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Cold Spring Harbor Course, 2009

Course Module Description

Key Value
Course Name: Cold Spring Harbor Course
Module Created: 2009/08/06
Author(s): Ion Moraru, Les Loew, Boris Slepchenko, Jim Schaff
Institutions University of Connecticut Health Center, Farmington, CT
Keywords: Modeling, quantitative, compartmental, spatial model
UG Course Level: Intermediate
Tool(s): Virtual Cell
Other tool(s):  
Course Abstract Cold Spring Harbor has started a Computational Cell Biology Course. The presentations and exercises in the modules below were prepared by faculty at the Center for Cell Analysis and Modeling. The course students included were mostly graduate students and post-docs who have a background in cell biology, biochemistry, mathematics, physics, and computer science. The lectures help these students in creating, running, and analyzing or interpreting numerical models (virtual experiments) in the Virtual Cell. All course models are available in the public folders of Education in the VCell. To access a model from this course, launch VCELL (Release or Beta), click on File > Open > BioModel... or MathModel... > Education. Another way to access models is to right-click on the related VCML file and "Save Target As" somewhere on your computer as a ".vcml" file then "Open" or double-click on the file to open. The file should open in VCell if VCell software is installed. If problems occur, take a look at VirtualCellPage. The Powerpoints (turned into pdf), VCell models, exercises, and further readings, are all available to you on this page!

Teaching Module Description

Key Value
Module Name: VCell - a Platform for Quantitative Modeling in Cell Biology
Author(s): Ion Moraru
Institution: UConn Health Center, Farmington, CT
Module Biology Topic: Quantitative Modeling
Keywords: quantitative, model, VCell, biophysics, cell biology, scope, capabilities
UG Course Level: Intermediate
Tool(s): Virtual Cell
Module Created: 2009/07/24

Quantitative Modeling in the Virtual Cell

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Abstract In this presentation the VCell platform, scope and capabilities are presented. An overview of VCell includes the software architechture, database, user interface, and how it is used in quantitative cell biology. How is VCell relevant to a cell biologist or biophysicist? How is it used? The typical workflow of a BioModel is highlighted. This presentation focuses on the software.
Physiology 04Moraru_VC_Introduction.pdf: This presentation gives an overview of the VCell capabilities in a concise way, for the audience to get the big picture of the scope of VCell. VCell is primarily used to model cellular physiology.
Model description What you learn from this exercise is how to create a simple Biomodel and Geometry using the Virtual Cell. There are two types ofd exercises, those that load existing models and others that create a model from scratch. They help people learn to do BioModels, MathModels, and simulations of biological cellular processes.
Model files Actin_Dendritic_Nucleation.vcml
cshl09_demo.vcml this demo model was used as a start of the exercise, without completion of reactions, math, spatial and compartmental application, nor a simulation run. A complete model with applications and simulations run can be found in Boris Slepchenko's module.
Model exercises 04Moraru-VC-Exercises.pdf
Further readings and references Trends in Cell Biology 13:570-576 (2003)
Vilar et al. 2002. PNAS

Teaching Module Description

Key Value
Module Name: VCell Analysing and Interpreting Experiments
Author(s): Les Loew
Institution: UConn Health Center, Farmington, CT
Module Biology Topic: VCell Analysis and Interpretation
Keywords: analysis, interpretation, Purkinje cell, dendritic spines
UG Course Level: Intermediate
Tool(s): Virtual Cell
Module Created: 2009/07/24

VCell Analysis and Interpretation

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Abstract This presentation extends the discussion of the uses of VCell in quantitative cell biology. From a hypothesis (model), a simulation can be run to predict cellular dynamics and experimental results. Some discussed examples include: bradykinin induced Calcium wave in a Neuroblastoma cell, kinetic analysis of receptor-activated phosphoinositide turnover, stimulation of PIP2 synthesis after hydrolysis, and stimulation of Gq pathway by bradykinin. One take-home message is VCell models are adaptable and reusable. The Virtual Cell can be used to analyze experiments that make use of fluorescent probes. The software can be used to identify the effects of the probe on the biology. VCell can help cell biologists test their hypothesis and understand complex experimental results.
Physiology 04Loew_VC_AnalysingInterpretingExperiments.pdf
Model description  
Model files PIP2_Hydrolysis_JCB_Submission.vcml
Model exercises 04Loew_VC_EveningExercises.pdf
04Brown_VC_SmithExamples.pdf : The models and simulations for Brown et al (2008) can be found in the Teaching Module VCellExercises.
Further readings and references

Trends in Cell Biology 13:570-576 (2003)
Fink C et al. 1999. JCB
Fink C et al. 2000. BioPhys J
Xu et al. 2003. JCB
Stauffer TP et al. 1998. Curr Biol. 8(6):343-346
Varnai P et al. 1998. J Cell Biol
Hirose K et al. 1999. Science
van der Wal et al. 2001. J Biol Chem
Brown et al. 2008. Biophys J.
Hausser et al. 2004. J Neurosci
Vecellio et al. 2000. Eur J Neurosci
Math description of Ca dynamics in neuroblastoma
Brown public models

Teaching Module Description

Key Value
Module Name: Compartmental Modeling with VCell
Author(s): Boris M. Slepchenko
Institution: UConn Health Center, Farmington, CT
Module Biology Topic: Compartmental Modeling
Keywords: compartmental, VCell, deterministic, stochastic, instability, simulation
UG Course Level: Intermediate
Tool(s): Virtual Cell
Module Created: 2009/07/24

Compartmental Modeling with VCell

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Abstract Compartmental modeling in VCell can consist of stochastic or deterministic simulations. This module explains what "stiff" systems are, what hybrid solvers do and provides real life examples. The stochastic simulation of non-spatial (compartmental) models can be run as well as multi-compartmental models. These are elaborated by doing VCell exercises.
Physiology 04Slepchenko_VC_CompartmentModeling.pdf: The Compartmental Modeling presentation includes VCell compartmental simulations at a glance, deterministic simulations, and stochastic simulations. The authors of these materials focus on the work of Vilar et al (circadian clocks) and Slepchencko and Terasaki (Oocytes and the cell cycle).
Model description stochastic and deterministic simulations in detail
Model files MichaelisMenten.vcml
CSH_09_circadian_clock.vcml (BioModel)
Vilar2002_Oscillator.vcml (MathModel)
CSH_09_G2_M_simple.vcml In the first Teaching Module, titled "VCell - a Platform for Quantitative Modeling in Cell Biology," students worked on the physiology of the Vilar et al 2002 model and a demo was shown. In this exercise, students completed the model as deterministic and stochastic applications, to make a compartmental model.
Model exercise VC Exercises.pdf
Further readings and references Vecellio et al. 2000. Eur J Neurosci
Salis H et al. 2006. BMC Bioinformatics
Vilar et al. PNAS. 2002
Okumura et al. 2002. Nat Cell Biol.
Slepchenko & Terasaki. 2004. Curr Opin Gen Dev
Slepchenko & Terasaki. 2003. Mol Biol Cell
Novak & Tyson. 1993. J Cell Sci

Teaching Module Description

Key Value
Module Name: Spatial Modeling with VCell
Author(s): Jim Schaff
Institution: UConn Health Center, Farmington, CT
Module Biology Topic: Spatial Modeling
Keywords: spatial, VCell, PIP2, diffusion, FRAP, geometry, 2D, 3D
UG Course Level: Advanced
Tool(s): Virtual Cell
Module Created: 2009/7/24

Spatial Modeling with VCell

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Abstract This lecture introduces the mathematical and physical consideration for spatial simulations in the VCell. PH-GFP fluorescence measurements of PIP2 and FRAP are used as examples of simple spatial models. Exercises on volume units, diffusion, advection, boundary conditions, and geometries are used to extend understanding and analysis of demonstrated models.
Physiology 04Schaff_VC_SpatialModelingAndExercise.pdf: Fluorescent analysis of the concentration and diffusion of second messenger molecules.
Model description PH-GFP fluorescence, FRAP, the concentration and diffusion of second messenger molecules, 2D, 3D
Model description PH-GFP fluorescence, FRAP, diffusion, boundary conditions, volume units
Model files PH-GFP-probe-only.vcml: Start the exercise with this model.
PH_GFP_Start.vcml is a complete version of the exercise.
Model exercises 04Schaff_VC_SpatialModelingAndExercise.pdf: For the exercise on Slide 12, open the PH-GFP-probe-only.vcml model. For the exercise on Slide 15, open the PH-GFP-Start.vcml model.
Further readings and references Stauffer TP et al.1998. Current Biology 8(6):343-346
Varnai P et al 2008 JCB 143(2):501-510


--Main.KhanhNguyen - 2009-08-06

Topic attachments
I Attachment Action Size Date Who Comment
PDFpdf 04Brown_VC_SmithExamples.pdf manage 11.5 K 2009-09-25 - 09:38 KhanhNguyen  
PDFpdf 04Loew_VC_AnalysingInterpretingExperiments.pdf manage 7381.0 K 2009-08-06 - 06:22 KhanhNguyen 04 Loew - VC Analysing Interpreting Experiments
PDFpdf 04Loew_VC_EveningExercises.pdf manage 70.3 K 2009-08-22 - 04:10 KhanhNguyen  
PDFpdf 04Moraru-VC-Exercises.pdf manage 139.6 K 2009-08-06 - 18:12 KhanhNguyen 04 Moraru VCell Exercises
PDFpdf 04Moraru_VC_Introduction.pdf manage 12851.1 K 2009-08-06 - 18:02 KhanhNguyen 04 Moraru VCell Introduction
PDFpdf 04Schaff_VC_SpatialModelingAndExercise.pdf manage 1986.8 K 2009-08-22 - 04:02 KhanhNguyen  
PDFpdf 04Slepchenko_VC_CompartmentModeling.pdf manage 1804.8 K 2009-08-22 - 04:11 KhanhNguyen  
PDFpdf 04Slepchenko_VC_Exercises.pdf manage 64.3 K 2009-08-22 - 04:03 KhanhNguyen  
Unknown file formatvcml Actin_Dendritic_Nucleation.vcml manage 1350.2 K 2009-08-06 - 18:21 KhanhNguyen Moraru exercise from Les folder: Actin Dendritic Nucleation
Unknown file formatvcml CSH_09_G2_M_simple.vcml manage 60.7 K 2009-09-25 - 08:36 KhanhNguyen  
Unknown file formatvcml CSH_09_circadian_clock.vcml manage 61.1 K 2009-09-25 - 09:48 KhanhNguyen  
Unknown file formatvcml CSH_09_multiple_compartments.vcml manage 11.9 K 2009-09-25 - 08:36 KhanhNguyen  
Unknown file formatvcml MichaelisMenten.vcml manage 23.9 K 2009-09-25 - 09:45 KhanhNguyen  
Unknown file formatvcml PH_GFP_Start.vcml manage 52.7 K 2009-09-25 - 09:58 KhanhNguyen  
Unknown file formatvcml PIP2_Hydrolysis_JCB_Submission.vcml manage 168.0 K 2009-09-25 - 09:25 KhanhNguyen  
Unknown file formatvcml Vilar2002_Oscillator.vcml manage 81.9 K 2009-09-25 - 08:41 KhanhNguyen  
Unknown file formatvcml cshl09_demo.vcml manage 21.6 K 2009-09-25 - 08:36 KhanhNguyen  
Unknown file formatvcml purkinge9_3D_crop776634105.vcml manage 26.0 K 2009-09-25 - 09:26 KhanhNguyen  
Topic revision: r32 - 2011-05-30 - 14:17:49 - RaquellHolmes
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