BIOL398-03/S13:Week 14

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==== Creating your model input file ====
==== Creating your model input file ====
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* Your first task will be to create a model input file using the Dahlquist lab data you have been working with.
+
Your first task will be to create a model input file using the Dahlquist lab data with which you have been working.
-
* Your file will be similar to the [http://openwetware.org/images/7/77/Full_schade_data.xls sample data input file] that you used last week, but with your expression data and network.  You should download this file, change the name, and edit it to include your data.
+
 
-
* The first thing you need to do is determine the transcription factors that you are including in your network.  You are going to use the "transposed" Regulation Matrix that you generated from YEASTRACT in the [[BIOL398-03/S13:Week 12 | Week 12 Assignment]].
+
For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual wiki page that records all the manipulations you perform on the data.
-
** Copy the transposed matrix from your Regulation Matrix file and paste it into the worksheets called "network", "network_weights", and "network_thresholds".
+
 
-
** Note that the transcription factor names have to be in the same format across the top row and first column, like CIN5, not Cin5p, so you will need to change the format of the names in the top row.
+
# Your file will be similar to the [http://openwetware.org/images/7/77/Full_schade_data.xls sample data input file] that you used last week, but with your expression data and network.  You should download this file, change the name, and edit it to include your data.  Make sure that you include your last name in the filename.
-
** It may be easier for you if you put the transcription factors in alphabetical order (using the sort feature in Excel), but whether you leave your list the same as it is from the YEASTRACT assignment or in alphabetical order, make sure it is the same order for all of the worksheets.
+
# The first thing you need to do is determine the transcription factors that you are including in your network.  You are going to use the "transposed" Regulation Matrix that you generated from YEASTRACT in the [[BIOL398-03/S13:Week 12 | Week 12 Assignment]].
-
* The next worksheet to edit is the one called "degradation_rates".
+
#* Copy the transposed matrix from your Regulation Matrix file and paste it into the worksheets called "network", "network_weights", and "network_thresholds".
-
** Paste your list of transcription factors from your "network" sheet into the column named "StandardName".  You will need to look up the "SystematicName" of your genes.  YEASTRACT has a feature that will allow you to paste your list of standard names in to retrieve the systematic names [http://www.yeastract.com/formorftogene.php here].
+
#* Note that the transcription factor names have to be in the same format across the top row and first column, like CIN5, not Cin5p, so you will need to change the format of the names in the top row.
-
** [[Media:Belle_TF_DegradationRates.xls | Degradation rates for transcription factors from Belle et. all (2006)]].
+
#* It may be easier for you if you put the transcription factors in alphabetical order (using the sort feature in Excel), but whether you leave your list the same as it is from the YEASTRACT assignment or in alphabetical order, make sure it is the same order for all of the worksheets.
 +
#* '''''IMPORTANT:'''''  If you are working with the wild type data, you are finished with this sheet.  However, if you are working with one of the deletion strains, you need to delete the row and column corresponding to the transcription factor that is deleted in your strain.  Do not leave any empty rows or columns in your matrix after you do this.
 +
# The next worksheet to edit is the one called "degradation_rates".
 +
#* Paste your list of transcription factors from your "network" sheet into the column named "StandardName".  You will need to look up the "SystematicName" of your genes.  YEASTRACT has a feature that will allow you to paste your list of standard names in to retrieve the systematic names [http://www.yeastract.com/formorftogene.php here].
 +
#* Next, you will need to look up the degradation rates for your list of transcription factors.  These rates have been calculated from protein half-life data from a paper by Belle et al. (2006).  Look up the rates for your transcription factors from [[Media:Belle_TF_DegradationRates.xls | this file]] and include them in your "degradation_rates" worksheet.
 +
#* If a transcription factor does not appear in the file above, use the value "0.027182242" for the degradation rate.
 +
# The next worksheet to edit is the one called "production_rates".
 +
#* Paste the "SystematicName" and "StandardName" columns rom your "degradation_rates" sheet into the "production_rates" sheet.
 +
#* The production rates we are using for the model are two times the degradation rate.  Compute these values from your degradation rates and paste the values into the column titled "ProductionRate".
 +
# The next sheet to edit is called "log2_concentrations".
 +
#* Paste the SystematicName and StandardName columns from one of your previous sheets into this one.
 +
#* This data in this sheet is the Average Log Fold Changes from your [[BIOL398-03/S13:Week 9 | Week 9 Assignment]].  We are only going to use the cold shock timepoints for the modeling.  Thus your column headings for the data should be "15", "30", and "60".  You will then need to look up the average log fold changes from your previous spreadsheet to include here.
 +
# The next sheet to edit is called "concentration_sigmas".
 +
#* This sheet contains the standard deviations of the expression data from your [[BIOL398-03/S13:Week 9 | Week 9 Assignment]].
 +
#* We did not actually perform this calculation yet in the previous assignment.  Using your spreadsheet from the [[BIOL398-03/S13:Week 9 | Week 9 Assignment]], go to the "statistics" worksheet.  Calculate the standard deviation for each of the cold shock timepoints using the <code>STDEV</code> function in Excel.  (''Remember, do '''not''' use <code>STDEVP</code>.'')
 +
#* Copy and paste the values into this worksheet.
 +
# Leave the "optimization_parameters" worksheet alone for now.
 +
# The next sheet to edit is the one called "simulation_times".
 +
#* You will simulate the expression in five minute increments from 0 to 60 minutes.  Thus, the top row should read:  "time", "0", "5", "10", ..., "60".<!--Edit, fill, series-->
 +
# The last sheet you will need to modify is called "network_b".
 +
#* Paste in the list of standard names for your transcription factors from one of your previous sheets.  Note that this sheet does not have a column for the systematic name.
 +
#* The "threshold" value for each gene should be "0.000".
 +
# When you have completed the modifications to your file, upload it to [http://lionshare.lmu.edu LionShare] and send Dr. Dahlquist and Dr. Fitzpatrick and e-mail with a link to the file.  Your assignment will not be considered complete until we have successfully downloaded the correct file from you.  If you need assistance with LionShare, please ask well ahead of the assignment deadline.
== Shared Journal Assignment ==
== Shared Journal Assignment ==

Current revision

BIOL398-03: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

Home       People        LionShare       Help      

This journal entry is due on Friday, April 26 at midnight PDT (Thursday night/Friday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Contents

Individual Journal Assignment

  • Store this journal entry as "username Week 14" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. (HINT: you can do all of this easily by adding them to your template and then using the template on your pages.)
    • Link to your journal entry from your user page.
    • Link back from your journal entry to your user page.
    • Link to this assignment from your journal entry.
    • Don't forget to add the "BIOL398-03/S13" category to the end of your wiki page.

Tasks

Creating your model input file

Your first task will be to create a model input file using the Dahlquist lab data with which you have been working.

For your assignment this week, you will keep an electronic laboratory notebook on your individual wiki page that records all the manipulations you perform on the data.

  1. Your file will be similar to the sample data input file that you used last week, but with your expression data and network. You should download this file, change the name, and edit it to include your data. Make sure that you include your last name in the filename.
  2. The first thing you need to do is determine the transcription factors that you are including in your network. You are going to use the "transposed" Regulation Matrix that you generated from YEASTRACT in the Week 12 Assignment.
    • Copy the transposed matrix from your Regulation Matrix file and paste it into the worksheets called "network", "network_weights", and "network_thresholds".
    • Note that the transcription factor names have to be in the same format across the top row and first column, like CIN5, not Cin5p, so you will need to change the format of the names in the top row.
    • It may be easier for you if you put the transcription factors in alphabetical order (using the sort feature in Excel), but whether you leave your list the same as it is from the YEASTRACT assignment or in alphabetical order, make sure it is the same order for all of the worksheets.
    • IMPORTANT: If you are working with the wild type data, you are finished with this sheet. However, if you are working with one of the deletion strains, you need to delete the row and column corresponding to the transcription factor that is deleted in your strain. Do not leave any empty rows or columns in your matrix after you do this.
  3. The next worksheet to edit is the one called "degradation_rates".
    • Paste your list of transcription factors from your "network" sheet into the column named "StandardName". You will need to look up the "SystematicName" of your genes. YEASTRACT has a feature that will allow you to paste your list of standard names in to retrieve the systematic names here.
    • Next, you will need to look up the degradation rates for your list of transcription factors. These rates have been calculated from protein half-life data from a paper by Belle et al. (2006). Look up the rates for your transcription factors from this file and include them in your "degradation_rates" worksheet.
    • If a transcription factor does not appear in the file above, use the value "0.027182242" for the degradation rate.
  4. The next worksheet to edit is the one called "production_rates".
    • Paste the "SystematicName" and "StandardName" columns rom your "degradation_rates" sheet into the "production_rates" sheet.
    • The production rates we are using for the model are two times the degradation rate. Compute these values from your degradation rates and paste the values into the column titled "ProductionRate".
  5. The next sheet to edit is called "log2_concentrations".
    • Paste the SystematicName and StandardName columns from one of your previous sheets into this one.
    • This data in this sheet is the Average Log Fold Changes from your Week 9 Assignment. We are only going to use the cold shock timepoints for the modeling. Thus your column headings for the data should be "15", "30", and "60". You will then need to look up the average log fold changes from your previous spreadsheet to include here.
  6. The next sheet to edit is called "concentration_sigmas".
    • This sheet contains the standard deviations of the expression data from your Week 9 Assignment.
    • We did not actually perform this calculation yet in the previous assignment. Using your spreadsheet from the Week 9 Assignment, go to the "statistics" worksheet. Calculate the standard deviation for each of the cold shock timepoints using the STDEV function in Excel. (Remember, do not use STDEVP.)
    • Copy and paste the values into this worksheet.
  7. Leave the "optimization_parameters" worksheet alone for now.
  8. The next sheet to edit is the one called "simulation_times".
    • You will simulate the expression in five minute increments from 0 to 60 minutes. Thus, the top row should read: "time", "0", "5", "10", ..., "60".
  9. The last sheet you will need to modify is called "network_b".
    • Paste in the list of standard names for your transcription factors from one of your previous sheets. Note that this sheet does not have a column for the systematic name.
    • The "threshold" value for each gene should be "0.000".
  10. When you have completed the modifications to your file, upload it to LionShare and send Dr. Dahlquist and Dr. Fitzpatrick and e-mail with a link to the file. Your assignment will not be considered complete until we have successfully downloaded the correct file from you. If you need assistance with LionShare, please ask well ahead of the assignment deadline.

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 14 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL398-03/S13" category to the end of the wiki page (if someone has not already done so).

Reflection

Reflect back on your learning for this project and for the entire semester and answer the following:

  1. What is the value of combining biological and mathematical approaches to scientific questions?
  2. Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?
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