v1.10

This release adds a minor check to warn the user in the event that running the model with the same input workbook will overwrite output files from a previous run (#144). This release also includes fixes to the OutputTest.m script.

v1.9

This release entails changes aimed at paying off our technical debt as we move forward to work on newer features. This includes changes to our test suite, and the addition of bug fixes along with their corresponding tests. Michalis-Menten has also been disabled as there is not sufficient testing as of now. Issues addressed in this release include #289, #380, #352, #353, #361, #375, #376, #380, and #397.

v1.8

This release includes a major revision of the data structure to support missing expression data values (#310, #311, #313) and a cleanup of global variables.

v1.4.4

GRNmap v1.4.4 includes the following:

• Routine bug fixes
• Implementation of a testing framework (#136, #194, #196)

Note that these changes should not affect the user experience, but has resulted in more robust code.

v1.4.2

• The MATLAB runtime library has been included in the executable for this release, which was missing from the v1.4 release (#180).
• GRNmap now supports up to 12 different strains when creating expression graphs (#163).
• The bug that occurred where the optimization diagnostic figure was not saved when the optimization had fewer than 100 iterations was fixed (#132, #175).

v1.4

GRNmap v1.4 includes the following new features and bug fixes:

• The input file can now be located in a directory that contains space characters in the directory name (#93), or on the Desktop (#94).
• We have standardized the format of the input and output Excel workbooks, making them more readable. See the wiki pages: https://github.com/kdahlquist/GRNmap/wiki/How-to-format-the-input-file-for-GRNmap-v1.4-and-above and https://github.com/kdahlquist/GRNmap/wiki/How-to-interpret-the-output-file-for-GRNmap, respectively for details (#119).
  • optimization_parameters variables previously named "time", "simtime", and "Sigmoid" have been renamed as "expression_timepoints", "simulation_timepoints", and "production_function", respectively (#119).
  • The deleted genes/strains are now determined by GRNmap so the "Deletion" parameter is no longer needed in the optimization_parameter sheet (#52).
  • The mean squared error calculation for each individual gene in each strain is now produced in the optimization_diagnostics sheet instead of the sum of squares of error (#106, #165).
• The current LSE value for each iteration is now shown in the optimization_diagnostics window (#86).
• The optimization_diagnostic graph is now saved correctly when the number of iterations of the estimation is less than 100 (#123).
• Fixed bug when the estimate_params = 0 (#118).
• GRNmap can now perform multiple successive runs for fine tuning of the optimization parameter, alpha. When L_curve is set to 1 in the optimization_parameters worksheet, GRNmap will complete 16 successive runs with the alpha values of 0.8, 0.5, 0.2, 0.1, 0.08, 0.05, 0.02, 0.01, 0.008, 0.005, 0.002, 0.001, 0.0008, 0.0005, 0.0002, and 0.0001. The user supplied initial guesses are used for the first run; all subsequent runs use the output from the previous run as the initial guesses for that run. By plotting the least squared error against the penalty term (found in the optimization_diagnostics sheet of the output file), the user can create an L-curve by which the appropriate alpha value for future estimation runs can be determined from the "elbow" of the curve (#168).
• The test suite has been updated to reflect recent changes in the package and now uses proper setUp and tearDown methods so that the tests can run faster (#139).
• All of the test files have been converted to the .xlsx format (#126).
• The test files have been updated accordingly (i.e., variable names that are obsolete have been removed) after implementing the above changes (#129).

Note that the MATLAB Runtime Library was left out of the executable for this release by mistake. Users of the executable are directed to use release v1.4.2 instead.

v1.2

GRNmap v1.2 includes the following new features and bug fixes:

• Estimation for the threshold parameter in the sigmoidal model for genes with no input has been fixed (#111).
• Optimization parameters in the test files have been changed to be compatible with the updated code (#74).
• Updates to the unit testing framework include the following (#37):
  • Test if input files have been read correctly.
  • Test if necessary output worksheets exist.
  • Test if graphs are outputted
• "optimizationDiagnostics.jpg" has been changed to "optimization_diagnostics.jpg"

v1.0.8

GRNmap v1.0.8 includes the following new features and bug fixes:

• Input/Output worksheet names have been changed. (#88)
• "concentration_sigmas" input worksheet deleted from test_files folder because they are no longer used. (#89)
• Optimized threshold is now outputted when fix_b = 0. (#90)
• Optimized production rates are now outputted when fix_P = 0. (#94)
• Standard deviations of input expressions are now outputted. (#102)
• Documentation of input/output worksheets described above have been updated in the wiki. (#4)
• We have added 16 new test input sheets for each combination of optimization parameters Sigmoid, estimateParams, makeGraphs, fix_b, and fix_P (#74)

v1.0.6

GRNmap v1.0.6 includes the following new features and bug fixes:

• The input Microsoft Excel workbook is now not required to be in the same directory as the GRNmodel code and can now be located in any folder (#44).
• A bug was fixed where the last graph generated was not being automatically saved; now all graphs are saved in the same folder as the input workbook (#45).
• The input test files were updated to comply with changes made to the optimization parameter variable names made in release v1.0.4 (#60).
• Ensured that all temporary information is cleared between consecutive estimation or simulation runs (#51).
  -GRNmap now outputs the log₂ expression values generated from the forward simulation of the model as individual worksheets for each strain. The worksheets are named with the convention "_log2_optimized_expression". (#40).
• The test file structure and naming convention has been implemented as documented in the wiki (https://github.com/kdahlquist/GRNmap/wiki/Naming-Convention-and-Test-Files-Organization) (#61).

v1.0.4

GRNmap v1.0.4 includes the following new features and bug fixes:

• The requirements for the "optimization_parameters" worksheet in the input Microsoft Excel workbook have been modified as follows:
  • The name of the parameter iestimate has been replaced with estimateParams.
  • The name of the parameter igraph has been replaced with makeGraphs.
  • These changes were made to make the parameter names more descriptive.
• The output workbook now contains all of the worksheets from the input workbook (issue #28).
• The output workbook now includes worksheets for all of the parameters that were estimated by GRNmap. These output sheets have names that begin with "out_".