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Module Name: VCell Exercises
Author(s): Sherry Ann Brown and Sofya Borinskaya
Institutions: University of Connecticut Health Center, Farmington, CT
Module Biology Topic: Biochemical reactions
Other Biology:  
Keywords: Edit to enter key words for biology
UG Course Level: Beginner
Tool(s): Virtual Cell
Other tool: Vcell.org or VirtualCellPage
Module Created: 2009/07/01

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Abstract Four exercises provided in the attached PDF ask students to create simple reactions within the Virtual Cell. Students are asked to evaluate steady state for a single species, isomerization and buffering of calcium
Physiology biochemical reactions
Model description Deterministic models
Model files CSHL_CCB_VCell_Example_1.vcml
CSHL_CCB_VCell_Example_1___simulations_completed.vcml
CSHL_CCB_VCell_Example_2.vcml
CSHL_CCB_VCel_Example_2___simulations_completed.vcml
CSHL_CCB_VCell_Example_3.vcml
CSHL_CCB_VCell_Example_3___simulations_completed.vcml
CSHL_CCB_VCell_Example_4.vcml
CSHL_CCB_VCell_Example_4___simulations_completed.vcml
All exercise models are available in via the Virtual Cell in the shared/public folder of Brown. Note that these models were created with VCell 4.7
Model exercises 04Brown_VC_SmithExamples.pdf contains four detailed exercises. Each exercise consist of two VCell model: one incomplete and one complete. The first is the model as it would be created prior to running simulations and the model with simulations that examine different model or simulation parameters. The "completed" is essentially the desired simulation results for the exercise.
Further reading and references: Brown et al. 2008. Biophys J.
Brown public models

CategoryModule

  • CSHL_CCB_VCell_Ex_6.jpg:
    CSHL_CCB_VCell_Ex_6.jpg

-- RaquellHolmes - 01 Jul 2009
Topic attachments
I Attachment Action Size Date Who Comment
PDFpdf 04Brown_VC_SmithExamples.pdf manage 11.5 K 2009-08-22 - 04:10 KhanhNguyen  
Unknown file formatvcml CSHL_CCB_VCel_Example_2___simulations_completed.vcml manage 7.6 K 2009-07-13 - 20:06 UnknownUser  
JPEGjpg CSHL_CCB_VCell_Ex_6.jpg manage 668.5 K 2009-07-01 - 16:38 UnknownUser  
Unknown file formatvcml CSHL_CCB_VCell_Example_1.vcml manage 6.2 K 2009-07-01 - 17:08 UnknownUser  
Unknown file formatvcml CSHL_CCB_VCell_Example_1___simulations_completed.vcml manage 9.9 K 2009-07-01 - 18:20 UnknownUser  
Unknown file formatvcml CSHL_CCB_VCell_Example_2.vcml manage 6.4 K 2009-07-13 - 20:07 UnknownUser  
Unknown file formatvcml CSHL_CCB_VCell_Example_3.vcml manage 8.1 K 2009-07-13 - 20:07 UnknownUser  
Unknown file formatvcml CSHL_CCB_VCell_Example_3___simulations_completed.vcml manage 9.3 K 2009-07-13 - 20:08 UnknownUser  
Unknown file formatvcml CSHL_CCB_VCell_Example_4.vcml manage 12.7 K 2009-07-13 - 20:19 UnknownUser  
Unknown file formatvcml CSHL_CCB_VCell_Example_4___simulations_completed.vcml manage 11.8 K 2009-09-25 - 10:11 KhanhNguyen  
Unknown file formatvcml real_purkinje_3D.vcml manage 126.6 K 2009-09-25 - 10:12 KhanhNguyen  
Topic revision: r10 - 2011-03-03 - 03:58:38 - IonMoraru
 
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