Computational Cell Biology - User contributions [en]

Template:Virtual Cell Exercises

2007-12-20T21:39:48Z

Raquell: /* '''Materials Needed''' */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become familiar with the Virtual Cell user interface and commands. What is outlined below is the experimental context and homework assignment that accompanies the tutorial.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

==='''Experimental principle'''===
Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

====Learning Goals====
''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

===='''Materials Needed'''====

ALG: Image stack, image analysis data
*To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

*Image stack for extracting values using Image J:
**Download and unzip image stack (Coming Soon).
***Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data [[mailto:rholmes@uchc.edu| email Dr.Holmes]].

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region, [Fi(-)]. See spreadsheet of FRAP Homework obtained from [[mailto:rholmes@uchc.edu| Dr.Holmes]].

[[image:FiINaROI.jpg]]

===='''BLG Tasks'''====

1. In excel, plot the data as a time series. Compare the plots, normalize based on t/msqi.
*To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

2. Compare results to Virtual Cell FRAP simulation created in Tutorial

What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T21:37:14Z

Raquell:

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become familiar with the Virtual Cell user interface and commands. What is outlined below is the experimental context and homework assignment that accompanies the tutorial.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

==='''Experimental principle'''===
Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

====Learning Goals====
''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

===='''Materials Needed'''====

ALG: Image stack, image analysis data
*To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

*Image stack for extracting values using Image J:
**Download and unzip image stack (Coming Soon).
***Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region, [Fi(-)]. See Spreadsheet [[media:FRAP_Homework.xls| FRAP Homework data coming]] [[mailto:rholmes@uchc.edu| email Dr.Holmes]] for the data.

[[image:FiINaROI.jpg]]

===='''BLG Tasks'''====

1. In excel, plot the data as a time series. Compare the plots, normalize based on t/msqi.
*To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

2. Compare results to Virtual Cell FRAP simulation created in Tutorial

What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T21:35:06Z

Raquell: /* '''Materials Needed:''' */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become familiar with the Virtual Cell user interface and commands. What is outlined below is the experimental context and homework assignment that accompanies the tutorial.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

==='''Experimental principle'''===
Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

====Learning Goals====
''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

===='''Materials Needed'''====

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region, [Fi(-)]. See Spreadsheet [[media:FRAP_Homework.xls| FRAP Homework data coming]] [[mailto:rholmes@uchc.edu| email Dr.Holmes]] for the data.

[[image:FiINaROI.jpg]]

===='''BLG Tasks'''====

1. In excel, plot the data as a time series. Compare the plots, normalize based on t/msqi.
*To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

2. Compare results to Virtual Cell FRAP simulation created in Tutorial

What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T21:34:50Z

Raquell: /* '''Materials Needed:''' */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become familiar with the Virtual Cell user interface and commands. What is outlined below is the experimental context and homework assignment that accompanies the tutorial.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

==='''Experimental principle'''===
Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

====Learning Goals====
''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

===='''Materials Needed:'''====

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region, [Fi(-)]. See Spreadsheet [[media:FRAP_Homework.xls| FRAP Homework data coming]] [[mailto:rholmes@uchc.edu| email Dr.Holmes]] for the data.

[[image:FiINaROI.jpg]]

===='''BLG Tasks'''====

1. In excel, plot the data as a time series. Compare the plots, normalize based on t/msqi.
*To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

2. Compare results to Virtual Cell FRAP simulation created in Tutorial

What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T21:34:06Z

Raquell:

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become familiar with the Virtual Cell user interface and commands. What is outlined below is the experimental context and homework assignment that accompanies the tutorial.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

==='''Experimental principle'''===
Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

====Learning Goals====
''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

===='''Materials Needed:'''====

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region, [Fi(-)]. See Spreadsheet [[media:FRAP_Homework.xls| FRAP Homework data coming]] [[mailto:rholmes@uchc.edu| email Dr.Holmes]] for the data.

[[image:FiINaROI.jpg]]

'''BLG Tasks:'''

1. In excel, plot the data as a time series. Compare the plots, normalize based on t/msqi.
*To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

2. Compare results to Virtual Cell FRAP simulation created in Tutorial
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T21:32:48Z

Raquell: /* '''Experimental principle:''' */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

==='''Experimental principle'''===
Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

====Learning Goals====
''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

===='''Materials Needed:'''====

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region, [Fi(-)]. See Spreadsheet [[media:FRAP_Homework.xls| FRAP Homework data coming]] [[mailto:rholmes@uchc.edu| email Dr.Holmes]] for the data.

[[image:FiINaROI.jpg]]

'''BLG Tasks:'''

1. In excel, plot the data as a time series. Compare the plots, normalize based on t/msqi.
*To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

2. Compare results to Virtual Cell FRAP simulation created in Tutorial
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T21:32:32Z

Raquell: /* '''Materials Needed:''' */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

==='''Experimental principle:'''===
Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

====Learning Goals====
''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

===='''Materials Needed:'''====

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region, [Fi(-)]. See Spreadsheet [[media:FRAP_Homework.xls| FRAP Homework data coming]] [[mailto:rholmes@uchc.edu| email Dr.Holmes]] for the data.

[[image:FiINaROI.jpg]]

'''BLG Tasks:'''

1. In excel, plot the data as a time series. Compare the plots, normalize based on t/msqi.
*To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

2. Compare results to Virtual Cell FRAP simulation created in Tutorial
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T18:55:27Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

==='''Experimental principle:'''===
Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

====Learning Goals====
''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

===='''Materials Needed:'''====

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region, [Fi(-)]. See Spreadsheet [[media:FRAP_Homework.xls| FRAP Homework data coming]] [[mailto:rholmes@uchc.edu| email Dr.Holmes]] for the data.

[[image:FiINaROI.jpg]]

'''BLG Tasks:'''

1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.
*To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T18:48:04Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

==='''Experimental principle:'''=== Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

====Learning Goals====
''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

===='''Materials Needed:'''====

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region, [Fi(-)]. See Spreadsheet [[media:FRAP_Homework.xls| FRAP Homework data coming]] [[mailto:rholmes@uchc.edu| email Dr.Holmes]] for the data.

[[image:FiINaROI.jpg]]

'''BLG Tasks:'''

1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.
*To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Exercises

2007-12-20T18:46:45Z

Raquell:

{{Cell Cycle Exercises}}

====Evaluation Forms====
[[Media:EvaluationCellCycleAndModeling.pdf|Evaluation Tool for Cell Cycle and Modeling Course Module]]

==Virtual Cell Exercises==

===Virtual Cell and Key Concepts===
{{Virtual Cell Exercises}}

Exercises

2007-12-20T18:46:22Z

Raquell:

{{Cell Cycle Exercises}}

===Evaluation Forms===
[[Media:EvaluationCellCycleAndModeling.pdf|Evaluation Tool for Cell Cycle and Modeling Course Module]]

==Virtual Cell Exercises==

===Virtual Cell and Key Concepts===
{{Virtual Cell Exercises}}

Template:Virtual Cell Exercises

2007-12-20T18:44:43Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

'''Materials Needed:'''

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region, [Fi(-)]. See Spreadsheet [[media:FRAP_Homework.xls| FRAP Homework data coming]] [[mailto:rholmes@uchc.edu| email Dr.Holmes]] for the data.

[[image:FiINaROI.jpg]]

'''BLG Tasks:'''

1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.
*To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T18:36:53Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

'''Materials Needed:'''

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region, [Fi(-)]. See Spreadsheet [[media:FRAP_Homework.xls| FRAP Homework data]]

[[image:FiINaROI.jpg]]

'''BLG Tasks:'''

1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.
*To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T18:29:49Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

'''Materials Needed:'''

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

[[image:FiINaROI.jpg]]

To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

'''BLG Tasks:'''

1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T18:29:00Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

'''Materials Needed:'''

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

[[image:FiINaROI.jpg]]

To normalize data across images [[image:FiINaROI.jpg]] vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

File:FiINaROI.jpg

2007-12-20T18:26:19Z

Raquell: Equation for calculating change in fluorescent intensity over time within a given space (geometry).

Equation for calculating change in fluorescent intensity over time within a given space (geometry).

Template:Virtual Cell Exercises

2007-12-20T18:25:11Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

'''Materials Needed:'''

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

[[media:FiINaROI.jpg]]

To normalize data across images vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T18:13:06Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

'''Materials Needed:'''

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

'''(See print out for equations)'''

To normalize data across images vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T18:12:39Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

'''Materials Needed:'''

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:

-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

'''(See print out for equations)'''

To normalize data across images vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T18:11:10Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

'''Materials Needed:'''

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:
-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

'''(See print out for equations)'''

To normalize data across images vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T18:10:24Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

'''Materials Needed:'''

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:
-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

'''(See print out for equations)'''

To normalize data across images vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T18:09:35Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

Needed:

ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:
-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
*Download and unzip image stack (Coming Soon).
**Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

*Image analysis:
**Use image analysis software to extract pixel values for fluoresence intensity

BLG: Download excel spreadsheet of fluorescent intensity data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

'''(See print out for equations)'''

To normalize data across images vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T18:06:47Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

''Basic learning goals (BLG):''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced learning goals (ALG):''
*extract data values from image files
*compare experimental data to multiple biological, computational models i.e. free diffusion, diffusion with binding, immobile fractions, etc.

Needed:
BLG:
ALG: Image stack, image analysis data
To obtain image stack in lab the following are needed:
-Fluorescent microscope -fluorescent probe -labeled cell -camera -image capture and analysis software (e.g. ImageJ).

Image stack for extracting values using Image J:
Download and unzip image stack (Coming Soon).
*Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

Image analysis:
1. Use image analysis software to extract pixel values for fluoresence intensity
2. Download excel spreadsheet of data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

'''(See print out for equations)'''

To normalize data across images vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T17:53:55Z

Raquell:

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

''Basic learning goals:''
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

''Advanced goals:''
Needed: Image stack, image analysis data

To obtain Image stack:
1. Fluorescent microscope, fluorescent probe, labeled cell, camera, image capture software (ImageJ).
2. Download and unzip image stack (available after workshop). Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

Image analysis:
1. Use image analysis software to extract pixel values for fluoresence intensity
2. Download excel spreadsheet of data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

'''(See print out for equations)'''

To normalize data across images vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T17:52:33Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

'''Experimental principle:''' Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a population of molecules over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity (recover) over time as the molecules diffuse.

Basic learning goals:
*To have students do data analysis
*To become familiar with constructing a simple model in Virtual Cell.

Advanced goals:
Needed: Image stack, image analysis data

To obtain Image stack:
1. Fluorescent microscope, fluorescent probe, labeled cell, camera, image capture software (ImageJ).
2. Download and unzip image stack (available after workshop). Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

Image analysis:
1. Use image analysis software to extract pixel values for fluoresence intensity
2. Download excel spreadsheet of data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

'''(See print out for equations)'''

To normalize data across images vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T17:41:14Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
*Biology: diffusion, compartments

*Experiments: time series, fluorescent microscopy, wave lengths, lasers

*Data Analysis: image capture, image analysis

Photobleaching experimental principle: Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a molecule over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity over time as the molecules diffuse in (Virtual Cell FRAP Tutorial).

Needed: Image stack, image analysis data

To obtain Image stack:
1. Fluorescent microscope, fluorescent probe, labeled cell, camera, image capture software (ImageJ).
2. Download and unzip image stack (available after workshop). Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

Image analysis:
1. Use image analysis software to extract pixel values for fluoresence intensity
2. Download excel spreadsheet of data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

'''(See print out for equations)'''

To normalize data across images vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T17:40:28Z

Raquell: /* Relevance of FRAP to courses */

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
Biology: diffusion, compartments

Experiments: time series, fluorescent microscopy, wave lengths, lasers

Data Analysis: image capture, image analysis

Photobleaching experimental principle: Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a molecule over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity over time as the molecules diffuse in (Virtual Cell FRAP Tutorial).

Needed: Image stack, image analysis data

To obtain Image stack:
1. Fluorescent microscope, fluorescent probe, labeled cell, camera, image capture software (ImageJ).
2. Download and unzip image stack (available after workshop). Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

Image analysis:
1. Use image analysis software to extract pixel values for fluoresence intensity
2. Download excel spreadsheet of data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

'''(See print out for equations)'''

To normalize data across images vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Template:Virtual Cell Exercises

2007-12-20T17:39:44Z

Raquell:

'''This exercise draws on a Virtual Cell Tutorial that can be found at the Virtual Cell website [http://vcell.org/login/login.html]'''

The first tutorial is based on FRAP. We use the [http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf FRAP Tutorial] to become with the Virtual Cell user interface and commands.

===Relevance of FRAP to courses===
'''Course Relevance:''' Cell Biology, Biochemistry

'''Concepts'''
Biology: diffusion, compartments
Experiments: time series, fluorescent microscopy, wave lengths, lasers
Data Analysis: image capture, image analysis

Photobleaching experimental principle: Fluorescence Recovery After Photobleaching (FRAP) is a fluorescent optical technique used to measure the dynamics of a molecule over time and chemical changes of molecular species. The fluorescently labeled molecules are visualized through an epifluorescent or confocal microscope using low light excitation. The excitation light is focused onto a small region of molecules and pulsed to a high intensity in order to photobleach the fluorophore within the illuminated region. A blackened area of photobleached molecules surrounded by fluorescently labeled molecules that are not photobleached will result from the high intensity light. The molecules that are not photobleached will diffuse, providing they can, into this region. The blackened area will gradually increase in intensity over time as the molecules diffuse in (Virtual Cell FRAP Tutorial).

Needed: Image stack, image analysis data

To obtain Image stack:
1. Fluorescent microscope, fluorescent probe, labeled cell, camera, image capture software (ImageJ).
2. Download and unzip image stack (available after workshop). Images are essentially wide field fluorescent images. They were collected with an open pin hole on confocal microscope.

Image analysis:
1. Use image analysis software to extract pixel values for fluoresence intensity
2. Download excel spreadsheet of data (available post workshop).

Data Set: The first postbleach image is at 0 time ( t=0). For each set of data (i=1,..,4), we give the number of microns squared in the bleach region (msqi), and the average pre-bleach fluorescence within the same region. [Fi(-)].

'''(See print out for equations)'''

To normalize data across images vs. (t/msqi)

'''Tasks:'''
1. In excel, plot the data as a time series. To compare the plots, normalize based on t/msqi.

2. Compare results to Virtual Cell FRAP simulation
What is needed in the simulation for an accurate comparison to experiment?

Exercises

2007-12-20T17:27:55Z

Raquell:

{{Cell Cycle Exercises}}

==Virtual Cell Exercises==

===Virtual Cell and Key Concepts===
{{Virtual Cell Exercises}}

===Evaluation Forms===
[[Media:EvaluationCellCycleAndModeling.pdf|Evaluation Tool for Cell Cycle and Modeling Course Module]]

References for workshop exercises

2007-12-20T15:40:12Z

Raquell: Protected "References for workshop exercises" [edit=autoconfirmed:move=autoconfirmed]

===Cell Cycle===
Hunt and Murray, ''Cell Cycle''

Sha W., et al. 2003. Hysteresis Drives Cell-Cycle Transitions in Xenopus Leavis Egg Extracts. PNAS 100: 975-980.

Tyson J.J., 1991. Modeling the Cell Division Cycle. PNAS 88: 7328-7332.

Goldbeter A., 1991. A Minimal Cascade Model for the Mitotic Oscillator. PNAS 88: 9107-9111.

===Virtual Cell Tutorials===
All Virtual Cell Tutorials can be found at the [http://vcell.org/login/login.html software download site] or [http://vcell.org/login/model_vcell.html "How to Model"] page.

---[http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf Fluorescent Recovery After Photobleaching]

---[http://vcell.org/userdocs/Rel/Tutorial_FacilitatedCalciumDiffusion.pdf Faciliated Calcium Diffusion]

---[http://vcell.org/userdocs/Rel/Tutorial_FacilitatedCalciumDiffusion.pdf Membrane Potential]

The links for tutorials have been updated to point to the most up to date version.

===Virtual Cell Software Guides===
[http://www.vcell.org/login/VCell%20Quick%20Start%20Guide.pdf Quick tips]

[http://vcell.org/userdocs/Rel/VCellQuickStartGuide.pdf User Guide for Current Release Version of VCell]

References for workshop exercises

2007-12-20T15:39:53Z

Raquell:

References for workshop exercises

2007-12-20T15:38:36Z

Raquell:

===Cell Cycle===
Hunt and Murray, ''Cell Cycle''

Sha W., et al. 2003. Hysteresis Drives Cell-Cycle Transitions in Xenopus Leavis Egg Extracts. PNAS 100: 975-980.

Tyson J.J., 1991. Modeling the Cell Division Cycle. PNAS 88: 7328-7332.

Goldbeter A., 1991. A Minimal Cascade Model for the Mitotic Oscillator. PNAS 88: 9107-9111.

===Virtual Cell Tutorials===
All Virtual Cell Tutorials can be found at the [http://vcell.org/login/login.html software download site] or [http://vcell.org/login/model_vcell.html "How to Model"] page.

---[http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf Fluorescent Recovery After Photobleaching]

---[http://vcell.org/userdocs/Rel/Tutorial_FacilitatedCalciumDiffusion.pdf Faciliated Calcium Diffusion]

---[http://vcell.org/userdocs/Rel/Tutorial_FacilitatedCalciumDiffusion.pdf Membrane Potential]

The links for tutorials have been updated to point to the most up to date version.

===Virtual Cell Software Guides===
[http://www.vcell.org/login/VCell%20Quick%20Start%20Guide.pdf Quick tips]

[http://www.vcell.org/login/user_guide_4_1.pdf User Guide 4.1]

References for workshop exercises

2007-12-20T15:38:01Z

Raquell:

===Cell Cycle===
Hunt and Murray, ''Cell Cycle''

Sha W., et al. 2003. Hysteresis Drives Cell-Cycle Transitions in Xenopus Leavis Egg Extracts. PNAS 100: 975-980.

Tyson J.J., 1991. Modeling the Cell Division Cycle. PNAS 88: 7328-7332.

Goldbeter A., 1991. A Minimal Cascade Model for the Mitotic Oscillator. PNAS 88: 9107-9111.

===Virtual Cell Tutorials===
All Virtual Cell Tutorials can be found at the [http://vcell.org/login/login.html software download site] or [http://vcell.org/login/model_vcell.html "How to Model"] page.

---[http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf Fluorescent Recovery After Photobleaching]

---[http://vcell.org/userdocs/Rel/Tutorial_FacilitatedCalciumDiffusion.pdf Faciliated Calcium Diffusion]

---[http://www.vcell.org/login/membrane_potential.pdf Membrane Potential]

The links for tutorials have been updated to point to the most up to date version.

===Virtual Cell Software Guides===
[http://www.vcell.org/login/VCell%20Quick%20Start%20Guide.pdf Quick tips]

[http://www.vcell.org/login/user_guide_4_1.pdf User Guide 4.1]

References for workshop exercises

2007-12-20T15:35:56Z

Raquell: /* Virtual Cell Tutorials */

===Cell Cycle===
Hunt and Murray, ''Cell Cycle''

Sha W., et al. 2003. Hysteresis Drives Cell-Cycle Transitions in Xenopus Leavis Egg Extracts. PNAS 100: 975-980.

Tyson J.J., 1991. Modeling the Cell Division Cycle. PNAS 88: 7328-7332.

Goldbeter A., 1991. A Minimal Cascade Model for the Mitotic Oscillator. PNAS 88: 9107-9111.

===Virtual Cell Tutorials===
All Virtual Cell Tutorials can be found at the [http://vcell.org/login/login.html software download site] or [http://vcell.org/login/model_vcell.html "How to Model"] page.

---[http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf Fluorescent Recovery After Photobleaching]

---[http://www.vcell.org/login/facil_ca_dif.pdf Faciliated Diffusion]

---[http://www.vcell.org/login/membrane_potential.pdf Membrane Potential]

===Virtual Cell Software Guides===
[http://www.vcell.org/login/VCell%20Quick%20Start%20Guide.pdf Quick tips]

[http://www.vcell.org/login/user_guide_4_1.pdf User Guide 4.1]

References for workshop exercises

2007-12-20T15:31:56Z

Raquell:

===Cell Cycle===
Hunt and Murray, ''Cell Cycle''

Sha W., et al. 2003. Hysteresis Drives Cell-Cycle Transitions in Xenopus Leavis Egg Extracts. PNAS 100: 975-980.

Tyson J.J., 1991. Modeling the Cell Division Cycle. PNAS 88: 7328-7332.

Goldbeter A., 1991. A Minimal Cascade Model for the Mitotic Oscillator. PNAS 88: 9107-9111.

===Virtual Cell Tutorials===
All Virtual Cell Tutorials can be found at the [http://vcell.org/login/login.html software download site] or [http://vcell.org/login/model_vcell.html "How to Model"] page.

+++[http://vcell.org/userdocs/Rel/Tutorial_SimpleFRAP.pdf Fluorescent Recovery After Photobleaching]

+++[http://www.vcell.org/login/facil_ca_dif.pdf Faciliated Diffusion]

++[http://www.vcell.org/login/membrane_potential.pdf Membrane Potential]

===Virtual Cell Software Guides===
[http://www.vcell.org/login/VCell%20Quick%20Start%20Guide.pdf Quick tips]

[http://www.vcell.org/login/user_guide_4_1.pdf User Guide 4.1]

References for workshop exercises

2007-12-20T15:23:50Z

Raquell:

Exercise rationale

2007-12-19T15:49:29Z

Raquell: Protected "Exercise rationale" [edit=autoconfirmed:move=autoconfirmed]

The goal of this section is to have you and students work with more than one set of parameter values and to see different behaviors arise.The number of choices are constrained to decrease the overall number of results reviewed by the instructor. However, the range of results is still large.

How to use this website?

2007-12-19T15:37:48Z

Raquell: Protected "How to use this website?" [edit=autoconfirmed:move=autoconfirmed]

This site was built for the Canisius College workshop. The pages are fixed as a reference.

Presentations from the workshop are linked from the [[workshop schedule| Workshop schedule]]. Information and links to materials that may be of use during and after the workshop are available[[workshop resources| Workshop resource pages]].

Editing a wiki site is very easy.
If you have suggestions or requests regarding layout or content, please [[contact| contact me]].

The [[Links to additional training opportunities| training opportunities]] page will continue to be updated

How to use this website?

2007-12-19T15:37:37Z

Raquell:

How to use this website?

2007-12-19T15:33:33Z

Raquell:

This site was built for the Canisius College workshop. The pages are fixed as a reference.

Presentations from the workshop are linked from the [[workshop schedule| Workshop schedule]]. Information and links to materials that may be of use during and after the workshop are available[[workshop resources| Workshop resource pages]].

Editing a wiki site is very easy.
If you have suggestions or requests regarding layout or content, please [[contact| contact me]].

The training opportunities page will continue to be updated

References for workshop exercises

2007-12-19T15:29:43Z

Raquell: Unprotected "References for workshop exercises"

===Cell Cycle===
Hunt and Murray, ''Cell Cycle''

Sha W., et al. Hysteresis Drives Cell-Cycle Transitions in Xenopus Leavis Egg Extracts

Tyson J.J., Modeling the Cell Division Cycle

Goldbeter A., A Minimal Cascade Model for the Mitotic Oscillator

===Virtual Cell Tutorials===
[http://www.vcell.org/login/frap.pdf Fluorescent Recovery After Photobleaching]

[http://www.vcell.org/login/facil_ca_dif.pdf Faciliated Diffusion]

[http://www.vcell.org/login/membrane_potential.pdf Membrane Potential]

===Virtual Cell Software Guides===
[http://www.vcell.org/login/VCell%20Quick%20Start%20Guide.pdf Quick tips]

[http://www.vcell.org/login/user_guide_4_1.pdf User Guide 4.1]

References for workshop exercises

2007-12-19T15:25:19Z

Raquell: /* Cell Cycle */

Virtual Cell: Cellular compartments, transport and image data

2007-12-19T15:21:54Z

Raquell: Protected "Virtual Cell: Cellular compartments, transport and image data" [edit=autoconfirmed:move=autoconfirmed]

[http://raquell.us/ccb/CanisiusCollege_AC.ppt Introduction to Virtual Cell] Slides provided by Ann Cowan of University Connecticut Health Center, Center for Cell Analysis and Modeling, and modified by Raquell Holmes.

Modeling basics: The cell cycle and modeling with Stella

2007-12-19T15:21:09Z

Raquell: Protected "Modeling basics: The cell cycle and modeling with Stella" [edit=autoconfirmed:move=autoconfirmed]

[[Media:ModelingCellCycleGoldbeter.pdf| Modeling the Cell Cycle presentation. PDF format]]

Modeling the cell cycle was taught as part of a research based undergraduate course: Cellular, Developmental Biology at Beloit College. This presentation provides an overview of the content presented during the class, exercises performed and student final projects.

===sample evaluation tool===
The four week project was evaluated with the following Likert-scale tool to determine student perceptions and understanding of modeling as well as key concepts about the cell cycle.

[[Media:EvaluationCellCycleAndModeling.pdf| Evaluation Tool]]

Schedule

2007-12-19T15:20:46Z

Raquell: Protected "Schedule" [edit=autoconfirmed:move=autoconfirmed]

Computational science education

2007-12-19T15:19:43Z

Raquell: Protected "Computational science education" [edit=autoconfirmed:move=autoconfirmed]

====List of undergraduate programs with [[computational X |computational X]]====
[http://www.krellinst.org/services/technology/CSE_survey/undergraduate.html Krell Institute CSE Survey]

====Introductory materials on modeling dynamic biological systems====
[http://www.ccam.uchc.edu/ccb/SiteExercises.htm Exercises for kinetics in models of cell cycle and glycolysis] Created by Raquell M. Holmes

[http://eot.bu.edu/ccb/Metabolic/Exercises/index.htm Introductory kinetics exercises in glycolysis] Created by Raquell M. Holmes

[http://www.bioinformaticsservices.com/bis/resources/cybertext/IBcont.html Online book for kinetic modeling] Created by Robert Phair

Computational science education

2007-12-19T15:19:25Z

Raquell:

Literature on teaching

2007-12-19T15:15:13Z

Raquell: Protected "Literature on teaching" [edit=autoconfirmed:move=autoconfirmed]

*Bio 2010. Transforming Undergraduate Education for further Research Biologists. Washington D.C. NHS. National Research Council (2003). [http://books.nap.edu/catalog.php?record_id=10497 Book]

*Microscopy Images as Interactive Tools in Cell Modeling and Cell Biology Education. Cell Biology Education 3, 99-110. Araujo-Jorge, T.C., Cardona, T.S., Coutinho, Cl’audia M.L.M., Henriques-Pons, A., Meirelles, R.M.S., Mendes, C. L.S., Coutinho, C.M.L.M., Aguiar, L.E.V., Meirelles, M.D.N.L, Castro, S.L.D., Barbosa, H.S., Luz, M.R.M.P. (2003) [http://www.lifescied.org/cgi/content/abstract/3/2/99 article]

*Computer Simulations Improve University Instructional Laboratories. Cell Biology Education Vol. 3, 263-269. Evans, C., Gibbons, N.J., Griffin, D.K., Payne, A., Shah. K. (2004) [http://www.lifescied.org/cgi/content/abstract/3/4/263 article]

*Investigations of Protein Structure and Function Using the Scientific Literature: An Assignment for Undergraduate Cell Physiology Course. Cell Biology Education 2, 248-255. Mulnix, A.B. (2003). [http://www.lifescied.org/cgi/content/abstract/2/4/248 article]

*Learning Cell Biology as a Team: A Project-Based Approach to Upper-Division Cell Biology. Cell Biology Education 1, p145-153. Wright R and Boggs J (2002) [http://www.lifescied.org/cgi/content/abstract/1/4/145 article]

*Learning How Scientists Work: Experiential Research Projects to Promote Cell Biology Learning and Scientific Process Skills. DebBurman SK (2002) [http://www.lifescied.org/cgi/content/abstract/1/4/154 article]

*Performing as Scientists: An improvisational approach to student research and faculty collaboration. Bioscene 32 (1), 23-29. Holmes R.M. and Qureshi M.M. (2006) [http://acube.org/volume_32/index.html article]

*Approaches to Cell Biology Teaching: Learning Content in Context: Problem - Based Learning. Cell Biology Education Summer 2003; 2: 73-81. Allen, D. and Tanner, M. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=162197 article]

*Ten equations that changed biology: mathematics in problem- solving biology curricula. BioScene vol 23, 11-36. Jungck, J. (1997) [http://papa.indstate.edu/amcbt/volume_23/v23-1p11-36.pdf article]

*Elements of Computational Science and Engineering Education. SIAM Rev., vol. 45, no. 4, pp. 787–805. Yassar O. and Landau R.H. (2003)

Literature on teaching

2007-12-19T15:14:45Z

Raquell:

Links to modeling databases

2007-12-19T15:13:23Z

Raquell: Protected "Links to modeling databases" [edit=autoconfirmed:move=autoconfirmed]

[http://jjj.biochem.sun.ac.za/database/index.html JWS Online]
JWS Online is a Systems Biology tool for simulation of kinetic models from a curated model database.

[http://www.ebi.ac.uk/biomodels/ BioModels Database at EBI]
BioModels is a collection of published models that can be viewed online and downloaded in multiple file formats for use with different simulation tools.

[http://www.vcell.org/login/modeling_links.html List of simulation tools and databases compiled by CCAM]

[http://yeastpheromonemodel.org Yeast Pheromone Model Documentation Wiki]

[http://sbml.org/index.psp List of SBML compatable simulators]

Resources

2007-12-19T15:13:12Z

Raquell: Protected "Resources" [edit=autoconfirmed:move=autoconfirmed]