   
*You can find old announcements [[Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals/old announcements| here]]
*You can find old announcements [[Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals/old announcements| here]]
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==[[Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals/Practical_1|Practical 1]]: Introduction (3h)==
==[[Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals/Practical_1|Practical 1]]: Introduction (3h)==
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* Short Presentation: "All the models are wrong, but some of them are useful", George Box.
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* '''Short Presentation''': "All the models are wrong, but some of them are useful", George Box.
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* Short Presentation: [[Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals/CellDesigner_Tutorial | CellDesigner Crash Course]]  
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* '''Short Presentation''': [[Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals/CellDesigner_Tutorial | CellDesigner Crash Course]]  
** Features and GUI
** Features and GUI
** Kinetic Simulations
** Kinetic Simulations
** SBML
** SBML
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* Hands-on: Build your first kinetic models.
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* '''Hands-on''': Build your first kinetic models.
==[[Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals/Practical_2|Practical 2]]: Gene Expression Modelling (3h)==
==[[Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals/Practical_2|Practical 2]]: Gene Expression Modelling (3h)==
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* Positive and Negative Feedback Gene Expression
* Positive and Negative Feedback Gene Expression
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==[[Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals/Practical_3|Practical 3]]: Genetic Circuits Modelling (3h)==
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==[[Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals/Practical_3|Practical 3]]: Genetic Circuit Modelling (3h)==
* Genetic Inverter Characterisation
* Genetic Inverter Characterisation
* Repressilator Characterisation
* Repressilator Characterisation
* Mystery Device Characterisation
* Mystery Device Characterisation

Current revision

Synthetic Biology (Spring2008): Computer Modelling Practicals

Home        CellDesigner Tutorial        Practical 1        Practical 2        Practical 3        Schedule        Back to Synthetic Biology Course       

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Spring 2008

Instructor: Vincent Rouilly.

Room: Biochemistry building, 310.

Welcome!

Announcements

  • Vincent 08:43, 5 February 2008 (CST): Practical 2 has been rescheduled, and will run this thurs (7th Feb) from 9-12 in room 311 Biochem.
  • Johnsy 04:57, 31 January 2008 (CST): Practical 2 Postponed until further notice.
  • Vincent 11:08, 18 January 2008 (CST): First practical report due on Monday 21st January, before 5pm. You can submit by emailing to me (PDF or Word format).
  • Vincent 06:43, 18 January 2008 (CST): Practical-2 re-run planned on January 31st. Practical-2 report not due before February 7th, 5pm.
  • Vincent 04:06, 15 January 2008 (CST): Computer Lab, planned on Tuesday 15th Jan POSTPONED . Computer Lab on Thursday 17th Jan (9-12), CONFIRMED
  • Registration to OpenWetWare required (Join OWW)
  • You can find old announcements here

Computer Lab Overview

Practical 1: Introduction (3h)

  • Short Presentation: "All the models are wrong, but some of them are useful", George Box.
  • Short Presentation: CellDesigner Crash Course
    • Features and GUI
    • Kinetic Simulations
    • SBML
  • Hands-on: Build your first kinetic models.

Practical 2: Gene Expression Modelling (3h)

  • Constitutive Gene Expression
  • Activated and Repressed Gene Expression
  • Positive and Negative Feedback Gene Expression

Practical 3: Genetic Circuit Modelling (3h)

  • Genetic Inverter Characterisation
  • Repressilator Characterisation
  • Mystery Device Characterisation
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