From 4c4f703c574bf3f689eff427b1aeac76bf51adb4 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Fri, 21 Nov 2025 10:04:23 -0500
Subject: [PATCH 1/6] feature(response-curve): Enable configuration for
 response curve analysis

---
 R/constants.R                                 |  8 +-
 R/module-statmodel-server.R                   | 38 +++++++++
 R/statmodel-ui-comparisons.R                  | 18 +++-
 R/statmodel-ui-headers.R                      |  4 +-
 .../test-statmodel-ui-options-contrasts.R     | 16 ++++
 tests/testthat/test-utils-statmodel-server.R  | 84 +++++++++++++++++++
 6 files changed, 162 insertions(+), 6 deletions(-)

diff --git a/R/constants.R b/R/constants.R
index cf9224f..d4b8c45 100644
--- a/R/constants.R
+++ b/R/constants.R
@@ -8,12 +8,16 @@ NAMESPACE_STATMODEL = list(
   comparisons_custom_pairwise_choice2 = "comparisons_custom_pairwise_choice2", 
   comparisons_all_vs_one_choice = "comparisons_all_vs_one_choice", 
   comparisons_custom_nonpairwise_name = "comparisons_custom_nonpairwise_name",
-  comparisons_custom_nonpairwise_weights = "comparisons_custom_nonpairwise_weights"
+  comparisons_custom_nonpairwise_weights = "comparisons_custom_nonpairwise_weights",
+  comparisons_response_curve_choice = "comparisons_response_curve_choice",
+  comparisons_response_curve_xaxis = "comparisons_response_curve_xaxis",
+  comparisons_response_curve_amount = "comparisons_response_curve_amount"
 )
 
 CONSTANTS_STATMODEL = list(
   comparison_mode_all_pairwise = "comparison_mode_all_pairwise", 
   comparison_mode_all_vs_one = "comparison_mode_all_vs_one",
   comparison_mode_custom_pairwise = "comparison_mode_custom_pairwise",
-  comparison_mode_custom_nonpairwise = "comparison_mode_custom_nonpairwise"
+  comparison_mode_custom_nonpairwise = "comparison_mode_custom_nonpairwise",
+  comparison_mode_response_curve = "comparison_mode_response_curve"
 )
\ No newline at end of file
diff --git a/R/module-statmodel-server.R b/R/module-statmodel-server.R
index a1643e2..a2b33f4 100644
--- a/R/module-statmodel-server.R
+++ b/R/module-statmodel-server.R
@@ -32,6 +32,8 @@ get_contrast_panel_ui <- function(mode, ns) {
     build_all_pairwise_panel(ns)
   } else if (mode == CONSTANTS_STATMODEL$comparison_mode_custom_nonpairwise) {
     build_custom_nonpairwise_panel(ns)
+  } else if (mode == CONSTANTS_STATMODEL$comparison_mode_response_curve) {
+    build_response_curve_panel(ns)
   } else {
     NULL
   }
@@ -69,6 +71,17 @@ render_custom_non_pairwise_inputs = function(output, session, condition_list) {
   })
 }
 
+render_response_curve_inputs = function(output, session, condition_list) {
+  ns = session$ns
+  
+  output[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]] = renderUI({
+    selectInput(ns(NAMESPACE_STATMODEL$comparisons_response_curve_choice), 
+                "Condition:", 
+                condition_list()
+    )
+  })
+}
+
 # Todo: Add helper function to render dose response curve inputs
 
 validate_contrast_inputs = function(input, contrast_mode, condition_list) {
@@ -202,6 +215,27 @@ build_all_pair_contrast = function(input, condition_list, contrast, comp_list, r
   return(contrast$matrix)
 }
 
+build_response_curve_matrix = function(input, contrast) {
+  if (is.null(contrast$matrix)) {
+    contrast$matrix = data.frame(
+      Condition = input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]],
+      X_axis = input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]],
+      Amount = input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]],
+      stringsAsFactors = FALSE
+    )
+  } else {
+    contrast$matrix = rbind(contrast$matrix, data.frame(
+      Condition = input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]],
+      X_axis = input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]],
+      Amount = input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]],
+      stringsAsFactors = FALSE
+    ))
+    contrast$matrix = rbind(contrast$matrix[!duplicated(contrast$matrix$Condition),])
+  }
+  
+  return(contrast$matrix)
+}
+
 # Todo: Add helper function to build dose response curve mapper matrix
 
 # ============================================================================
@@ -467,6 +501,7 @@ statmodelServer = function(id, parent_session, loadpage_input, qc_input,
       render_all_against_one_inputs(output, session, condition_list)
       render_custom_pairwise_inputs(output, session, condition_list)
       render_custom_non_pairwise_inputs(output, session, condition_list)
+      render_response_curve_inputs(output, session, condition_list)
       
       Rownames = eventReactive(input[[NAMESPACE_STATMODEL$comparisons_submit]], {
                                    req(input[[NAMESPACE_STATMODEL$comparison_mode]])
@@ -509,6 +544,9 @@ statmodelServer = function(id, parent_session, loadpage_input, qc_input,
             } else if (input[[NAMESPACE_STATMODEL$comparison_mode]] == CONSTANTS_STATMODEL$comparison_mode_all_pairwise) {
               contrast$matrix = build_all_pair_contrast(
                 input, condition_list(), contrast, comp_list, row(), loadpage_input())
+            } else if (input[[NAMESPACE_STATMODEL$comparison_mode]] == CONSTANTS_STATMODEL$comparison_mode_response_curve) {
+              contrast$matrix = build_response_curve_matrix(
+                  input, contrast)
             }
             
             enable("calculate")
diff --git a/R/statmodel-ui-comparisons.R b/R/statmodel-ui-comparisons.R
index d2278cf..d4ba098 100644
--- a/R/statmodel-ui-comparisons.R
+++ b/R/statmodel-ui-comparisons.R
@@ -23,13 +23,14 @@ create_contrast_radio_buttons <- function(ns) {
       "1. Define comparisons - contrast matrix",
       class = "icon-wrapper",
       icon("question-circle", lib = "font-awesome"),
-      div("Define what conditions you want to compare here.", class = "icon-tooltip")
+      div("Define what conditions you want to compare here", class = "icon-tooltip")
     ),
     c(
       "All possible pairwise comparisons" = CONSTANTS_STATMODEL$comparison_mode_all_pairwise, 
       "Compare all against one" = CONSTANTS_STATMODEL$comparison_mode_all_vs_one, 
       "Create custom pairwise comparisons" = CONSTANTS_STATMODEL$comparison_mode_custom_pairwise,
-      "Create custom non-pairwise comparisons" = CONSTANTS_STATMODEL$comparison_mode_custom_nonpairwise
+      "Create custom non-pairwise comparisons" = CONSTANTS_STATMODEL$comparison_mode_custom_nonpairwise,
+      "Create response curves" = CONSTANTS_STATMODEL$comparison_mode_response_curve
     ),
     selected = character(0)
   )
@@ -78,4 +79,17 @@ build_custom_nonpairwise_panel <- function(ns) {
     actionButton(ns(NAMESPACE_STATMODEL$comparisons_submit), "Add"),
     actionButton(ns(NAMESPACE_STATMODEL$comparisons_clear), "Clear matrix")
   )
+}
+
+#' Create panel for configuring response curve metadata
+#' @noRd
+build_response_curve_panel <- function(ns) {
+  tagList(
+    h5("Set up response curve configuration:"),
+    uiOutput(ns(NAMESPACE_STATMODEL$comparisons_response_curve_choice)),
+    textInput(ns(NAMESPACE_STATMODEL$comparisons_response_curve_xaxis), "X-Axis Label:", placeholder = "e.g., Dosage, Time"),
+    numericInput(ns(NAMESPACE_STATMODEL$comparisons_response_curve_amount), "Response:", value = NULL, step = 0.1),
+    actionButton(ns(NAMESPACE_STATMODEL$comparisons_submit), "Add Entry"),
+    actionButton(ns(NAMESPACE_STATMODEL$comparisons_clear), "Clear All Data")
+  )
 }
\ No newline at end of file
diff --git a/R/statmodel-ui-headers.R b/R/statmodel-ui-headers.R
index c3db71c..d948937 100644
--- a/R/statmodel-ui-headers.R
+++ b/R/statmodel-ui-headers.R
@@ -28,8 +28,8 @@ create_custom_styles <- function() {
 create_header_section <- function() {
   tagList(
     headerPanel("Statistical modeling and inference"),
-    p("In this tab a statistical model is built in three steps:"),
-    p("(i) Create a contrast matrix with the correct Group comparisons,"), 
+    p("In this tab, build your statistical model in three steps:"),
+    p("(i) Create a contrast matrix for a group comparison or set up a configuration for a response curve analysis,"), 
     p("(ii) generate the model and "),
     p("(iii) view result plots."),
     p("More info ", a("here", href="https://www.rdocumentation.org/packages/MSstats/versions/3.4.0/topics/groupComparisonPlots"))
diff --git a/tests/testthat/test-statmodel-ui-options-contrasts.R b/tests/testthat/test-statmodel-ui-options-contrasts.R
index 08e497b..ee93e24 100644
--- a/tests/testthat/test-statmodel-ui-options-contrasts.R
+++ b/tests/testthat/test-statmodel-ui-options-contrasts.R
@@ -52,4 +52,20 @@ test_that("build_custom_nonpairwise_panel creates correct UI structure", {
   expect_true(grepl(">Clear matrix<", html, fixed = TRUE))
   expect_s3_class(ui, "shiny.tag.list")
   expect_length(ui, 5)
+})
+
+test_that("build_response_curve_panel creates correct UI structure", {
+  ns <- function(id) paste0("statmodel-", id)
+  ui <- build_response_curve_panel(ns)
+  html <- as.character(ui)
+  expect_true(grepl("<h5>Set up response curve configuration:</h5>", html, fixed = TRUE))
+  expect_true(grepl(NAMESPACE_STATMODEL$comparisons_response_curve_choice, html, fixed = TRUE))
+  expect_true(grepl(NAMESPACE_STATMODEL$comparisons_response_curve_xaxis, html, fixed = TRUE))
+  expect_true(grepl(NAMESPACE_STATMODEL$comparisons_response_curve_amount, html, fixed = TRUE))
+  expect_true(grepl(NAMESPACE_STATMODEL$comparisons_submit, html, fixed = TRUE))
+  expect_true(grepl(NAMESPACE_STATMODEL$comparisons_clear, html, fixed = TRUE))
+  expect_true(grepl(">Add Entry<", html, fixed = TRUE))
+  expect_true(grepl(">Clear All Data<", html, fixed = TRUE))
+  expect_s3_class(ui, "shiny.tag.list")
+  expect_length(ui, 6)
 })
\ No newline at end of file
diff --git a/tests/testthat/test-utils-statmodel-server.R b/tests/testthat/test-utils-statmodel-server.R
index 3b53ac8..e5d0284 100644
--- a/tests/testthat/test-utils-statmodel-server.R
+++ b/tests/testthat/test-utils-statmodel-server.R
@@ -374,4 +374,88 @@ test_that("get_contrast_panel_ui returns correct UI for each mode", {
   expect_null(get_contrast_panel_ui(NULL, ns))
   expect_null(get_contrast_panel_ui(character(0), ns))
   expect_null(get_contrast_panel_ui("invalid", ns))
+})
+
+
+test_that("build_response_curve_matrix when contrast$matrix is NULL", {
+  input <- list()
+  input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]] <- "Control"
+  input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]] <- "Dose"
+  input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]] <- 0
+  
+  contrast <- list(matrix = NULL)
+  result <- build_response_curve_matrix(input, contrast)
+  
+  expect_equal(nrow(result), 1)
+  expect_equal(ncol(result), 3)
+  expect_equal(result$Condition, "Control")
+  expect_equal(result$X_axis, "Dose")
+  expect_equal(result$Amount, 0)
+})
+
+test_that("build_response_curve_matrix appends row to existing response matrix", {
+  input <- list()
+  input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]] <- "T5"
+  input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]] <- "Time"
+  input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]] <- 5
+  
+  contrast <- list(
+    matrix = data.frame(
+      Condition = "Control",
+      X_axis = "Time",
+      Amount = 0,
+      stringsAsFactors = FALSE
+    )
+  )
+  
+  result <- build_response_curve_matrix(input, contrast)
+  
+  expect_equal(nrow(result), 2)
+  expect_equal(result$Condition[2], "T5")
+  expect_equal(result$X_axis[2], "Time")
+  expect_equal(result$Amount[2], 5)
+})
+
+test_that("build_response_curve_matrix removes duplicate conditions in response matrix, keep first occurrence", {
+  input <- list()
+  input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]] <- "Control"
+  input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]] <- "Time"
+  input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]] <- 1
+  
+  contrast <- list(
+    matrix = data.frame(
+      Condition = c("Control", "T15"),
+      X_axis = c("Time", "Time"),
+      Amount = c(0, 15),
+      stringsAsFactors = FALSE
+    )
+  )
+  
+  result <- build_response_curve_matrix(input, contrast)
+  
+  expect_equal(nrow(result), 2)
+  control_row <- result[result$Condition == "Control", ]
+  expect_equal(control_row$X_axis, "Time")
+  expect_equal(control_row$Amount, 0)
+})
+
+test_that("build_response_curve_matrix handles multiple unique x-axes correctly", {
+  input <- list()
+  input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]] <- "Group_C"
+  input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]] <- "pH"
+  input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]] <- 7.5
+  
+  contrast <- list(
+    matrix = data.frame(
+      Condition = c("Group_A", "Group_B"),
+      X_axis = c("Temperature", "Pressure"),
+      Amount = c(25, 100),
+      stringsAsFactors = FALSE
+    )
+  )
+  
+  result <- build_response_curve_matrix(input, contrast)
+  
+  expect_equal(nrow(result), 3)
+  expect_true(all(c("Group_A", "Group_B", "Group_C") %in% result$Condition))
 })
\ No newline at end of file

From 3e45d0e1f39acc9b660900bb558b0779d6b4b755 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Fri, 21 Nov 2025 10:25:35 -0500
Subject: [PATCH 2/6] address coderabbit validation comments

---
 R/module-statmodel-server.R | 29 +++++++++++++++++++++++++----
 1 file changed, 25 insertions(+), 4 deletions(-)

diff --git a/R/module-statmodel-server.R b/R/module-statmodel-server.R
index a2b33f4..843e0ac 100644
--- a/R/module-statmodel-server.R
+++ b/R/module-statmodel-server.R
@@ -97,6 +97,16 @@ validate_contrast_inputs = function(input, contrast_mode, condition_list) {
     validate(
       need(wt_sum == 0, "The contrast weights should sum up to 0")
     )
+  } else if (contrast_mode == CONSTANTS_STATMODEL$comparison_mode_response_curve) {
+    x_axis <- input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]]
+    amount <- input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]]
+    
+    validate(
+      need(!is.null(x_axis) && trimws(x_axis) != "", 
+           "Please define an X-axis variable"),
+      need(!is.null(amount) && !is.na(amount), 
+           "Please provide a valid amount")
+    )
   }
 }
 
@@ -216,18 +226,29 @@ build_all_pair_contrast = function(input, condition_list, contrast, comp_list, r
 }
 
 build_response_curve_matrix = function(input, contrast) {
+  x_axis <- input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]]
+  amount <- input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]]
+  
+  if (is.null(x_axis) || trimws(x_axis) == "") {
+    return(contrast$matrix)
+  }
+  
+  if (is.null(amount) || is.na(amount)) {
+    return(contrast$matrix)
+  }
+  
   if (is.null(contrast$matrix)) {
     contrast$matrix = data.frame(
       Condition = input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]],
-      X_axis = input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]],
-      Amount = input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]],
+      X_axis = x_axis,
+      Amount = amount,
       stringsAsFactors = FALSE
     )
   } else {
     contrast$matrix = rbind(contrast$matrix, data.frame(
       Condition = input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]],
-      X_axis = input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]],
-      Amount = input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]],
+      X_axis = x_axis,
+      Amount = amount,
       stringsAsFactors = FALSE
     ))
     contrast$matrix = rbind(contrast$matrix[!duplicated(contrast$matrix$Condition),])

From 0ccbcabc988e3a5dab1c676f4971cc1273be1077 Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Fri, 21 Nov 2025 15:08:38 -0500
Subject: [PATCH 3/6] change condition to group in tables

---
 R/module-statmodel-server.R                  |  8 ++++----
 tests/testthat/test-utils-statmodel-server.R | 14 +++++++-------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/R/module-statmodel-server.R b/R/module-statmodel-server.R
index 843e0ac..4674512 100644
--- a/R/module-statmodel-server.R
+++ b/R/module-statmodel-server.R
@@ -76,7 +76,7 @@ render_response_curve_inputs = function(output, session, condition_list) {
   
   output[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]] = renderUI({
     selectInput(ns(NAMESPACE_STATMODEL$comparisons_response_curve_choice), 
-                "Condition:", 
+                "Group:", 
                 condition_list()
     )
   })
@@ -239,19 +239,19 @@ build_response_curve_matrix = function(input, contrast) {
   
   if (is.null(contrast$matrix)) {
     contrast$matrix = data.frame(
-      Condition = input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]],
+      GROUP = input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]],
       X_axis = x_axis,
       Amount = amount,
       stringsAsFactors = FALSE
     )
   } else {
     contrast$matrix = rbind(contrast$matrix, data.frame(
-      Condition = input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]],
+      GROUP = input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]],
       X_axis = x_axis,
       Amount = amount,
       stringsAsFactors = FALSE
     ))
-    contrast$matrix = rbind(contrast$matrix[!duplicated(contrast$matrix$Condition),])
+    contrast$matrix = rbind(contrast$matrix[!duplicated(contrast$matrix$GROUP),])
   }
   
   return(contrast$matrix)
diff --git a/tests/testthat/test-utils-statmodel-server.R b/tests/testthat/test-utils-statmodel-server.R
index e5d0284..fa97240 100644
--- a/tests/testthat/test-utils-statmodel-server.R
+++ b/tests/testthat/test-utils-statmodel-server.R
@@ -388,7 +388,7 @@ test_that("build_response_curve_matrix when contrast$matrix is NULL", {
   
   expect_equal(nrow(result), 1)
   expect_equal(ncol(result), 3)
-  expect_equal(result$Condition, "Control")
+  expect_equal(result$GROUP, "Control")
   expect_equal(result$X_axis, "Dose")
   expect_equal(result$Amount, 0)
 })
@@ -401,7 +401,7 @@ test_that("build_response_curve_matrix appends row to existing response matrix",
   
   contrast <- list(
     matrix = data.frame(
-      Condition = "Control",
+      GROUP = "Control",
       X_axis = "Time",
       Amount = 0,
       stringsAsFactors = FALSE
@@ -411,7 +411,7 @@ test_that("build_response_curve_matrix appends row to existing response matrix",
   result <- build_response_curve_matrix(input, contrast)
   
   expect_equal(nrow(result), 2)
-  expect_equal(result$Condition[2], "T5")
+  expect_equal(result$GROUP[2], "T5")
   expect_equal(result$X_axis[2], "Time")
   expect_equal(result$Amount[2], 5)
 })
@@ -424,7 +424,7 @@ test_that("build_response_curve_matrix removes duplicate conditions in response
   
   contrast <- list(
     matrix = data.frame(
-      Condition = c("Control", "T15"),
+      GROUP = c("Control", "T15"),
       X_axis = c("Time", "Time"),
       Amount = c(0, 15),
       stringsAsFactors = FALSE
@@ -434,7 +434,7 @@ test_that("build_response_curve_matrix removes duplicate conditions in response
   result <- build_response_curve_matrix(input, contrast)
   
   expect_equal(nrow(result), 2)
-  control_row <- result[result$Condition == "Control", ]
+  control_row <- result[result$GROUP == "Control", ]
   expect_equal(control_row$X_axis, "Time")
   expect_equal(control_row$Amount, 0)
 })
@@ -447,7 +447,7 @@ test_that("build_response_curve_matrix handles multiple unique x-axes correctly"
   
   contrast <- list(
     matrix = data.frame(
-      Condition = c("Group_A", "Group_B"),
+      GROUP = c("Group_A", "Group_B"),
       X_axis = c("Temperature", "Pressure"),
       Amount = c(25, 100),
       stringsAsFactors = FALSE
@@ -457,5 +457,5 @@ test_that("build_response_curve_matrix handles multiple unique x-axes correctly"
   result <- build_response_curve_matrix(input, contrast)
   
   expect_equal(nrow(result), 3)
-  expect_true(all(c("Group_A", "Group_B", "Group_C") %in% result$Condition))
+  expect_true(all(c("Group_A", "Group_B", "Group_C") %in% result$GROUP))
 })
\ No newline at end of file

From 0dc9021132c90f6beb4e0854bf5be52ed8f0eb43 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Mon, 1 Dec 2025 18:43:10 -0500
Subject: [PATCH 4/6] set up default parsing from MSstatsResponse

---
 NAMESPACE                                     |  1 +
 R/module-statmodel-server.R                   | 36 ++------
 R/statmodel-ui-comparisons.R                  |  7 +-
 .../test-statmodel-ui-options-contrasts.R     |  7 +-
 tests/testthat/test-utils-statmodel-server.R  | 84 ++-----------------
 5 files changed, 16 insertions(+), 119 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 9e72d74..f61c14a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -48,6 +48,7 @@ importFrom(MSstatsPTM,SkylinetoMSstatsPTMFormat)
 importFrom(MSstatsPTM,SpectronauttoMSstatsPTMFormat)
 importFrom(MSstatsPTM,dataProcessPlotsPTM)
 importFrom(MSstatsPTM,groupComparisonPlotsPTM)
+importFrom(MSstatsResponse,convertGroupToNumericDose)
 importFrom(arrow,read_parquet)
 importFrom(data.table,copy)
 importFrom(dplyr,`%>%`)
diff --git a/R/module-statmodel-server.R b/R/module-statmodel-server.R
index 4674512..1b35263 100644
--- a/R/module-statmodel-server.R
+++ b/R/module-statmodel-server.R
@@ -225,35 +225,10 @@ build_all_pair_contrast = function(input, condition_list, contrast, comp_list, r
   return(contrast$matrix)
 }
 
-build_response_curve_matrix = function(input, contrast) {
-  x_axis <- input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]]
-  amount <- input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]]
-  
-  if (is.null(x_axis) || trimws(x_axis) == "") {
-    return(contrast$matrix)
-  }
-  
-  if (is.null(amount) || is.na(amount)) {
-    return(contrast$matrix)
-  }
-  
-  if (is.null(contrast$matrix)) {
-    contrast$matrix = data.frame(
-      GROUP = input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]],
-      X_axis = x_axis,
-      Amount = amount,
-      stringsAsFactors = FALSE
-    )
-  } else {
-    contrast$matrix = rbind(contrast$matrix, data.frame(
-      GROUP = input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]],
-      X_axis = x_axis,
-      Amount = amount,
-      stringsAsFactors = FALSE
-    ))
-    contrast$matrix = rbind(contrast$matrix[!duplicated(contrast$matrix$GROUP),])
-  }
-  
+#' @importFrom MSstatsResponse convertGroupToNumericDose
+build_response_curve_matrix = function(contrast, condition_list) {
+  condition_to_metadata_table = convertGroupToNumericDose(condition_list)
+  contrast$matrix = data.frame(GROUP = condition_list, condition_to_metadata_table)
   return(contrast$matrix)
 }
 
@@ -522,7 +497,6 @@ statmodelServer = function(id, parent_session, loadpage_input, qc_input,
       render_all_against_one_inputs(output, session, condition_list)
       render_custom_pairwise_inputs(output, session, condition_list)
       render_custom_non_pairwise_inputs(output, session, condition_list)
-      render_response_curve_inputs(output, session, condition_list)
       
       Rownames = eventReactive(input[[NAMESPACE_STATMODEL$comparisons_submit]], {
                                    req(input[[NAMESPACE_STATMODEL$comparison_mode]])
@@ -567,7 +541,7 @@ statmodelServer = function(id, parent_session, loadpage_input, qc_input,
                 input, condition_list(), contrast, comp_list, row(), loadpage_input())
             } else if (input[[NAMESPACE_STATMODEL$comparison_mode]] == CONSTANTS_STATMODEL$comparison_mode_response_curve) {
               contrast$matrix = build_response_curve_matrix(
-                  input, contrast)
+                  contrast, condition_list())
             }
             
             enable("calculate")
diff --git a/R/statmodel-ui-comparisons.R b/R/statmodel-ui-comparisons.R
index d4ba098..9df89b7 100644
--- a/R/statmodel-ui-comparisons.R
+++ b/R/statmodel-ui-comparisons.R
@@ -86,10 +86,7 @@ build_custom_nonpairwise_panel <- function(ns) {
 build_response_curve_panel <- function(ns) {
   tagList(
     h5("Set up response curve configuration:"),
-    uiOutput(ns(NAMESPACE_STATMODEL$comparisons_response_curve_choice)),
-    textInput(ns(NAMESPACE_STATMODEL$comparisons_response_curve_xaxis), "X-Axis Label:", placeholder = "e.g., Dosage, Time"),
-    numericInput(ns(NAMESPACE_STATMODEL$comparisons_response_curve_amount), "Response:", value = NULL, step = 0.1),
-    actionButton(ns(NAMESPACE_STATMODEL$comparisons_submit), "Add Entry"),
-    actionButton(ns(NAMESPACE_STATMODEL$comparisons_clear), "Clear All Data")
+    actionButton(ns(NAMESPACE_STATMODEL$comparisons_submit), "Setup Metadata"),
+    actionButton(ns(NAMESPACE_STATMODEL$comparisons_clear), "Reset")
   )
 }
\ No newline at end of file
diff --git a/tests/testthat/test-statmodel-ui-options-contrasts.R b/tests/testthat/test-statmodel-ui-options-contrasts.R
index ee93e24..4f870fb 100644
--- a/tests/testthat/test-statmodel-ui-options-contrasts.R
+++ b/tests/testthat/test-statmodel-ui-options-contrasts.R
@@ -59,13 +59,8 @@ test_that("build_response_curve_panel creates correct UI structure", {
   ui <- build_response_curve_panel(ns)
   html <- as.character(ui)
   expect_true(grepl("<h5>Set up response curve configuration:</h5>", html, fixed = TRUE))
-  expect_true(grepl(NAMESPACE_STATMODEL$comparisons_response_curve_choice, html, fixed = TRUE))
-  expect_true(grepl(NAMESPACE_STATMODEL$comparisons_response_curve_xaxis, html, fixed = TRUE))
-  expect_true(grepl(NAMESPACE_STATMODEL$comparisons_response_curve_amount, html, fixed = TRUE))
   expect_true(grepl(NAMESPACE_STATMODEL$comparisons_submit, html, fixed = TRUE))
   expect_true(grepl(NAMESPACE_STATMODEL$comparisons_clear, html, fixed = TRUE))
-  expect_true(grepl(">Add Entry<", html, fixed = TRUE))
-  expect_true(grepl(">Clear All Data<", html, fixed = TRUE))
   expect_s3_class(ui, "shiny.tag.list")
-  expect_length(ui, 6)
+  expect_length(ui, 3)
 })
\ No newline at end of file
diff --git a/tests/testthat/test-utils-statmodel-server.R b/tests/testthat/test-utils-statmodel-server.R
index fa97240..86a34cd 100644
--- a/tests/testthat/test-utils-statmodel-server.R
+++ b/tests/testthat/test-utils-statmodel-server.R
@@ -377,85 +377,15 @@ test_that("get_contrast_panel_ui returns correct UI for each mode", {
 })
 
 
-test_that("build_response_curve_matrix when contrast$matrix is NULL", {
-  input <- list()
-  input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]] <- "Control"
-  input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]] <- "Dose"
-  input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]] <- 0
+test_that("build_response_curve_matrix returns correct columns", {
+  condition_list = c("Dasatinib_001nM", "Dasatinib_001uM", "DMSO")
   
   contrast <- list(matrix = NULL)
-  result <- build_response_curve_matrix(input, contrast)
-  
-  expect_equal(nrow(result), 1)
-  expect_equal(ncol(result), 3)
-  expect_equal(result$GROUP, "Control")
-  expect_equal(result$X_axis, "Dose")
-  expect_equal(result$Amount, 0)
-})
-
-test_that("build_response_curve_matrix appends row to existing response matrix", {
-  input <- list()
-  input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]] <- "T5"
-  input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]] <- "Time"
-  input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]] <- 5
-  
-  contrast <- list(
-    matrix = data.frame(
-      GROUP = "Control",
-      X_axis = "Time",
-      Amount = 0,
-      stringsAsFactors = FALSE
-    )
-  )
-  
-  result <- build_response_curve_matrix(input, contrast)
-  
-  expect_equal(nrow(result), 2)
-  expect_equal(result$GROUP[2], "T5")
-  expect_equal(result$X_axis[2], "Time")
-  expect_equal(result$Amount[2], 5)
-})
-
-test_that("build_response_curve_matrix removes duplicate conditions in response matrix, keep first occurrence", {
-  input <- list()
-  input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]] <- "Control"
-  input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]] <- "Time"
-  input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]] <- 1
-  
-  contrast <- list(
-    matrix = data.frame(
-      GROUP = c("Control", "T15"),
-      X_axis = c("Time", "Time"),
-      Amount = c(0, 15),
-      stringsAsFactors = FALSE
-    )
-  )
-  
-  result <- build_response_curve_matrix(input, contrast)
-  
-  expect_equal(nrow(result), 2)
-  control_row <- result[result$GROUP == "Control", ]
-  expect_equal(control_row$X_axis, "Time")
-  expect_equal(control_row$Amount, 0)
-})
-
-test_that("build_response_curve_matrix handles multiple unique x-axes correctly", {
-  input <- list()
-  input[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]] <- "Group_C"
-  input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]] <- "pH"
-  input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]] <- 7.5
-  
-  contrast <- list(
-    matrix = data.frame(
-      GROUP = c("Group_A", "Group_B"),
-      X_axis = c("Temperature", "Pressure"),
-      Amount = c(25, 100),
-      stringsAsFactors = FALSE
-    )
-  )
-  
-  result <- build_response_curve_matrix(input, contrast)
+  result <- build_response_curve_matrix(contrast, condition_list)
   
   expect_equal(nrow(result), 3)
-  expect_true(all(c("Group_A", "Group_B", "Group_C") %in% result$GROUP))
+  expect_equal(ncol(result), 3)
+  expect_true("GROUP" %in% colnames(result))
+  expect_true("drug" %in% colnames(result))
+  expect_true("dose_nM" %in% colnames(result))
 })
\ No newline at end of file

From 732e5f497ce2cfe0dae89067445752803cb86322 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Mon, 1 Dec 2025 19:00:26 -0500
Subject: [PATCH 5/6] add description file

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 88e82c2..abdfb0d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,7 +27,7 @@ Depends: R (>= 4.2)
 Imports: shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly, data.table, Hmisc,
   MSstats, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl,
   ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics, mockery, MSstatsBioNet,
-  shinydashboard, arrow, tools
+  shinydashboard, arrow, tools, MSstatsResponse
 Suggests: 
     rmarkdown,
     tinytest,

From 4ce844f6594adc1a9cbba4cfb32b14f43b538d15 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Mon, 1 Dec 2025 19:03:36 -0500
Subject: [PATCH 6/6] remove dead code

---
 R/constants.R               |  5 +----
 R/module-statmodel-server.R | 21 ---------------------
 2 files changed, 1 insertion(+), 25 deletions(-)

diff --git a/R/constants.R b/R/constants.R
index d4b8c45..3385c1c 100644
--- a/R/constants.R
+++ b/R/constants.R
@@ -8,10 +8,7 @@ NAMESPACE_STATMODEL = list(
   comparisons_custom_pairwise_choice2 = "comparisons_custom_pairwise_choice2", 
   comparisons_all_vs_one_choice = "comparisons_all_vs_one_choice", 
   comparisons_custom_nonpairwise_name = "comparisons_custom_nonpairwise_name",
-  comparisons_custom_nonpairwise_weights = "comparisons_custom_nonpairwise_weights",
-  comparisons_response_curve_choice = "comparisons_response_curve_choice",
-  comparisons_response_curve_xaxis = "comparisons_response_curve_xaxis",
-  comparisons_response_curve_amount = "comparisons_response_curve_amount"
+  comparisons_custom_nonpairwise_weights = "comparisons_custom_nonpairwise_weights"
 )
 
 CONSTANTS_STATMODEL = list(
diff --git a/R/module-statmodel-server.R b/R/module-statmodel-server.R
index 1b35263..5dd9b57 100644
--- a/R/module-statmodel-server.R
+++ b/R/module-statmodel-server.R
@@ -71,17 +71,6 @@ render_custom_non_pairwise_inputs = function(output, session, condition_list) {
   })
 }
 
-render_response_curve_inputs = function(output, session, condition_list) {
-  ns = session$ns
-  
-  output[[NAMESPACE_STATMODEL$comparisons_response_curve_choice]] = renderUI({
-    selectInput(ns(NAMESPACE_STATMODEL$comparisons_response_curve_choice), 
-                "Group:", 
-                condition_list()
-    )
-  })
-}
-
 # Todo: Add helper function to render dose response curve inputs
 
 validate_contrast_inputs = function(input, contrast_mode, condition_list) {
@@ -97,16 +86,6 @@ validate_contrast_inputs = function(input, contrast_mode, condition_list) {
     validate(
       need(wt_sum == 0, "The contrast weights should sum up to 0")
     )
-  } else if (contrast_mode == CONSTANTS_STATMODEL$comparison_mode_response_curve) {
-    x_axis <- input[[NAMESPACE_STATMODEL$comparisons_response_curve_xaxis]]
-    amount <- input[[NAMESPACE_STATMODEL$comparisons_response_curve_amount]]
-    
-    validate(
-      need(!is.null(x_axis) && trimws(x_axis) != "", 
-           "Please define an X-axis variable"),
-      need(!is.null(amount) && !is.na(amount), 
-           "Please provide a valid amount")
-    )
   }
 }