GRNmap Testing Report 16 Test Files 2015-06-01: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
(→‎Data & Observations: add error that appeared)
(→‎Data & Observations: be more specific)
Line 232: Line 232:
*The optimized_threshold_b sheet was only produced when fixb-0 and the model with Sigmoidal.
*The optimized_threshold_b sheet was only produced when fixb-0 and the model with Sigmoidal.
*The weights for the Sigmoidal were all about the same value. The MM was always larger, with the fixP-0 being much larger in the case of ACE2-->ACE2 and AFT2-->AFT2 and MM fixP-1 was much larger when CIN5-->FHL1. The MM fixP-1  had an opposite sign than all of the Sigmoidal, but the weight was of a small magnitude.  
*The weights for the Sigmoidal were all about the same value. The MM was always larger, with the fixP-0 being much larger in the case of ACE2-->ACE2 and AFT2-->AFT2 and MM fixP-1 was much larger when CIN5-->FHL1. The MM fixP-1  had an opposite sign than all of the Sigmoidal, but the weight was of a small magnitude.  
*When the new sheet was run on the newest beta version the following Matlab error appeared
*When the new workbook with updated sheet names with the newest beta version (4:39 pm)the following Matlab error appeared
<code>Error using  *  
<code>Error using  *  
Inner matrix dimensions must agree.
Inner matrix dimensions must agree.

Revision as of 17:03, 1 June 2015

GRNmap Testing Report

  • Date started: 2015-06-01
  • GRNmap code: GRNmap-beta branch downloaded from Github at 10:43 am 2015-06-01
    • Changes were made to the GRNmap-beta branch which was downloaded at 4:39 pm 2015-06-01
  • MATLAB Version: 2014b
  • Model was run computer (from door): Row#2 4

Input, Output, and Images

  1. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph
  2. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph
  3. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_graph
  4. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph
  5. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_graph
  6. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph
  7. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_graph
  8. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph
  9. 4-genes_6-edges_artificial-data_Sigmoidal_forward_graph
  10. 4-genes_6-edges_artificial-data_Sigmoidal_forward_no-graph
  11. 4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph
  12. 4-genes_6-edges_artificial-data_MM_estimation_fixP-1_no-graph
  13. 4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph
  14. 4-genes_6-edges_artificial-data_MM_estimation_fixP-0_no-graph
  15. 4-genes_6-edges_artificial-data_MM_forward_graph
  16. 4-genes_6-edges_artificial-data_MM_forward_no-graph

Methods

Selecting the GRNmap Version and Base Input Sheet

  1. Download the GRNmap-beta branch version from Github by downloading the zip file.
  2. Move it to the desktop and unzip by right-clicking on it and choosing 7-zip > Extract here.
  3. Open the unzipped "GRNmap-beta branch" folder and find the folder "test_files" then navigate to "estimation_tests" and open the file "4-genes_6-edges_artificial-data_Sigmoid_estimation.xls"
    • We compared "4-genes_6-edges_artificial-data_Sigmoid_estimation.xls" and "4-genes_6-edges_artificial-data_Sigmoid_forward.xlsx" and found them to contain different data points and different time points, so the "4-genes_6-edges_artificial-data_Sigmoid_estimation.xls" was chosen as the base for the 16 test files.

Editing the Optimization Parameters for each Input

  • There are sixteen different input sheets that need to be tested. The "optimization parameters" worksheet is adjusted for each type. For all inputs, the following optimization parameters will be left as they were originally entered
    • "alpha" should be 1.00E-10
    • "kk_max" should be 1
    • "MaxIter" should be 1e08
    • "TolFun" should be 1e-10
    • "MaxFunEval" should be 1e08
    • "TolX" should be 1e-10
    • For the parameter "time" (Cell A13), should have "0.4", "0.8", "1.2", and "1.4"
    • For the parameter "Strain" (Cell A14), make sure it says "dcin5", making sure that the capitalization and spelling is the same as the worksheet containing that strain's expression data.
    • For the parameter "Sheet" (Cell A15), give the number of the worksheet from left to right that your "Strain" log2 expression data is in. This should be the fourth sheet.
    • For the parameter "Deletion", leave the zero in cell B15 (corresponding to wt). In cell C15, put a number corresponding to the position in the list of gene names that the gene that was deleted appears. This should be the number three in the list (disregard the column header in this count and only consider the actual gene names themselves).
    • For the parameter, "simtime", the row should read: 0, 0.1, 0.2, 0.3 <...fill by steps of 0.1...>, 2, each number in a different cell.
  • The parameters "Sigmoid","estimateParams", "makeGraphs","fix_P", and "fix_b" will be different for each input sheet.
  1. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph
    • "Sigmoid" should be 1
    • "estimateParams" should be 1
    • "makeGraphs" should be 1
    • "fix_P" should be 0
    • "fix_b" should be 0
  2. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_no-graph
    • "Sigmoid" should be 1
    • "estimateParams" should be 1
    • "makeGraphs" should be 0
    • "fix_P" should be 0
    • "fix_b" should be 0
  3. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_graph
    • "Sigmoid" should be 1
    • "estimateParams" should be 1
    • "makeGraphs" should be 1
    • "fix_P" should be 1
    • "fix_b" should be 0
  4. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-1_no-graph
    • "Sigmoid" should be 1
    • "estimateParams" should be 1
    • "makeGraphs" should be 0
    • "fix_P" should be 1
    • "fix_b" should be 0
  5. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_graph
    • "Sigmoid" should be 1
    • "estimateParams" should be 1
    • "makeGraphs" should be 1
    • "fix_P" should be 0
    • "fix_b" should be 1
  6. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-0_no-graph
    • "Sigmoid" should be 1
    • "estimateParams" should be 1
    • "makeGraphs" should be 0
    • "fix_P" should be 0
    • "fix_b" should be 1
  7. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_graph
    • "Sigmoid" should be 1
    • "estimateParams" should be 1
    • "makeGraphs" should be 1
    • "fix_P" should be 1
    • "fix_b" should be 1
  8. 4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-1_fixP-1_no-graph
    • "Sigmoid" should be 1
    • "estimateParams" should be 1
    • "makeGraphs" should be 0
    • "fix_P" should be 1
    • "fix_b" should be 1
  9. 4-genes_6-edges_artificial-data_Sigmoidal_forward_graph
    • "Sigmoid" should be 1
    • "estimateParams" should be 0
    • "makeGraphs" should be 1
    • "fix_P" should be 0
    • "fix_b" should be 1
  10. 4-genes_6-edges_artificial-data_Sigmoidal_forward_no-graph
    • "Sigmoid" should be 1
    • "estimateParams" should be 0
    • "makeGraphs" should be 0
    • "fix_P" should be 0
    • "fix_b" should be 1
  11. 4-genes_6-edges_artificial-data_MM_estimation_fixP-1_graph
    • "Sigmoid" should be 0
    • "estimateParams" should be 1
    • "makeGraphs" should be 1
    • "fix_P" should be 1
    • "fix_b" should be 0
  12. 4-genes_6-edges_artificial-data_MM_estimation_fixP-1_no-graph
    • "Sigmoid" should be 0
    • "estimateParams" should be 1
    • "makeGraphs" should be 0
    • "fix_P" should be 1
    • "fix_b" should be 0
  13. 4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph
    • "Sigmoid" should be 0
    • "estimateParams" should be 1
    • "makeGraphs" should be 1
    • "fix_P" should be 0
    • "fix_b" should be 0
  14. 4-genes_6-edges_artificial-data_MM_estimation_fixP-0_no-graph
    • "Sigmoid" should be 0
    • "estimateParams" should be 1
    • "makeGraphs" should be 0
    • "fix_P" should be 0
    • "fix_b" should be 0
  15. 4-genes_6-edges_artificial-data_MM_forward_graph
    • "Sigmoid" should be 0
    • "estimateParams" should be 0
    • "makeGraphs" should be 1
    • "fix_P" should be 1
    • "fix_b" should be 0
  16. 4-genes_6-edges_artificial-data_MM_forward_no-graph
    • "Sigmoid" should be 0
    • "estimateParams" should be 0
    • "makeGraphs" should be 0
    • "fix_P" should be 1
    • "fix_b" should be 0

Running GRNmap

You will now finally run the GRNmap model on each input workbook created above.

  1. Open MATLAB and navigate to the "matlab" subfolder in the "GRNmap-beta" folder on the desktop
  2. Move the input sheet that you would like to run into this folder.
  3. In MATLAB type the command "GRNmodel" and select the input sheet of study
  4. Once the model has finished running, plots showing the expression over time for all of the genes in the network will appear if "makeGraphs" was set to 1. The plots will automatically be saved as *.jpg files in the same folder as your input file. Compile the figures into a folder following the naming convention described earlier. Compress this folder by right clicking then selecting "7-zip" and "Add to archive...". Make sure the archive format is "zip."
  5. Upload the .xlsx output sheet and the zipped folder with the output plots onto openwetware.
  6. In between each run type "close all" and "clear all" into MATLAB

Updating GRNmap on Github

  1. Download "Git" from this link
  2. Go through the instillation process (no changes needed)
  3. Once installed open "Git Bash" from the programs menu on the computer
  4. To have the GRNmap folder to edit on the desktop type cd Desktop then press enter
  5. To clone into GRNmap type git clone https://github.com/kdahlquist/GRNmap.git then press enter
  6. To edit GRNmap, type cd GRNmap then press enter
  7. To edit the Beta version, type git checkout beta
  8. There will now be a file on the desktop titled "GRNmap" where you can put the updated test files and then upload them to github
  9. Create two new folders in the "test_files" subfolder called "sixteen_tests" and "sixteen_tests_output"
    • The "sixteen_tests" contains the input sheets and the "sixteen_tests_output" contains the output sheet.
  10. To update the GRNmap on the web
    • Type git checkout beta then press enter
    • Type git status then press enter will show the changes that you made in red
    • Type git add test_files/s then press enter
    • Type git add test_files/s then press tab. The code should then read git add test_files/sixteen_tests/ then press space and type git add test_files/s again then tab so it reads git add test_files/sixteen_tests_output/ then type an underscore to indicate you're done.
    • Type git status then press enter
    • Type git commit -m "add sixteen combinations of input files and their output files" or a description of the change that was made then press enter
      • I made a typo and wrote "coombinations instead of combinations", unfortunately
    • In order to configure the computer to your user name Type git config --global user.name "github username" then press enter and then type git config --global user.email "email used for github" then press enter
    • To update anything that was changed while you were working type git pull then press enter
    • To update the website with your changes type git push then press enter and enter your username and password when prompted.
  11. Comment on Issue 74 on Github explaining what was done and change the label to "review requested" and select Dr. Dahlquist.

Adjust Input Sheets to Correct for Change to Sheet Name

  1. Change sheet names "wt" and "dcin5" to "wt_log2_expression" and "dcin5_log2_expression"
  2. Save and rerun on Matlab

Data & Observations

  • Summary statistics
  • Every difference between graph and no graph was 0.
  • The optimized_production_rate sheet was only produced when fixP-0.
  • The optimized_threshold_b sheet was only produced when fixb-0 and the model with Sigmoidal.
  • The weights for the Sigmoidal were all about the same value. The MM was always larger, with the fixP-0 being much larger in the case of ACE2-->ACE2 and AFT2-->AFT2 and MM fixP-1 was much larger when CIN5-->FHL1. The MM fixP-1 had an opposite sign than all of the Sigmoidal, but the weight was of a small magnitude.
  • When the new workbook with updated sheet names with the newest beta version (4:39 pm)the following Matlab error appeared

Error using * Inner matrix dimensions must agree.

Error in general_least_squares_error (line 94) L = L + alpha*(wts')*wts + alpha*(b-bp)'*(b-bp) + alpha*sum(proratep(:))^2;

Error in lse (line 53) GRNstruct.GRNOutput.lse_0 = general_least_squares_error(initial_guesses);

Error in GRNmodel (line 32) GRNstruct = lse(GRNstruct);


Dahlquist Lab Navigation

Retrieved from "https://openwetware.org/mediawiki/index.php?title=GRNmap_Testing_Report_16_Test_Files_2015-06-01&oldid=887134"