BIOL398-04/S15:Week 13

This journal entry is due on Tuesday, April 21 at midnight PDT (Monday night/Tuesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

NOTE: this page is under construction.

Individual Journal Assignment

• Store this journal entry as "username Week 13" (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: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.)
  • 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 "BIOL398-04/S15" category to the end of your wiki page.

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 and the answers to the questions throughout the protocol. We will be working on the protocols in class on this week. Whatever you do not finish in class will be homework to be completed by the Week 13 journal deadline.

REMINDER: you should "turn on" the file extensions using the instructions found on the Help page before beginning today's work.

Create the Input Excel Workbook for the Model

1. Your file will be similar to the file "Input_4_gene_forward_correct_params.xlsx" that you used in class on Tuesday, but with your expression data and network. You should download this file, change the name, and edit it to include your data. Make sure to give it a meaningful filename that includes your last name or initials. (The file can be found in this zipped file on LionShare.)
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 "network" sheet and paste it into the worksheets called "network" and "network_weights".
   • Note that the transcription factor names have to be in the same order and same format across the top row and first column. CIN5 does not match Cin5p, so the latter will need to be changed to CIN5 if you have not already done so.
   • 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.
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 initial guesses for 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. Next you will input the expression data for the wild type strain and the other strain your partner is using (dcin5, dgln3, dhmo1, dzap1, spar).
   • Put the wild type data in the sheet called "wt".
   • The sample spreadsheet has a worksheet named "dcin5". Change this name to match the strain you are using (listed above). The instructions below should be followed for each strain sheet.
   • Paste the SystematicName and StandardName columns from one of your previous sheets into this one.
   • This data in this sheet is the Log Fold Changes for each replicate and each timepoint from your Week 11 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". There will be multiple columns for each timepoint (typically 4) to represent the replicate data, but they will all have the same name. For example, you may have four columns with the header "15".
   • Copy and paste the data from your Week 11 spreadsheet into this one. Make sure that the genes are in the same order as in the other sheets.
6. We will only be editing parts of the "optimization_parameters" worksheet.
   • For the parameter "time" (Cell A13), replace what is in the sample file with "15", "30", and "60", since these are the timepoints we have in our data.
   • For the parameter "Strain" (Cell A14), replace "dcin5" with the name of the second strain you are using, making sure that the capitalizaiton and spelling is the same as what you named the worksheet containing that strain's expression data.
   • For the parameter "simtime", you perform the forward simulation of the expression in five minute increments from 0 to 60 minutes. Thus, this row should read: "simtime", "0", "5", "10", ..., "60".
7. 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.
   • Cell A1 in the sample files has the text "rows genes affected/cols genes controlling". I believe you can either have this text in cell A1 or "StandardName".
   • The "threshold" value for each gene should be "0".
8. 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.

Appendix: Full explanation of the optimization_parameters sheet

Shared Journal Assignment

• Store your shared journal entry in the shared Class Journal Week 13 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 "BIOL398-04/S15" category to the end of the wiki page (if someone has not already done so).