From 978bf6f6edad35df4e05043b80110856b9f87434 Mon Sep 17 00:00:00 2001
From: Patrick Chwalek <patrickchwalek@gmail.com>
Date: Sun, 6 Nov 2022 15:50:43 -0500
Subject: [PATCH 01/10] added code to skip day if power loss during task and to
 skip multiple days if blackout longer than 1 day

---
 .../MicroPET_Launch_code.ino                   | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino
index 42f10ea..751f857 100644
--- a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
+++ b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
@@ -521,19 +521,25 @@ void recoverSystemStart(){
   /* (1) check for hard faults */
   //  (1.1) if system failed during an experiment, generate fault
   if(systemStateStructVar.testDayComplete != 1){
-    Serial.println("System was interrupted during an experiment! No way to resume!");
-    while(1);
-    return;
+    Serial.print("System was interrupted during experiment: ");
+    Serial.println(systemStateStructVar.testDay);
   }
 
   //  (1.2) if system paused for longer than test day interval, generate fault
   uint32_t timeSinceLastExperiment = rtc.now().unixtime() - systemStateStructVar.epoch;
+  uint16_t skipDays;
   if(timeSinceLastExperiment >= DELAY_SECONDS_PER_EXPERIMENT){
-    Serial.println("System was off for longer than experiment interval! No way to resume!");
-    while(1);
-    return;
+    Serial.println("System was off for longer than experiment interval!");
+
+    skipDays = int( timeSinceLastExperiment / DELAY_SECONDS_PER_EXPERIMENT );
+    for(int i = 0; i < skipDays; i++){
+      systemStateStructVar.testDay++;
+      Serial.print(" Skipping day: ");
+      Serial.println(systemStateStructVar.testDay);
+    }
   }
 
+  timeSinceLastExperiment = int( timeSinceLastExperiment % DELAY_SECONDS_PER_EXPERIMENT );
   //  (1.3) check if tests had already ended
   if(systemStateStructVar.testDay == TOTAL_EXPERIMENTS - 1){
     Serial.println("Power failure occured after experiment finished! No reason to resume!");

From f933194f9246dac047d9a5286593db56006a48df Mon Sep 17 00:00:00 2001
From: Patrick Chwalek <patrickchwalek@gmail.com>
Date: Sun, 6 Nov 2022 16:05:58 -0500
Subject: [PATCH 02/10] added SD card power failure logging

---
 Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino
index 751f857..3d93328 100644
--- a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
+++ b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
@@ -523,6 +523,7 @@ void recoverSystemStart(){
   if(systemStateStructVar.testDayComplete != 1){
     Serial.print("System was interrupted during experiment: ");
     Serial.println(systemStateStructVar.testDay);
+    saveExperimentalLog("System was interrupted during experiment: " + String(systemStateStructVar.testDay));
   }
 
   //  (1.2) if system paused for longer than test day interval, generate fault
@@ -536,6 +537,8 @@ void recoverSystemStart(){
       systemStateStructVar.testDay++;
       Serial.print(" Skipping day: ");
       Serial.println(systemStateStructVar.testDay);
+
+      saveExperimentalLog(" Skipping day: " + String(systemStateStructVar.testDay));
     }
   }
 
@@ -543,6 +546,9 @@ void recoverSystemStart(){
   //  (1.3) check if tests had already ended
   if(systemStateStructVar.testDay == TOTAL_EXPERIMENTS - 1){
     Serial.println("Power failure occured after experiment finished! No reason to resume!");
+
+    saveExperimentalLog("Power failure occured after experiment finished! No reason to resume!");
+
     while(1);
     return;
   }

From 8e59023a6f261b5d359a058532ed9d0b49f33d60 Mon Sep 17 00:00:00 2001
From: Patrick Chwalek <patrickchwalek@gmail.com>
Date: Mon, 7 Nov 2022 12:11:33 -0500
Subject: [PATCH 03/10] added code if day 1 is interrupted, restart day_1

---
 Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino
index 3d93328..e79a2aa 100644
--- a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
+++ b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
@@ -524,6 +524,13 @@ void recoverSystemStart(){
     Serial.print("System was interrupted during experiment: ");
     Serial.println(systemStateStructVar.testDay);
     saveExperimentalLog("System was interrupted during experiment: " + String(systemStateStructVar.testDay));
+
+    if(systemStateStructVar.testDay == 1){
+      Serial.print("Restarting entire experiment since lost power on day 1");
+      saveExperimentalLog("Restarting entire experiment since lost power on day 1");
+      day_1();
+      return;
+    }
   }
 
   //  (1.2) if system paused for longer than test day interval, generate fault

From c45e4b44cc7400d9423394508510032fd271ee7c Mon Sep 17 00:00:00 2001
From: Patrick Chwalek <patrickchwalek@gmail.com>
Date: Mon, 7 Nov 2022 12:14:10 -0500
Subject: [PATCH 04/10] added systemState boolean toggle

---
 Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino
index e79a2aa..2b247da 100644
--- a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
+++ b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
@@ -529,6 +529,7 @@ void recoverSystemStart(){
       Serial.print("Restarting entire experiment since lost power on day 1");
       saveExperimentalLog("Restarting entire experiment since lost power on day 1");
       day_1();
+      systemState = true;
       return;
     }
   }
@@ -572,6 +573,8 @@ void recoverSystemStart(){
 //  }
 
   Serial.println("System has recovered gracefully!");
+
+  systemState = true;
 }
 
 

From f3c3ac03dedf9155df62f32db795b4f6abd2acae Mon Sep 17 00:00:00 2001
From: pat pataranutaporn <patpat@mit.edu>
Date: Tue, 8 Nov 2022 09:47:32 -0600
Subject: [PATCH 05/10] finish the dummy code

---
 .DS_Store                                     | Bin 10244 -> 10244 bytes
 Teensey Code/.DS_Store                        | Bin 12292 -> 12292 bytes
 .../MicroPET_Launch_code.ino                  |  29 ++++++++----------
 3 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/.DS_Store b/.DS_Store
index 4cf95a961c4bf3c78477898b04f76f1cd4268314..5331ff2b652fe5f238ff9d6e2ab47e151f2cc362 100644
GIT binary patch
delta 56
zcmZn(XbITRBh0vKa<6b9w^Vhtk)@fAf}ye5WOfl*#-7QJLh_8glM7^IHYbWK;oi)y
M@QY>he-UP8000~jng9R*

delta 45
zcmZn(XbITRBRsiUpp?zRTt~s&a5ATe>||j<mB|LelADu7mT+%oRrtfQnOT&X82~^f
B49x%l

diff --git a/Teensey Code/.DS_Store b/Teensey Code/.DS_Store
index 7f003d2e8396a9e54ef1eaa6d75c4b0cd724c824..2f270885c2e85f27b6d6e08845e2146cadfe4dac 100644
GIT binary patch
delta 68
zcmZokXi3;`Re*8V<O!mM+)~xmMwVte3WmmJlLG{08G9z@3Cc6}ZtfGT=G)Azu!?=M
Si<sWzhvG_`Sv5AmIEnxkxE4_W

delta 50
ycmZokXi3;`RbX-?Q|aUxLhhR<3s&%L=2Te2&e%1%QA}s@6LICutQs2-TqOYSf)Z;0

diff --git a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino
index 2b247da..5162285 100644
--- a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
+++ b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
@@ -664,13 +664,20 @@ void day_1() {
   saveExperimentalLog("Executing Day 1");
 
 
- // =============== SAFETY MECHANISM ================
-  // DUMMY TASK
+ // =============== ENZYME EXP =====================
 
-  //EXP1
-  moveLiquid (experimentOne, e_buffer, chamberA, 2000);  //buffer to chamber A - 2 ml (flexible)
-  //EXP2
-  moveLiquid (experimentTwo, e_buffer, chamberA, 2000);  //buffer to chamber A - 2 ml (flexible)
+  //DUMMY CODE
+  moveLiquid (experimentOne, e_buffer, chamberA, 1000);  //buffer to chamber A - 1 ml (flexible)
+  moveLiquid (experimentTwo, e_buffer, chamberA, 1000);  //buffer to chamber A - 1 ml (flexible)
+  Serial.println("finish the summy code...");
+  saveExperimentalLog("Finish dummy code!");
+
+  //EXP1 - liquid in dummy code
+  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentOne, e_buffer, chamberA, 1525);  //buffer to chamber A - 1.525 ml (flexible)
+  //EXP2 - liquid in dummy code
+  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentTwo, e_buffer, chamberA, 1525);  //buffer to chamber A - 1.525 ml (flexible)
 
 
  // =============== MICROBE EXP =====================
@@ -692,16 +699,6 @@ void day_1() {
   motorSensorBrdCtrl(3, halt);
 
 
- // =============== ENZYME EXP =====================
-
-  //EXP1
-  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
-  moveLiquid (experimentOne, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
-  //EXP2
-  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
-  moveLiquid (experimentTwo, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
-
-
  // =============== UPDATE STATUS ===================
   systemStateStructVar.testDayComplete = 1;
   saveStateToSD(&systemStateStructVar);

From 103d8c586d49f44d58ed8e02930d98709bf73ee0 Mon Sep 17 00:00:00 2001
From: pat pataranutaporn <patpat@mit.edu>
Date: Tue, 8 Nov 2022 16:30:39 -0600
Subject: [PATCH 06/10] Update day test function + comments

---
 .../MicroPET_Launch_code.ino                  | 92 ++++++++++---------
 Teensey Code/move_liquid/move_liquid.ino      | 50 +++++++++-
 2 files changed, 93 insertions(+), 49 deletions(-)

diff --git a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino
index 5162285..2e311d5 100644
--- a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
+++ b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
@@ -612,6 +612,8 @@ bool checkForStartSerialCommand() {
         //Print the message (or do other things)
         Serial.println("Executing Test Script");
 
+
+
         day_functionTest();
       }
 
@@ -624,18 +626,14 @@ bool checkForStartSerialCommand() {
 }
 
 void day_functionTest(){
-
-  // DUMMY TASK
-
-  //EXP1
-  moveLiquid (experimentOne, e_buffer, chamberA, 2000);  //buffer to chamber A - 2 ml (flexible)
+  
   //EXP2
-  moveLiquid (experimentTwo, e_buffer, chamberA, 2000);  //buffer to chamber A - 2 ml (flexible)
-
-Serial.println("revival pumping...");
-motorSensorBrdCtrl(1, forward);
-delay (5000);
-motorSensorBrdCtrl(1, halt);
+  Serial.println("EXP2 revival pumping...");
+  saveExperimentalLog("EXP2 revived");
+  switchCollection(experimentTwo, waste);//back to waste bag
+  motorSensorBrdCtrl(1, forward);
+  delay (5000); //~10ML
+  motorSensorBrdCtrl(1, halt);
 
 }
 
@@ -669,7 +667,7 @@ void day_1() {
   //DUMMY CODE
   moveLiquid (experimentOne, e_buffer, chamberA, 1000);  //buffer to chamber A - 1 ml (flexible)
   moveLiquid (experimentTwo, e_buffer, chamberA, 1000);  //buffer to chamber A - 1 ml (flexible)
-  Serial.println("finish the summy code...");
+  Serial.println("finish the dummy code...");
   saveExperimentalLog("Finish dummy code!");
 
   //EXP1 - liquid in dummy code
@@ -1786,15 +1784,15 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
   if (experiment == 1 && origin == 0)
   {
     switch_conn_pin(BASEBD_J10_PIN2, LOW); //Experiment 1 valveA
-    Serial.println("_E1_exp1 move from e_buffer");
-    saveExperimentalLog("_E1_move from e_buffer");
+    Serial.println("E1_exp1 move from e_buffer");
+    saveExperimentalLog("E1_move from e_buffer");
   }
 
   if (experiment == 1 && origin == 1)
   {
     switch_conn_pin(BASEBD_J10_PIN2, HIGH); //Experiment 1 valveA
-    Serial.println("_E1 move from enzyme");
-    saveExperimentalLog("_E1_move from enzyme");
+    Serial.println("E1 move from enzyme");
+    saveExperimentalLog("E1_move from enzyme");
   }
 
   if (experiment == 1 && target == 2)
@@ -1802,7 +1800,7 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
     switch_conn_pin(BASEBD_J9_PIN2, HIGH); //Experiment 1 valveB high, waste line open
     int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 25uL at a time
     Serial.println("move to chamberA");
-    saveExperimentalLog("exp1_move to chamberA" + String(move_pulse * 25) + "uL");
+    saveExperimentalLog("E1_move to chamberA" + String(move_pulse * 25) + "uL");
     for (int i = 0; i <= move_pulse; i++) {
       switch_conn_pin(BASEBD_J10_PIN4, HIGH); //Experiment 1 pumpA
       digitalWrite(LED, HIGH);
@@ -1811,6 +1809,7 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
       digitalWrite(LED, LOW);
       delay(200);
       Serial.println( i * 25); //print out the moving volume
+      saveExperimentalLog("STEP_exp1_move to chamberA" + String(i * 25) + "uL");
     }
     switch_conn_pin(BASEBD_J10_PIN2, LOW); //Reset eperiment 1 valveA so enzyme is blocked
   }
@@ -1840,8 +1839,8 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
   if (experiment == 1 && origin == 3 && target == 4)
   {
     int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 25uL at a time
-    Serial.println("_E1 move to chamberB");
-    saveExperimentalLog("_E1_move to chamberB " + String(move_pulse * 25) + "uL");
+    Serial.println("E1 move to chamberB");
+    saveExperimentalLog("E1_move to chamberB " + String(move_pulse * 25) + "uL");
     for (int i = 0; i <= move_pulse; i++) {
       switch_conn_pin(BASEBD_J9_PIN4, HIGH); //Experiment 1 pumpB
       digitalWrite(LED, HIGH);
@@ -1850,6 +1849,7 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
       digitalWrite(LED, LOW);
       delay(200);
       Serial.println( i * 25); //print out the moving volume
+      saveExperimentalLog("STEP_E1_move to chamberB " + String(i * 25) + "uL");
     }
   //  switch_conn_pin(BASEBD_J9_PIN2, LOW); //Reset experiment 1 valveB so chamberA is blocked
   }
@@ -1859,23 +1859,23 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
   if (experiment == 2 && origin == 0)
   {
     switch_conn_pin(BASEBD_J12_PIN2, LOW); //Experiment 2 valveA
-    Serial.println("_E2 move from e_buffer");
-    saveExperimentalLog("_E2_move from e_buffer");
+    Serial.println("E2 move from e_buffer");
+    saveExperimentalLog("E2_move from e_buffer");
   }
 
   if (experiment == 2 && origin == 1)
   {
     switch_conn_pin(BASEBD_J12_PIN2, HIGH); //Experiment 2 valveA
-    saveExperimentalLog("_E2_move from enzyme");
-    Serial.println("_E2 move from Enzyme");
+    saveExperimentalLog("E2_move from enzyme");
+    Serial.println("E2 move from Enzyme");
   }
 
   if (experiment == 2 && target == 2)
   {
     switch_conn_pin(BASEBD_J11_PIN2, HIGH); //Experiment 2 valveB high, waste line open
     int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 25uL at a time
-    Serial.println("_E2 move to chamberA");
-    saveExperimentalLog("_E2_move to chamberA " + String(move_pulse * 25) + "uL");
+    Serial.println("E2 move to chamberA");
+    saveExperimentalLog("E2_move to chamberA " + String(move_pulse * 25) + "uL");
     for (int i = 0; i <= move_pulse; i++) {
       switch_conn_pin(BASEBD_J12_PIN4, HIGH); //Experiment 2 pumpA
       digitalWrite(LED, HIGH);
@@ -1884,6 +1884,7 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
       digitalWrite(LED, LOW);
       delay(200);
       Serial.println( i * 25);
+      saveExperimentalLog("STEP_E2_move to chamberA " + String(i * 25) + "uL");
     }
     switch_conn_pin(BASEBD_J12_PIN2, LOW); //Reset xperiment 1 valveA so enzyme is blocked
   }
@@ -1914,8 +1915,8 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
   if (experiment == 2 && origin == 3 && target == 4)
    {
       int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 35uL at a time
-      Serial.println("_E2 media move to chamberB");
-      saveExperimentalLog("_E2_media_move to chamberB " + String(move_pulse * 25) + "uL");
+      Serial.println("E2 media move to chamberB");
+      saveExperimentalLog("E2_media_move to chamberB " + String(move_pulse * 25) + "uL");
       for (int i = 0; i <= move_pulse; i++){
       switch_conn_pin(BASEBD_J11_PIN4, HIGH); //Experiment 2 pumpB
       digitalWrite(LED, HIGH);
@@ -1924,6 +1925,7 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
       digitalWrite(LED, LOW);
       delay(200);
       Serial.println( i * 25);
+      saveExperimentalLog("STEP_E2_media_move to chamberB " + String(i * 25) + "uL");
       }
     }
 }
@@ -1933,23 +1935,23 @@ void switchCollection(int experiment, int bag)
   if (experiment == 1 && bag == 0)
   {
     switch_conn_pin(BASEBD_J5_PIN4, LOW); //Experiment 1 waste V6
-    Serial.println("exp1 open waste bag");
-    saveExperimentalLog("exp1_opem waste bag");
+    Serial.println("E1 open waste bag");
+    saveExperimentalLog("E1_opem waste bag");
   }
   if (experiment == 1 && bag == 1)
   {
     switch_conn_pin(BASEBD_J5_PIN4, HIGH); //NOT V6
     switch_conn_pin(BASEBD_J5_PIN2, LOW); //Experiment 1 preservativeOne V5
-    Serial.println("exp1 open preservativeOne bag");
-    saveExperimentalLog("exp1_open preservativeOne bag");
+    Serial.println("E1 open preservativeOne bag");
+    saveExperimentalLog("E1_open preservativeOne bag");
   }
   if (experiment == 1 && bag == 2)
   {
     switch_conn_pin(BASEBD_J5_PIN4, HIGH); //NOT V6
     switch_conn_pin(BASEBD_J5_PIN2, HIGH); //NOT V5
     switch_conn_pin(BASEBD_J3_PIN4, LOW); ////Experiment 1 preservativeTwo V4
-    Serial.println("exp1 open preservativeTwo bag");
-    saveExperimentalLog("exp1_open preservativeTwo bag");
+    Serial.println("E1 open preservativeTwo bag");
+    saveExperimentalLog("E1_open preservativeTwo bag");
   }
   if (experiment == 1 && bag == 3)
   {
@@ -1958,7 +1960,7 @@ void switchCollection(int experiment, int bag)
     switch_conn_pin(BASEBD_J3_PIN4, HIGH); //NOT V4
     switch_conn_pin(BASEBD_J3_PIN2, LOW); //Experiment 1 preservativeThree V3
     Serial.println("open preservativeThree bag");
-    saveExperimentalLog("exp1_open preservativeThree bag");
+    saveExperimentalLog("E1_open preservativeThree bag");
   }
     if (experiment == 1 && bag == 4)
   {
@@ -1967,7 +1969,7 @@ void switchCollection(int experiment, int bag)
     switch_conn_pin(BASEBD_J3_PIN4, HIGH); //NOT V4
     switch_conn_pin(BASEBD_J3_PIN2, HIGH); //NOT V3
     switch_conn_pin(BASEBD_J1_PIN4, LOW); //Experiment 1 preservativeFour V2
-    Serial.println("open preservativeFour bag");
+    Serial.println("E1_open preservativeFour bag");
     }
 
   //experiment two collection
@@ -1975,23 +1977,23 @@ void switchCollection(int experiment, int bag)
   if (experiment == 2 && bag == 0)
   {
     switch_conn_pin(BASEBD_J2_PIN2, LOW); //Experiment 2 waste V7
-    Serial.println("exp2 open waste bag");
-    saveExperimentalLog("exp2_opem waste bag");
+    Serial.println("E2 open waste bag");
+    saveExperimentalLog("E2_opem waste bag");
   }
   if (experiment == 2 && bag == 1)
   {
     switch_conn_pin(BASEBD_J2_PIN2, HIGH); //NOT V7
     switch_conn_pin(BASEBD_J2_PIN4, LOW); //Experiment 2 preservativeOne V8
-    Serial.println("exp2 open preservativeOne bag");
-    saveExperimentalLog("exp2_open preservativeOne bag");
+    Serial.println("E2 open preservativeOne bag");
+    saveExperimentalLog("E2_open preservativeOne bag");
   }
   if (experiment == 2 && bag == 2)
   {
     switch_conn_pin(BASEBD_J2_PIN2, HIGH); //NOT V7
     switch_conn_pin(BASEBD_J2_PIN4, HIGH); //NOT V8
     switch_conn_pin(BASEBD_J4_PIN2, LOW); ////Experiment 2 preservativeTwo V9
-    Serial.println("exp2 open preservativeTwo bag");
-    saveExperimentalLog("exp2_open preservativeTwo bag");
+    Serial.println("E2 open preservativeTwo bag");
+    saveExperimentalLog("E2_open preservativeTwo bag");
   }
   if (experiment == 2 && bag == 3)
   {
@@ -1999,8 +2001,8 @@ void switchCollection(int experiment, int bag)
   switch_conn_pin(BASEBD_J2_PIN4, HIGH); //NOT V8
   switch_conn_pin(BASEBD_J4_PIN2, HIGH); //NOT V9
   switch_conn_pin(BASEBD_J4_PIN4, LOW); //Experiment 2 preservativeThree V10
-  Serial.println("open preservativeThree bag");
-  saveExperimentalLog("exp2_open preservativeThree bag");
+  Serial.println("E2_open preservativeThree bag");
+  saveExperimentalLog("E2_open preservativeThree bag");
   }
 if (experiment == 2 && bag == 4)
 {
@@ -2009,8 +2011,8 @@ if (experiment == 2 && bag == 4)
   switch_conn_pin(BASEBD_J4_PIN2, HIGH); //NOT V9
   switch_conn_pin(BASEBD_J4_PIN4, HIGH); //NOT V10
   switch_conn_pin(BASEBD_J6_PIN2, LOW); //Experiment 2 preservativeFour V11
-  Serial.println("open preservativeFour bag");
-  saveExperimentalLog("exp2_open preservativeFour bag");
+  Serial.println("E2_open preservativeFour bag");
+  saveExperimentalLog("E2_open preservativeFour bag");
 }
 }
 
diff --git a/Teensey Code/move_liquid/move_liquid.ino b/Teensey Code/move_liquid/move_liquid.ino
index d645cab..db5e48a 100644
--- a/Teensey Code/move_liquid/move_liquid.ino	
+++ b/Teensey Code/move_liquid/move_liquid.ino	
@@ -202,16 +202,58 @@ void setup() {
     
 int stop_move = 0;
 
+//CHAM A
+
+//moveLiquid (experimentOne, enzyme, chamberA, 10000);
+//moveLiquid (experimentOne, e_buffer, chamberA, 10000);
+//moveLiquid (experimentTwo, enzyme, chamberA, 10000);
+//moveLiquid (experimentTwo, e_buffer, chamberA, 10000);
+
+//CHAM B EXP 1
+
+//switchCollection(experimentOne, waste);
+//moveLiquid (experimentOne, media, chamberB, 10000);
+
+//switchCollection(experimentOne, preservativeOne);
+//moveLiquid (experimentOne, media, chamberB, 10000);
+
+//switchCollection(experimentOne, preservativeTwo);
+//moveLiquid (experimentOne, media, chamberB, 10000);
+
+
+//switchCollection(experimentOne, preservativeThree);
+//moveLiquid (experimentOne, media, chamberB, 10000);
+
+//switchCollection(experimentOne, preservativeFour);
+//moveLiquid (experimentOne, media, chamberB, 10000);
+
+//CHAM B EXP 2
+
+//switchCollection(experimentTwo, waste);
+//moveLiquid (experimentTwo, media, chamberB, 10000);
+
+//switchCollection(experimentTwo, preservativeOne);
+//moveLiquid (experimentTwo, media, chamberB, 10000);
+
+//switchCollection(experimentTwo, preservativeTwo);
+//moveLiquid (experimentTwo, media, chamberB, 10000);
+
+//switchCollection(experimentTwo, preservativeThree);
+//moveLiquid (experimentTwo, media, chamberB, 10000);
+
+switchCollection(experimentTwo, preservativeFour);
+moveLiquid (experimentTwo, media, chamberB, 10000);
 
 
 }
 
 void loop() {
+//moveLiquid (experimentTwo, enzyme, chamberA, 5000);
 
-  Serial.println("revival pumping...");
-  motorSensorBrdCtrl(1, forward);
-  delay (5000);
-  motorSensorBrdCtrl(1, halt);
+//  Serial.println("revival pumping...");
+//  motorSensorBrdCtrl(1, forward);
+//  delay (5000);
+//  motorSensorBrdCtrl(1, halt);
   
 //Experiment1 liquid system cleaning
 // moveLiquid (experimentOne, e_buffer, chamberA, 50);

From 184dd94f690fa4cc254f7e3b7d0870a205d366bc Mon Sep 17 00:00:00 2001
From: pat pataranutaporn <patpat@mit.edu>
Date: Tue, 8 Nov 2022 16:40:00 -0600
Subject: [PATCH 07/10] fix second in day

---
 .DS_Store                                     | Bin 10244 -> 10244 bytes
 Teensey Code/.DS_Store                        | Bin 12292 -> 12292 bytes
 .../MicroPET_Launch_code.ino                  |   4 ++--
 3 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.DS_Store b/.DS_Store
index 5331ff2b652fe5f238ff9d6e2ab47e151f2cc362..2b4c2bb9e0f2b2cc37160e6fcb6a7642f027ea4a 100644
GIT binary patch
delta 77
zcmZn(XbIR*EiiexU@5zyv5tbFf%#-k5!uNOLMoHZ1)s7Tn!v?2I|%tOVpV7$EV(&Z
HWT7wsPSg~t

delta 133
zcmZn(XbIR*Ex@>Aa-VRax<qxgp^1Txf~i@pjzYDep{0e6f~A>dZ7nB<sItCwP<(by
zZeD)ZWOWgF#_q|cf-gjk3`}(t41r2O>P<{cbQCO%O(u(r7;jD$(qLrV1u~Xfs=C_9
d(hR81*laSVh%93d*nr;2dcrcBlSLK^0|4;gB#r<8

diff --git a/Teensey Code/.DS_Store b/Teensey Code/.DS_Store
index 2f270885c2e85f27b6d6e08845e2146cadfe4dac..bfc9c4641d9136515d78309ef1ea70f6137b3abd 100644
GIT binary patch
delta 50
zcmZokXi3;`RbcWW<x+M-V;u!U1M|uAgk&dMtEg<AELg#}nM+{}`{eEF0h`%0HUJso
FegMT=5oG`X

delta 68
zcmZokXi3;`Re*8V<cXq%+)~xmMwVte3WmmJlLG~18G9z@3(7P0ZtfSX=G)Azu$q0c
To0#t8N9rn@*)`TfIpT@{7{L~8

diff --git a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino
index 2e311d5..7525f66 100644
--- a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
+++ b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
@@ -220,8 +220,8 @@ String experimenta_log = "";
 unsigned int whichsensor = 0;
 
 #define SECONDS_IN_DAY 86400
-//#define DELAY_SECONDS_PER_EXPERIMENT SECONDS_IN_DAY
-#define DELAY_SECONDS_PER_EXPERIMENT 120 // 2 mins for the functional testing
+#define DELAY_SECONDS_PER_EXPERIMENT SECONDS_IN_DAY
+//#define DELAY_SECONDS_PER_EXPERIMENT 120 // 2 mins for the functional testing
 #define SERIAL_TIMEOUT 10000 //milliseconds
 
 const unsigned int MAX_MESSAGE_LENGTH = 12;

From 096d593f617062790c3a8689271f3824a3b46e9f Mon Sep 17 00:00:00 2001
From: pat pataranutaporn <patpat@mit.edu>
Date: Tue, 8 Nov 2022 16:57:25 -0600
Subject: [PATCH 08/10] Clear Day Function

---
 .../MicroPET_Launch_code/MicroPET_Launch_code.ino  | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino
index 7525f66..cf87179 100644
--- a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
+++ b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
@@ -627,14 +627,12 @@ bool checkForStartSerialCommand() {
 
 void day_functionTest(){
   
-  //EXP2
-  Serial.println("EXP2 revival pumping...");
-  saveExperimentalLog("EXP2 revived");
-  switchCollection(experimentTwo, waste);//back to waste bag
-  motorSensorBrdCtrl(1, forward);
-  delay (5000); //~10ML
-  motorSensorBrdCtrl(1, halt);
-
+  /////DAYFUNCTION
+  
+  /////DAYFUNCTION
+  
+  /////DAYFUNCTION
+  
 }
 
 

From c9ac1959a5756ad39ff693e2593bfc93d29471e9 Mon Sep 17 00:00:00 2001
From: pat pataranutaporn <patpat@mit.edu>
Date: Thu, 10 Nov 2022 17:13:34 -0600
Subject: [PATCH 09/10] FINAL LOAD CODE TO GO TO SPACE

---
 Teensey Code/.DS_Store                        | Bin 12292 -> 12292 bytes
 .../MicroPET_Launch_code.ino                  |   4 ++--
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Teensey Code/.DS_Store b/Teensey Code/.DS_Store
index bfc9c4641d9136515d78309ef1ea70f6137b3abd..475e69de2a0cf2d08f323029f0c59c1e42318e1e 100644
GIT binary patch
delta 19
acmZokXi3=MEy!l6qhM%gxj9g9vm5|E>;>Tf

delta 19
acmZokXi3=MEy!l9qhM%YzBy2Evm5|Emj&1W

diff --git a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino
index cf87179..a7e4d8b 100644
--- a/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
+++ b/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino	
@@ -453,10 +453,10 @@ void rtcInit() {
     Serial.println("RTC is NOT initialized, let's set the time!");
     // When time needs to be set on a new device, or after a power loss, the
     // following line sets the RTC to the date & time this sketch was compiled
-    rtc.adjust(DateTime(F(__DATE__), F(__TIME__)));
+    //rtc.adjust(DateTime(F(__DATE__), F(__TIME__)));
     // This line sets the RTC with an explicit date & time, for example to set
     // January 21, 2014 at 3am you would call:
-    // rtc.adjust(DateTime(2014, 1, 21, 3, 0, 0));
+    // rtc.adjust(DateTime(2022, 11, 10, 2, 3, 3));
     //
     // Note: allow 2 seconds after inserting battery or applying external power
     // without battery before calling adjust(). This gives the PCF8523's

From 55dc16c6f602f80cd0abca0a220d55b8b89fc20a Mon Sep 17 00:00:00 2001
From: pat pataranutaporn <patpat@mit.edu>
Date: Sat, 1 Jul 2023 10:46:52 -0400
Subject: [PATCH 10/10] Clean up the code

---
 .DS_Store                                     |  Bin 10244 -> 8196 bytes
 Teensey Code/mux_multi_sensor.zip             |  Bin 2843 -> 0 bytes
 archive/.DS_Store                             |  Bin 0 -> 10244 bytes
 {Python => archive/Python}/.idea/.gitignore   |    0
 {Python => archive/Python}/.idea/Python.iml   |    0
 .../inspectionProfiles/profiles_settings.xml  |    0
 {Python => archive/Python}/.idea/misc.xml     |    0
 {Python => archive/Python}/.idea/modules.xml  |    0
 {Python => archive/Python}/.idea/vcs.xml      |    0
 {Python => archive/Python}/main.py            |    0
 .../Teensey Code}/.DS_Store                   |  Bin 12292 -> 12292 bytes
 .../Teensey Code}/Clock_test/Clock_test.ino   |    0
 .../MicroPET_DressRehearsal_202202/.DS_Store  |  Bin
 .../MicroPET_DressRehearsal_202202.ino        |    0
 .../MicroPET_DressRehearsal_202204/.DS_Store  |  Bin
 .../MicroPET_DressRehearsal_202204.ino        |    0
 .../MicroPET_DressRehearsal_202206/.DS_Store  |  Bin
 .../MicroPET_DressRehearsal_202206.ino        |    0
 .../MicroPET_FunctionalTest_202201.ino        |    0
 .../MicroPET_FunctionalTest_202208.ino        |    0
 .../MicroPET_Integration_20211208.ino         |    0
 .../MicroPET_Launch_code/.DS_Store            |  Bin
 .../MicroPET_Launch_code.ino                  |    0
 .../Teensy_integration_1.ino                  |    0
 .../Teensy_integration_2.ino                  |    0
 .../Teensy_sensor_debug.ino                   |    0
 .../Teensy_sensor_test/.DS_Store              |  Bin
 .../Teensy_sensor_test/Teensy_sensor_test.ino |    0
 .../Teensy_test_RTC_/Teensy_test_RTC_.ino     |    0
 .../Teensy_writing_CSV/Teensy_writing_CSV.ino |    0
 .../Teensy_writing_file.ino                   |    0
 .../Teensey Code}/Time_test/Time_test.ino     |    0
 .../Teensey Code}/Topboard/Topboard.ino       |    0
 .../Teensey Code}/move_liquid/move_liquid.ino |    0
 .../mux_multi_sensor/mux_multi_sensor.ino     |    0
 .../switch_connector_pins.ino                 |    0
 .../teensy_test_var/teensy_test_var.ino       |    0
 launch_code/.DS_Store                         |  Bin 0 -> 6148 bytes
 launch_code/launch_code.ino                   | 2284 +++++++++++++++++
 39 files changed, 2284 insertions(+)
 delete mode 100644 Teensey Code/mux_multi_sensor.zip
 create mode 100644 archive/.DS_Store
 rename {Python => archive/Python}/.idea/.gitignore (100%)
 rename {Python => archive/Python}/.idea/Python.iml (100%)
 rename {Python => archive/Python}/.idea/inspectionProfiles/profiles_settings.xml (100%)
 rename {Python => archive/Python}/.idea/misc.xml (100%)
 rename {Python => archive/Python}/.idea/modules.xml (100%)
 rename {Python => archive/Python}/.idea/vcs.xml (100%)
 rename {Python => archive/Python}/main.py (100%)
 rename {Teensey Code => archive/Teensey Code}/.DS_Store (93%)
 rename {Teensey Code => archive/Teensey Code}/Clock_test/Clock_test.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/MicroPET_DressRehearsal_202202/.DS_Store (100%)
 rename {Teensey Code => archive/Teensey Code}/MicroPET_DressRehearsal_202202/MicroPET_DressRehearsal_202202.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/MicroPET_DressRehearsal_202204/.DS_Store (100%)
 rename {Teensey Code => archive/Teensey Code}/MicroPET_DressRehearsal_202204/MicroPET_DressRehearsal_202204.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/MicroPET_DressRehearsal_202206/.DS_Store (100%)
 rename {Teensey Code => archive/Teensey Code}/MicroPET_DressRehearsal_202206/MicroPET_DressRehearsal_202206.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/MicroPET_FunctionalTest_202201/MicroPET_FunctionalTest_202201.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/MicroPET_FunctionalTest_202208/MicroPET_FunctionalTest_202208.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/MicroPET_Integration_20211208/MicroPET_Integration_20211208.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/MicroPET_Launch_code/.DS_Store (100%)
 rename {Teensey Code => archive/Teensey Code}/MicroPET_Launch_code/MicroPET_Launch_code.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/Teensy_integration_1/Teensy_integration_1.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/Teensy_integration_2/Teensy_integration_2.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/Teensy_sensor_debug/Teensy_sensor_debug.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/Teensy_sensor_test/.DS_Store (100%)
 rename {Teensey Code => archive/Teensey Code}/Teensy_sensor_test/Teensy_sensor_test.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/Teensy_test_RTC_/Teensy_test_RTC_.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/Teensy_writing_CSV/Teensy_writing_CSV.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/Teensy_writing_file/Teensy_writing_file.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/Time_test/Time_test.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/Topboard/Topboard.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/move_liquid/move_liquid.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/mux_multi_sensor/mux_multi_sensor.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/switch_connector_pins/switch_connector_pins.ino (100%)
 rename {Teensey Code => archive/Teensey Code}/teensy_test_var/teensy_test_var.ino (100%)
 create mode 100644 launch_code/.DS_Store
 create mode 100644 launch_code/launch_code.ino

diff --git a/.DS_Store b/.DS_Store
index 2b4c2bb9e0f2b2cc37160e6fcb6a7642f027ea4a..f7cfe036da6010f0ea1411424a0e4da713d86c7d 100644
GIT binary patch
delta 437
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diff --git a/Teensey Code/mux_multi_sensor.zip b/Teensey Code/mux_multi_sensor.zip
deleted file mode 100644
index 0519e974060173abafa17c73a31a76e16645e6b2..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/launch_code/launch_code.ino b/launch_code/launch_code.ino
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--- /dev/null
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@@ -0,0 +1,2284 @@
+/***************************************************************************
+  Base Board Connection:
+  E1VA + E1PA - J10
+  E1VB + E1PB - J09
+  E2VA + E2PA - J12
+  E2VB + E2PB - J11
+  the valve board connector J1-6 are the same on the base board
+
+ ***************************************************************************/
+#include <TimeLib.h>
+#include <TimeAlarms.h>
+#include <Wire.h>
+#include <SPI.h>
+#include <Adafruit_Sensor.h>
+#include <Adafruit_BME280.h>
+#include <Adafruit_AS726x.h>
+#include <Adafruit_MCP23X17.h>
+#include "RTClib.h"
+
+/* Experiment Prototypes and supporting defines */
+#define TOTAL_EXPERIMENTS 26
+void day_1();
+void day_2();
+void day_3();
+void day_4();
+void day_5();
+void day_6();
+void day_7();
+void day_8();
+void day_9();
+void day_10();
+void day_11();
+void day_12();
+void day_13();
+void day_14();
+void day_15();
+void day_16();
+void day_17();
+void day_18();
+void day_19();
+void day_20();
+void day_21();
+void day_22();
+void day_23();
+void day_24();
+void day_25();
+void day_26();
+
+void (*experimentArray[TOTAL_EXPERIMENTS])() = {day_1, day_2, day_3, day_4, day_5, day_6, day_7, day_8, day_9, day_10, day_11, day_12, day_13, day_14, day_15, day_16, day_17, day_18, day_19, day_20, day_21, day_22, day_23, day_24, day_25, day_26};
+//Teensey 4.1 - SCL 19 - yellow /SDA 18 - blue
+
+#define BME_SCK 13
+#define BME_MISO 12
+#define BME_MOSI 11
+#define BME_CS 10
+#define SEALEVELPRESSURE_HPA (1013.25)
+
+RTC_PCF8523 rtc;
+
+uint16_t experimentIndex = 0;
+
+// Native I2C address of the mux
+#define MUX_ADDR    0x70
+// Native I2C address of both AS7262 sensors
+#define AS7262_ADDR 0x49
+// Native I2C address of both BME280 sensors
+#define BME280_ADDR 0x76
+// Sensor positions on the mux
+#define AS7262_SENSOR1  3
+#define AS7262_SENSOR2  0
+#define BME280_SENSOR1  2
+#define BME280_SENSOR2  1
+
+Adafruit_BME280 bme;
+Adafruit_AS726x ams;
+
+unsigned long delayTime;
+#define SEALEVELPRESSURE_HPA (1013.25)
+uint16_t sensorValues[AS726x_NUM_CHANNELS];
+
+//SD Card
+#include <SD.h>
+#include <SPI.h>
+
+typedef struct {
+  byte experimentStarted;
+  time_t epoch;
+  byte testDay;
+  byte testDayComplete;
+  byte testInterval;
+} systemStateStruct;
+
+File myFile;
+File expLogFile;
+const int chipSelect = BUILTIN_SDCARD;
+const int ledPin = 5;
+
+systemStateStruct systemStateStructVar = {0, 0, 0, 0};
+
+//IO ports
+
+#define MCP_ADDR0 0x20  // IC5 on base board
+#define MCP_ADDR1 0x21  // IC4 on base board
+#define MCP_ADDR2 0x22  // IC1 on sensor board
+
+enum motion { forward, reverse, halt };
+#define PUMP1_A 8
+#define PUMP1_B 9
+#define PUMP2_A 10
+#define PUMP2_B 11
+#define PUMP3_A 12
+#define PUMP3_B 13
+
+#define LED 13
+
+// Double check these pin assignments
+#define GPA0 0
+#define GPA1 1
+#define GPA2 2
+#define GPA3 3
+#define GPA4 4
+#define GPA5 5
+#define GPA6 6
+#define GPA7 7
+
+#define GPB0 8
+#define GPB1 9
+#define GPB2 10
+#define GPB3 11
+#define GPB4 12
+#define GPB5 13
+#define GPB6 14
+#define GPB7 15
+
+#define experimentOne 1
+#define experimentTwo 2
+
+#define e_buffer 0
+#define enzyme 1
+#define chamberA 2
+#define media 3
+#define chamberB 4
+
+#define waste 0
+#define preservativeOne 1
+#define preservativeTwo 2
+#define preservativeThree 3
+#define preservativeFour 4
+#define preservativeFive 5
+
+
+Adafruit_MCP23X17 mcp0;
+Adafruit_MCP23X17 mcp1;
+Adafruit_MCP23X17 mcp2;
+
+typedef enum {
+  // MCP0 - IC5 on base board
+  BASEBD_J4_PIN2 = 0,
+  BASEBD_J4_PIN4,
+  BASEBD_J3_PIN2,
+  BASEBD_J3_PIN4,
+  BASEBD_J2_PIN2,
+  BASEBD_J2_PIN4,
+  BASEBD_J1_PIN2,
+  BASEBD_J1_PIN4,
+  BASEBD_J5_PIN2,
+  BASEBD_J5_PIN4,
+  BASEBD_J6_PIN2,
+  BASEBD_J6_PIN4,
+  BASEBD_J7_PIN2,
+  BASEBD_J7_PIN4,
+  BASEBD_J8_PIN2,
+  BASEBD_J8_PIN4,
+
+  // MCP1 - IC4 on base board
+  BASEBD_J12_PIN2,
+  BASEBD_J12_PIN4,
+  BASEBD_J11_PIN2,
+  BASEBD_J11_PIN4,
+  BASEBD_J10_PIN2,
+  BASEBD_J10_PIN4,
+  BASEBD_J9_PIN2,
+  BASEBD_J9_PIN4,
+
+  //MCP2 - IC1 on sensor board
+  SENSEBD_J2_PIN1,
+  SENSEBD_J2_PIN2,
+  SENSEBD_J2_PIN3,
+  SENSEBD_J2_PIN4,
+  SENSEBD_J3_PIN1,
+  SENSEBD_J3_PIN2
+} CONN_PIN_T; // Connector and Pin type
+
+#define MCP1_PIN_OFFSET 16
+#define MCP2_PIN_OFFSET 16
+
+/****************************************/
+
+boolean switch_conn_pin(CONN_PIN_T conn_pin, byte level)
+{
+  if ((level != HIGH) && (level != LOW)) {
+    return false;
+  }
+
+  if (conn_pin <= BASEBD_J8_PIN4) {
+    mcp0.digitalWrite(conn_pin, level);
+  } else if (conn_pin <= BASEBD_J9_PIN4) {
+    mcp1.digitalWrite((conn_pin - MCP1_PIN_OFFSET), level);
+  } else if (conn_pin <= SENSEBD_J3_PIN2) {
+    mcp2.digitalWrite((conn_pin - MCP2_PIN_OFFSET), level);
+  } else {
+    return false;
+  }
+
+  return true;
+}
+
+
+String experimenta_log = "";
+unsigned int whichsensor = 0;
+
+#define SECONDS_IN_DAY 86400
+#define DELAY_SECONDS_PER_EXPERIMENT SECONDS_IN_DAY
+//#define DELAY_SECONDS_PER_EXPERIMENT 120 // 2 mins for the functional testing
+#define SERIAL_TIMEOUT 10000 //milliseconds
+
+const unsigned int MAX_MESSAGE_LENGTH = 12;
+bool systemState = 0;
+
+//AlarmID_t Alarm_Day1_ID;
+//AlarmID_t Alarm_Day2_ID;
+//AlarmID_t Alarm_Day3_ID;
+//AlarmID_t Alarm_Day4_ID;
+//AlarmID_t Alarm_Day5_ID;
+//AlarmID_t Alarm_Day6_ID;
+//AlarmID_t Alarm_Day7_ID;
+//AlarmID_t Alarm_Day8_ID;
+//AlarmID_t Alarm_Day9_ID;
+
+// Function to select a sensor
+void tcaselect(uint8_t sensor_addr) {
+  Wire.beginTransmission(MUX_ADDR);
+  Wire.write(1 << sensor_addr);
+  Wire.endTransmission();
+}
+
+void setup() {
+  pinMode(3, OUTPUT);
+  pinMode(4, OUTPUT);
+  pinMode(ledPin, OUTPUT);
+
+  Serial.begin(9600);
+
+  long unsigned startup_time = millis();
+  // the below code waits for a serial monitor session to be opened
+  // but times out in SERIAL_TIMEOUT milliseconds if none exist
+  while (!Serial) {
+    // timeout check
+    if ( (millis() - startup_time) > SERIAL_TIMEOUT) {
+      break;
+    }
+  }
+
+  Serial.println(F("Begin Serial"));
+
+  init_card();
+  initExpLogFile();
+  rtcInit();
+
+  pinMode(LED, OUTPUT);
+  // uncomment appropriate mcp.begin
+  if (!mcp0.begin_I2C(MCP_ADDR0)) {
+    Serial.println("Error initializing chip 0.");
+    // while (1);
+  }
+
+  if (!mcp1.begin_I2C(MCP_ADDR1)) {
+    Serial.println("Error initializing chip 1.");
+    // while (1);
+  }
+
+  // IC5 on base board
+  mcp0.pinMode(GPA0, OUTPUT);
+  mcp0.pinMode(GPA1, OUTPUT);
+  mcp0.pinMode(GPA2, OUTPUT);
+  mcp0.pinMode(GPA3, OUTPUT);
+  mcp0.pinMode(GPA4, OUTPUT);
+  mcp0.pinMode(GPA5, OUTPUT);
+  mcp0.pinMode(GPA6, OUTPUT);
+  mcp0.pinMode(GPA7, OUTPUT);
+
+  mcp0.pinMode(GPB0, OUTPUT);
+  mcp0.pinMode(GPB1, OUTPUT);
+  mcp0.pinMode(GPB2, OUTPUT);
+  mcp0.pinMode(GPB3, OUTPUT);
+  mcp0.pinMode(GPB4, OUTPUT);
+  mcp0.pinMode(GPB5, OUTPUT);
+  mcp0.pinMode(GPB6, OUTPUT);
+  mcp0.pinMode(GPB7, OUTPUT);
+
+  // IC4 on base board
+  mcp1.pinMode(GPA0, OUTPUT);
+  mcp1.pinMode(GPA1, OUTPUT);
+  mcp1.pinMode(GPA2, OUTPUT);
+  mcp1.pinMode(GPA3, OUTPUT);
+  mcp1.pinMode(GPA4, OUTPUT);
+  mcp1.pinMode(GPA5, OUTPUT);
+  mcp1.pinMode(GPA6, OUTPUT);
+  mcp1.pinMode(GPA7, OUTPUT);
+
+  //Revial
+
+    if (!mcp2.begin_I2C(MCP_ADDR2)) {
+     Serial.println("Error initializing chip 2.");
+  //   while (1);
+   }
+  Serial.println("setup revival pumping...");
+  mcp2.pinMode(PUMP1_A, OUTPUT);
+  mcp2.pinMode(PUMP1_B, OUTPUT);
+//    mcp.pinMode(PUMP2_A, OUTPUT);
+//    mcp.pinMode(PUMP2_B, OUTPUT);
+  mcp2.pinMode(PUMP3_A, OUTPUT);
+  mcp2.pinMode(PUMP3_B, OUTPUT);
+
+  // halt both motors upon initialization
+
+  motorSensorBrdCtrl(1, halt);
+  motorSensorBrdCtrl(3, halt);
+  Serial.println("revival pumping halted");
+
+
+// Set up the sensors
+  unsigned bme_status;
+  unsigned ams_status;
+
+  //Start the sensors line 1
+  tcaselect(BME280_SENSOR1);
+  delay(1000);
+  // start the sensor
+  bme_status = bme.begin();
+  ams_status = ams.begin();
+  delay(1000);
+
+    if(!ams_status){
+        Serial.println("could not connect to AS726x sensor1, Please check your wiring.");
+     //   while(1); delay(10);
+    }
+
+    if (!bme_status) {
+        Serial.println("Could not find a valid BME280 sensor1, check wiring, address, sensor ID!");
+     //   while (1) delay(10);
+    }
+
+  //Start the sensors line　2
+  tcaselect(BME280_SENSOR2);
+  delay(1000);
+  // start the sensor
+  bme_status = bme.begin();
+  ams_status = ams.begin();
+  delay(1000);
+
+    if(!ams_status){
+        Serial.println("could not connect to AS726x sensor2, Please check your wiring.");
+     //   while(1); delay(10);
+    }
+
+    if (!bme_status) {
+        Serial.println("Could not find a valid BME280 sensor2, check wiring, address, sensor ID!");
+     //   while (1) delay(10);
+    }
+
+
+    Serial.println("-- Default Test --");
+    delayTime = 1000;
+
+    Serial.println();
+
+    // EXPERIMENTAL SETUP
+
+    //STARTING DATE
+//    setTime(11,0,0,12,2,2022);  // hr,min,sec,day,mnth,yr
+    Serial.println("Setting time from RTC");
+    setTime(rtc.now().unixtime()); //sets time from RTC
+    Serial.print("Time is now: ");
+    Serial.println(now());
+
+    if(!grabStateFromSD(&systemStateStructVar)){
+        Serial.println("No log file exists so will create one!");
+        // no prior state exists so saving a new file with current rtc time
+        systemStateStructVar.experimentStarted = 0;
+        systemStateStructVar.epoch = rtc.now().unixtime();
+        saveStateToSD(&systemStateStructVar);
+    }
+    else if(systemStateStructVar.experimentStarted==0){
+      Serial.println("Previous log file exists but experiment hasn't started!");
+      // if a file exists and shows no prior experiment has started, update time
+        systemStateStructVar.experimentStarted = 0;
+        systemStateStructVar.epoch = rtc.now().unixtime();
+        saveStateToSD(&systemStateStructVar);
+    }
+    else if (systemStateStructVar.experimentStarted==1){
+      Serial.println("Power Failure Event Detected!");
+      // log file has shown that experiment has started already
+      // todo: implement schedule correction
+      systemState = true;
+      recoverSystemStart();
+    }
+
+    Serial.println("Start Looping...");
+
+  // EVERYDAY TASK
+  Alarm.timerRepeat(60, Taking_Sensor_Data);
+
+
+}
+
+
+//  for(int i = 1+systemStateStructVar.testDay; i<TOTAL_EXPERIMENTS; i++){
+//    Alarm.timerOnce(timeRemaining + inc*DELAY_SECONDS_PER_EXPERIMENT,(*experimentArray[i]));
+//    inc++;
+//  }
+
+void loop() {
+
+  //  digitalClockDisplay();
+  Alarm.delay(1000);
+
+  // if system has not already started, check for start condition via serial
+  if (!systemState && checkForStartSerialCommand()) {
+
+    // system has been commanded to start
+    day_1();
+
+    // set system state
+    systemState = true;
+  }
+}
+
+void rtcInit() {
+  if (! rtc.begin()) {
+    Serial.println("Couldn't find RTC");
+    Serial.flush();
+  }
+  else {
+    Serial.println("Found RTC");
+
+    // following line sets the RTC to the date & time this sketch was compiled
+    // Uncomment it when setting up the first time/change battery
+    //rtc.adjust(DateTime(F(__DATE__), F(__TIME__)));
+  }
+
+  if (! rtc.initialized() || rtc.lostPower()) {
+    Serial.println("RTC is NOT initialized, let's set the time!");
+    // When time needs to be set on a new device, or after a power loss, the
+    // following line sets the RTC to the date & time this sketch was compiled
+    //rtc.adjust(DateTime(F(__DATE__), F(__TIME__)));
+    // This line sets the RTC with an explicit date & time, for example to set
+    // January 21, 2014 at 3am you would call:
+    // rtc.adjust(DateTime(2022, 11, 10, 2, 3, 3));
+    //
+    // Note: allow 2 seconds after inserting battery or applying external power
+    // without battery before calling adjust(). This gives the PCF8523's
+    // crystal oscillator time to stabilize. If you call adjust() very quickly
+    // after the RTC is powered, lostPower() may still return true.
+  }
+
+  // When the RTC was stopped and stays connected to the battery, it has
+  // to be restarted by clearing the STOP bit. Let's do this to ensure
+  // the RTC is running.
+  rtc.start();
+
+  // The PCF8523 can be calibrated for:
+  //        - Aging adjustment
+  //        - Temperature compensation
+  //        - Accuracy tuning
+  // The offset mode to use, once every two hours or once every minute.
+  // The offset Offset value from -64 to +63. See the Application Note for calculation of offset values.
+  // https://www.nxp.com/docs/en/application-note/AN11247.pdf
+  // The deviation in parts per million can be calculated over a period of observation. Both the drift (which can be negative)
+  // and the observation period must be in seconds. For accuracy the variation should be observed over about 1 week.
+  // Note: any previous calibration should cancelled prior to any new observation period.
+  // Example - RTC gaining 43 seconds in 1 week
+  float drift = 43; // seconds plus or minus over oservation period - set to 0 to cancel previous calibration.
+  float period_sec = (7 * 86400);  // total obsevation period in seconds (86400 = seconds in 1 day:  7 days = (7 * 86400) seconds )
+  float deviation_ppm = (drift / period_sec * 1000000); //  deviation in parts per million (μs)
+  float drift_unit = 4.34; // use with offset mode PCF8523_TwoHours
+  // float drift_unit = 4.069; //For corrections every min the drift_unit is 4.069 ppm (use with offset mode PCF8523_OneMinute)
+  int offset = round(deviation_ppm / drift_unit);
+  rtc.calibrate(PCF8523_TwoHours, offset); // Un-comment to perform calibration once drift (seconds) and observation period (seconds) are correct
+  // rtc.calibrate(PCF8523_TwoHours, 0); // Un-comment to cancel previous calibration
+}
+
+//typedef union {
+//   systemStateStruct state;
+//   byte bytes [sizeof(systemStateStruct)];
+//}systemStateUnion;
+
+bool grabStateFromSD(systemStateStruct* input) {
+  if (SD.exists("logFile.txt")) {
+    File logFile = SD.open("logFile.txt", FILE_READ);
+    logFile.read((uint8_t *)input, sizeof(systemStateStruct));
+    logFile.close();
+    return true;
+  }
+  else {
+    return false;
+  }
+}
+
+void saveStateToSD(systemStateStruct* input) {
+  File logFile = SD.open("logFile.txt", FILE_WRITE);
+  logFile.seek(0); // overwrite existing file
+  logFile.write((uint8_t *)input, sizeof(systemStateStruct));
+  logFile.close();
+}
+
+/* Function for resuming system after unscheduled power loss */
+
+void recoverSystemStart(){
+
+  /* (1) check for hard faults */
+  //  (1.1) if system failed during an experiment, generate fault
+  if(systemStateStructVar.testDayComplete != 1){
+    Serial.print("System was interrupted during experiment: ");
+    Serial.println(systemStateStructVar.testDay);
+    saveExperimentalLog("System was interrupted during experiment: " + String(systemStateStructVar.testDay));
+
+    if(systemStateStructVar.testDay == 1){
+      Serial.print("Restarting entire experiment since lost power on day 1");
+      saveExperimentalLog("Restarting entire experiment since lost power on day 1");
+      day_1();
+      systemState = true;
+      return;
+    }
+  }
+
+  //  (1.2) if system paused for longer than test day interval, generate fault
+  uint32_t timeSinceLastExperiment = rtc.now().unixtime() - systemStateStructVar.epoch;
+  uint16_t skipDays;
+  if(timeSinceLastExperiment >= DELAY_SECONDS_PER_EXPERIMENT){
+    Serial.println("System was off for longer than experiment interval!");
+
+    skipDays = int( timeSinceLastExperiment / DELAY_SECONDS_PER_EXPERIMENT );
+    for(int i = 0; i < skipDays; i++){
+      systemStateStructVar.testDay++;
+      Serial.print(" Skipping day: ");
+      Serial.println(systemStateStructVar.testDay);
+
+      saveExperimentalLog(" Skipping day: " + String(systemStateStructVar.testDay));
+    }
+  }
+
+  timeSinceLastExperiment = int( timeSinceLastExperiment % DELAY_SECONDS_PER_EXPERIMENT );
+  //  (1.3) check if tests had already ended
+  if(systemStateStructVar.testDay == TOTAL_EXPERIMENTS - 1){
+    Serial.println("Power failure occured after experiment finished! No reason to resume!");
+
+    saveExperimentalLog("Power failure occured after experiment finished! No reason to resume!");
+
+    while(1);
+    return;
+  }
+
+  /* (2) setup timers */
+  uint32_t timeRemaining = DELAY_SECONDS_PER_EXPERIMENT - timeSinceLastExperiment;
+  experimentIndex = systemStateStructVar.testDay;
+  Alarm.timerOnce(timeRemaining,(*experimentArray[experimentIndex]));
+
+//  uint16_t inc = 0;
+//  for(int i = 1+systemStateStructVar.testDay; i<TOTAL_EXPERIMENTS; i++){
+//    Alarm.timerOnce(timeRemaining + inc*DELAY_SECONDS_PER_EXPERIMENT,(*experimentArray[i]));
+//    inc++;
+//  }
+
+  Serial.println("System has recovered gracefully!");
+
+  systemState = true;
+}
+
+
+bool checkForStartSerialCommand() {
+  bool startCondition = false;
+  while (Serial.available() > 0) {
+    //Create a place to hold the incoming message
+    static char message[MAX_MESSAGE_LENGTH];
+    static unsigned int message_pos = 0;
+
+    //Read the next available byte in the serial receive buffer
+    char inByte = Serial.read();
+    //Message coming in (check not terminating character) and guard for over message size
+    if ( inByte != '\n' && (message_pos < MAX_MESSAGE_LENGTH - 1) )
+    {
+      //Add the incoming byte to our message
+      message[message_pos] = inByte;
+      message_pos++;
+    }
+    //Full message received...
+    else
+    {
+      //Add null character to string
+      message[message_pos] = '\0';
+
+      if (strcmp(message, "START") == 0) {
+        startCondition = true;
+
+        //Print the message (or do other things)
+        Serial.println("Start Message Received");
+      }
+
+
+      if (strcmp(message, "TEST") == 0) {
+        //Print the message (or do other things)
+        Serial.println("Executing Test Script");
+
+
+
+        day_functionTest();
+      }
+
+      //Reset for the next message
+      message_pos = 0;
+    }
+  }
+
+  return startCondition;
+}
+
+void day_functionTest(){
+  
+  /////DAYFUNCTION
+  
+  /////DAYFUNCTION
+  
+  /////DAYFUNCTION
+  
+}
+
+
+void day_1() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+//==================================================
+//==================================================
+//==================================================
+//==================================================
+//==================================================
+// =============== UPDATE STATUS ===================
+  systemState = 1;
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 1;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 1");
+  saveExperimentalLog("Executing Day 1");
+
+
+ // =============== ENZYME EXP =====================
+
+  //DUMMY CODE
+  moveLiquid (experimentOne, e_buffer, chamberA, 1000);  //buffer to chamber A - 1 ml (flexible)
+  moveLiquid (experimentTwo, e_buffer, chamberA, 1000);  //buffer to chamber A - 1 ml (flexible)
+  Serial.println("finish the dummy code...");
+  saveExperimentalLog("Finish dummy code!");
+
+  //EXP1 - liquid in dummy code
+  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentOne, e_buffer, chamberA, 1525);  //buffer to chamber A - 1.525 ml (flexible)
+  //EXP2 - liquid in dummy code
+  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentTwo, e_buffer, chamberA, 1525);  //buffer to chamber A - 1.525 ml (flexible)
+
+
+ // =============== MICROBE EXP =====================
+
+  //EXP1
+  Serial.println("EXP1 revival pumping...");
+  saveExperimentalLog("EXP1 revived");
+  switchCollection(experimentOne, waste);//back to waste bag
+  motorSensorBrdCtrl(1, forward);
+  delay (5000); //~10ML
+  motorSensorBrdCtrl(1, halt);
+
+  //EXP2
+  Serial.println("EXP2 revival pumping...");
+  saveExperimentalLog("EXP2 revived");
+  switchCollection(experimentTwo, waste);//back to waste bag
+  motorSensorBrdCtrl(3, forward);
+  delay (5000); //~10ML
+  motorSensorBrdCtrl(3, halt);
+
+
+ // =============== UPDATE STATUS ===================
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 1 Finishes");
+  saveExperimentalLog("Day 1 Finishes");
+}
+
+void day_2() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 2;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 1");
+  saveExperimentalLog("Executing Day 1");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 2 Finishes");
+  saveExperimentalLog("Day 2 Finishes");
+
+
+
+}
+
+void day_3() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 3;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 3");
+  saveExperimentalLog("Executing Day 3");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+   Serial.println("Day 3 Finishes");
+  saveExperimentalLog("Day 3 Finishes");
+
+
+
+}
+
+void day_4() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 4;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 4");
+  saveExperimentalLog("Executing Day 4");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+  //EXP1
+  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentOne, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
+  //EXP2
+  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentTwo, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
+
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 4 Finishes");
+  saveExperimentalLog("Day 4 Finishes");
+
+
+}
+
+void day_5() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 5;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 5");
+  saveExperimentalLog("Executing Day 5");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 5 Finishes");
+  saveExperimentalLog("Day 5 Finishes");
+
+
+}
+
+void day_6() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 6;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 6");
+  saveExperimentalLog("Executing Day 6");
+
+
+ // =============== MICROBE EXP =====================
+
+ //EXP1
+  switchCollection(experimentOne, preservativeOne);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentOne, media, chamberB, 5000);//move medium to chamber B - 6ml
+  switchCollection(experimentOne, waste);//back to waste bag
+
+ //EXP2
+  switchCollection(experimentTwo, preservativeOne);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentTwo, media, chamberB, 5000);//move medium to chamber B - 6ml
+  switchCollection(experimentTwo, waste);//back to waste bag
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 6 Finishes");
+  saveExperimentalLog("Day 6 Finishes");
+
+
+}
+
+void day_7() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 7;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 7");
+  saveExperimentalLog("Executing Day 7");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ //EXP1
+  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentOne, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.525 ml (flexible)
+  //EXP2
+  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentTwo, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.525 ml (flexible)
+
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 7 Finishes");
+  saveExperimentalLog("Day 7 Finishes");
+
+
+}
+
+void day_8() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 8;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 8");
+  saveExperimentalLog("Executing Day 8");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 8 Finishes");
+  saveExperimentalLog("Day 8 Finishes");
+
+
+}
+
+void day_9() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 9;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 9");
+  saveExperimentalLog("Executing Day 9");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 9 Finishes");
+  saveExperimentalLog("Day 9 Finishes");
+
+
+}
+
+void day_10() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 10;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 10");
+  saveExperimentalLog("Executing Day 10");
+
+
+ // =============== MICROBE EXP =====================
+
+ //EXP1
+  switchCollection(experimentOne, preservativeOne);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentOne, media, chamberB, 5000);//move medium to chamber B - 6ml
+  Serial.println("Exp1_SDS collection");
+  saveExperimentalLog("Exp1_SDS collection");
+
+  switchCollection(experimentOne, preservativeFour);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentOne, media, chamberB, 10000);//move medium to chamber B - 6ml
+  switchCollection(experimentOne, waste);//back to waste bag
+
+
+
+ //EXP2
+  switchCollection(experimentTwo, preservativeOne);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentTwo, media, chamberB, 5000);//move medium to chamber B - 6ml
+  Serial.println("Exp2_SDS collection");
+  saveExperimentalLog("Exp2_SDS collection");
+
+  switchCollection(experimentTwo, preservativeFour);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentTwo, media, chamberB, 10000);//move medium to chamber B - 6ml
+  switchCollection(experimentTwo, waste);//back to waste bag
+
+
+ // =============== ENZYME EXP =====================
+
+ //EXP1
+  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentOne, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.525 ml (flexible)
+  //EXP2
+  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentTwo, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.525 ml (flexible)
+
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 10 Finishes");
+  saveExperimentalLog("Day 10 Finishes");
+
+
+}
+
+void day_11() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 11;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 11");
+  saveExperimentalLog("Executing Day 11");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 11 Finishes");
+  saveExperimentalLog("Day 11 Finishes");
+
+
+}
+
+void day_12() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 12;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 12");
+  saveExperimentalLog("Executing Day 12");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 12 Finishes");
+  saveExperimentalLog("Day 12 Finishes");
+
+
+}
+
+void day_13() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 13;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 13");
+  saveExperimentalLog("Executing Day 13");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ //EXP1
+  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentOne, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.525 ml (flexible)
+  //EXP2
+  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentTwo, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.525 ml (flexible)
+
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 13 Finishes");
+  saveExperimentalLog("Day 13 Finishes");
+
+
+}
+
+void day_14() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 14;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 14");
+  saveExperimentalLog("Executing Day 14");
+
+
+ // =============== MICROBE EXP =====================
+
+ //EXP1
+  switchCollection(experimentOne, preservativeTwo);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentOne, media, chamberB, 5000);//move medium to chamber B - 6ml
+  switchCollection(experimentOne, waste);//back to waste bag
+
+ //EXP2
+  switchCollection(experimentTwo, preservativeTwo);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentTwo, media, chamberB, 5000);//move medium to chamber B - 6ml
+  switchCollection(experimentTwo, waste);//back to waste bag
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 14 Finishes");
+  saveExperimentalLog("Day 14 Finishes");
+
+
+}
+
+void day_15() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 15;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 15");
+  saveExperimentalLog("Executing Day 15");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 15 Finishes");
+  saveExperimentalLog("Day 15 Finishes");
+
+
+}
+
+void day_16() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 16;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 16");
+  saveExperimentalLog("Executing Day 16");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ //EXP1
+  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentOne, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
+  //EXP2
+  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentTwo, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
+
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 16 Finishes");
+  saveExperimentalLog("Day 16 Finishes");
+
+
+}
+
+void day_17() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 17;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 17");
+  saveExperimentalLog("Executing Day 17");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 17 Finishes");
+  saveExperimentalLog("Day 17 Finishes");
+
+
+}
+
+void day_18() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 18;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 18");
+  saveExperimentalLog("Executing Day 18");
+
+
+ // =============== MICROBE EXP =====================
+
+ //EXP1
+  switchCollection(experimentOne, preservativeTwo);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentOne, media, chamberB, 5000);//move medium to chamber B - 6ml
+  switchCollection(experimentOne, waste);//back to waste bag
+
+ //EXP2
+  switchCollection(experimentTwo, preservativeTwo);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentTwo, media, chamberB, 5000);//move medium to chamber B - 6ml
+  switchCollection(experimentTwo, waste);//back to waste bag
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 18 Finishes");
+  saveExperimentalLog("Day 18 Finishes");
+
+
+}
+
+void day_19() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 19;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 19");
+  saveExperimentalLog("Executing Day 19");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ //EXP1
+  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentOne, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
+  //EXP2
+  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentTwo, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
+
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 19 Finishes");
+  saveExperimentalLog("Day 19 Finishes");
+
+
+}
+
+void day_20() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 20;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 20");
+  saveExperimentalLog("Executing Day 20");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 20 Finishes");
+  saveExperimentalLog("Day 20 Finishes");
+
+
+}
+
+void day_21() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 21;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 21");
+  saveExperimentalLog("Executing Day 21");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 21 Finishes");
+  saveExperimentalLog("Day 21 Finishes");
+
+
+}
+
+void day_22() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 22;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 22");
+  saveExperimentalLog("Executing Day 22");
+
+
+ // =============== MICROBE EXP =====================
+
+ //EXP1
+  switchCollection(experimentOne, preservativeThree);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentOne, media, chamberB, 5000);//move medium to chamber B - 6ml
+  switchCollection(experimentOne, waste);//back to waste bag
+
+ //EXP2
+  switchCollection(experimentTwo, preservativeThree);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentTwo, media, chamberB, 5000);//move medium to chamber B - 6ml
+  switchCollection(experimentTwo, waste);//back to waste bag
+
+
+ // =============== ENZYME EXP =====================
+
+ //EXP1
+  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentOne, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
+  //EXP2
+  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentTwo, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
+
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 22 Finishes");
+  saveExperimentalLog("Day 22 Finishes");
+
+
+}
+
+void day_23() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 23;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 23");
+  saveExperimentalLog("Executing Day 23");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 23 Finishes");
+  saveExperimentalLog("Day 23 Finishes");
+
+
+}
+
+void day_24() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 24;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 24");
+  saveExperimentalLog("Executing Day 24");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 24 Finishes");
+  saveExperimentalLog("Day 24 Finishes");
+
+
+}
+
+void day_25() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 25;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 25");
+  saveExperimentalLog("Executing Day 25");
+
+
+ // =============== MICROBE EXP =====================
+
+ // DO NOTHING
+
+ // =============== ENZYME EXP =====================
+
+ //EXP1
+  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentOne, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
+  //EXP2
+  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentTwo, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
+
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 25 Finishes");
+  saveExperimentalLog("Day 25 Finishes");
+
+
+}
+
+void day_26() {
+  // =============== SET == NEXT == ALARM ============ 
+  setNextAlarm();
+
+
+// =============== UPDATE === STATUS ===============
+
+  systemStateStructVar.experimentStarted = 1;
+  systemStateStructVar.epoch = rtc.now().unixtime();
+  systemStateStructVar.testDay = 26;
+  systemStateStructVar.testInterval = 1;
+  systemStateStructVar.testDayComplete = 0;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Executing Day 26");
+  saveExperimentalLog("Executing Day 26");
+
+
+ // =============== MICROBE EXP =====================
+
+ //EXP1
+  switchCollection(experimentOne, preservativeThree);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentOne, media, chamberB, 5000);//move medium to chamber B - 6ml
+  switchCollection(experimentOne, waste);//back to waste bag
+
+ //EXP2
+  switchCollection(experimentTwo, preservativeThree);//Open valve to preservative MRNA1 - with BKA
+  moveLiquid (experimentTwo, media, chamberB, 5000);//move medium to chamber B - 6ml
+  switchCollection(experimentTwo, waste);//back to waste bag
+
+
+ // =============== ENZYME EXP =====================
+
+ // DO NOTHING
+
+ // =============== UPDATE === STATUS ===============
+
+
+  systemStateStructVar.testDayComplete = 1;
+  saveStateToSD(&systemStateStructVar);
+
+  Serial.println("Day 26 Finishes");
+  saveExperimentalLog("Day 26 Finishes");
+
+
+}
+
+
+void setNextAlarm(){
+  experimentIndex++;
+  if(experimentIndex < TOTAL_EXPERIMENTS){
+    Alarm.timerOnce(DELAY_SECONDS_PER_EXPERIMENT, (*experimentArray[experimentIndex]));
+  }
+}
+
+
+void moveLiquid(int experiment, int origin, int target, float liquid_volume)
+{
+   //experiment ONE_Enyzme Part
+
+  if (experiment == 1 && origin == 0)
+  {
+    switch_conn_pin(BASEBD_J10_PIN2, LOW); //Experiment 1 valveA
+    Serial.println("E1_exp1 move from e_buffer");
+    saveExperimentalLog("E1_move from e_buffer");
+  }
+
+  if (experiment == 1 && origin == 1)
+  {
+    switch_conn_pin(BASEBD_J10_PIN2, HIGH); //Experiment 1 valveA
+    Serial.println("E1 move from enzyme");
+    saveExperimentalLog("E1_move from enzyme");
+  }
+
+  if (experiment == 1 && target == 2)
+  {
+    switch_conn_pin(BASEBD_J9_PIN2, HIGH); //Experiment 1 valveB high, waste line open
+    int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 25uL at a time
+    Serial.println("move to chamberA");
+    saveExperimentalLog("E1_move to chamberA" + String(move_pulse * 25) + "uL");
+    for (int i = 0; i <= move_pulse; i++) {
+      switch_conn_pin(BASEBD_J10_PIN4, HIGH); //Experiment 1 pumpA
+      digitalWrite(LED, HIGH);
+      delay(200);
+      switch_conn_pin(BASEBD_J10_PIN4, LOW); //Experiment 1 pumpA
+      digitalWrite(LED, LOW);
+      delay(200);
+      Serial.println( i * 25); //print out the moving volume
+      saveExperimentalLog("STEP_exp1_move to chamberA" + String(i * 25) + "uL");
+    }
+    switch_conn_pin(BASEBD_J10_PIN2, LOW); //Reset eperiment 1 valveA so enzyme is blocked
+  }
+  /* Uncomment and edit line above switch_conn_pin(BASEBD_J9_PIN2, HIGH); to LOW
+ if we want to control chamberA and waste flow
+  if (experiment == 1 && target == 0)
+  {
+    switch_conn_pin(BASEBD_J9_PIN2, HIGH); //Experiment 2 valveB high, go to waste
+    int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 25uL at a time
+    Serial.println("move to waste");
+    saveExperimentalLog("_move to waste " + move_pulse * 25 + "uL");
+    for (int i = 0; i <= move_pulse; i++) {
+      switch_conn_pin(BASEBD_J10_PIN4, HIGH); //Experiment 2 pumpA
+      digitalWrite(LED, HIGH);
+      delay(200);
+      switch_conn_pin(BASEBD_J10_PIN4, LOW); //Experiment 2 pumpA
+      digitalWrite(LED, LOW);
+      delay(200);
+      Serial.println( i * 25);
+    }
+    switch_conn_pin(BASEBD_J10_PIN2, LOW); //Reset experiment 2 valveA so enzyme is blocked
+  }
+*/
+
+//experiment One_BioCell Part
+
+  if (experiment == 1 && origin == 3 && target == 4)
+  {
+    int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 25uL at a time
+    Serial.println("E1 move to chamberB");
+    saveExperimentalLog("E1_move to chamberB " + String(move_pulse * 25) + "uL");
+    for (int i = 0; i <= move_pulse; i++) {
+      switch_conn_pin(BASEBD_J9_PIN4, HIGH); //Experiment 1 pumpB
+      digitalWrite(LED, HIGH);
+      delay(200);
+      switch_conn_pin(BASEBD_J9_PIN4, LOW); //Experiment 1 pumpB
+      digitalWrite(LED, LOW);
+      delay(200);
+      Serial.println( i * 25); //print out the moving volume
+      saveExperimentalLog("STEP_E1_move to chamberB " + String(i * 25) + "uL");
+    }
+  //  switch_conn_pin(BASEBD_J9_PIN2, LOW); //Reset experiment 1 valveB so chamberA is blocked
+  }
+
+  //experimentTWO, Enzyme
+
+  if (experiment == 2 && origin == 0)
+  {
+    switch_conn_pin(BASEBD_J12_PIN2, LOW); //Experiment 2 valveA
+    Serial.println("E2 move from e_buffer");
+    saveExperimentalLog("E2_move from e_buffer");
+  }
+
+  if (experiment == 2 && origin == 1)
+  {
+    switch_conn_pin(BASEBD_J12_PIN2, HIGH); //Experiment 2 valveA
+    saveExperimentalLog("E2_move from enzyme");
+    Serial.println("E2 move from Enzyme");
+  }
+
+  if (experiment == 2 && target == 2)
+  {
+    switch_conn_pin(BASEBD_J11_PIN2, HIGH); //Experiment 2 valveB high, waste line open
+    int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 25uL at a time
+    Serial.println("E2 move to chamberA");
+    saveExperimentalLog("E2_move to chamberA " + String(move_pulse * 25) + "uL");
+    for (int i = 0; i <= move_pulse; i++) {
+      switch_conn_pin(BASEBD_J12_PIN4, HIGH); //Experiment 2 pumpA
+      digitalWrite(LED, HIGH);
+      delay(200);
+      switch_conn_pin(BASEBD_J12_PIN4, LOW); //Experiment 2 pumpA
+      digitalWrite(LED, LOW);
+      delay(200);
+      Serial.println( i * 25);
+      saveExperimentalLog("STEP_E2_move to chamberA " + String(i * 25) + "uL");
+    }
+    switch_conn_pin(BASEBD_J12_PIN2, LOW); //Reset xperiment 1 valveA so enzyme is blocked
+  }
+
+  /* Uncomment and edit line above switch_conn_pin(BASEBD_J11_PIN2, HIGH); to LOW
+  if we want to control chamberA and waste flow
+    if (experiment == 2 && target == 0)
+    {
+      switch_conn_pin(BASEBD_J11_PIN2, HIGH); //Experiment 2 valveB high, go to waste
+      int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 25uL at a time
+      Serial.println("move to waste");
+      saveExperimentalLog("_move to waste " + move_pulse * 25 + "uL");
+      for (int i = 0; i <= move_pulse; i++) {
+        switch_conn_pin(BASEBD_J12_PIN4, HIGH); //Experiment 2 pumpA
+        digitalWrite(LED, HIGH);
+        delay(200);
+        switch_conn_pin(BASEBD_J12_PIN4, LOW); //Experiment 2 pumpA
+        digitalWrite(LED, LOW);
+        delay(200);
+        Serial.println( i * 25);
+      }
+      switch_conn_pin(BASEBD_J12_PIN2, LOW); //Reset xperiment 2 valveA so enzyme is blocked
+    }
+  */
+
+  //experimentTWO, Microbe
+
+  if (experiment == 2 && origin == 3 && target == 4)
+   {
+      int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 35uL at a time
+      Serial.println("E2 media move to chamberB");
+      saveExperimentalLog("E2_media_move to chamberB " + String(move_pulse * 25) + "uL");
+      for (int i = 0; i <= move_pulse; i++){
+      switch_conn_pin(BASEBD_J11_PIN4, HIGH); //Experiment 2 pumpB
+      digitalWrite(LED, HIGH);
+      delay(200);
+      switch_conn_pin(BASEBD_J11_PIN4, LOW); //Experiment 2 pumpB
+      digitalWrite(LED, LOW);
+      delay(200);
+      Serial.println( i * 25);
+      saveExperimentalLog("STEP_E2_media_move to chamberB " + String(i * 25) + "uL");
+      }
+    }
+}
+
+void switchCollection(int experiment, int bag)
+{
+  if (experiment == 1 && bag == 0)
+  {
+    switch_conn_pin(BASEBD_J5_PIN4, LOW); //Experiment 1 waste V6
+    Serial.println("E1 open waste bag");
+    saveExperimentalLog("E1_opem waste bag");
+  }
+  if (experiment == 1 && bag == 1)
+  {
+    switch_conn_pin(BASEBD_J5_PIN4, HIGH); //NOT V6
+    switch_conn_pin(BASEBD_J5_PIN2, LOW); //Experiment 1 preservativeOne V5
+    Serial.println("E1 open preservativeOne bag");
+    saveExperimentalLog("E1_open preservativeOne bag");
+  }
+  if (experiment == 1 && bag == 2)
+  {
+    switch_conn_pin(BASEBD_J5_PIN4, HIGH); //NOT V6
+    switch_conn_pin(BASEBD_J5_PIN2, HIGH); //NOT V5
+    switch_conn_pin(BASEBD_J3_PIN4, LOW); ////Experiment 1 preservativeTwo V4
+    Serial.println("E1 open preservativeTwo bag");
+    saveExperimentalLog("E1_open preservativeTwo bag");
+  }
+  if (experiment == 1 && bag == 3)
+  {
+    switch_conn_pin(BASEBD_J5_PIN4, HIGH); //NOT V6
+    switch_conn_pin(BASEBD_J5_PIN2, HIGH); //NOT V5
+    switch_conn_pin(BASEBD_J3_PIN4, HIGH); //NOT V4
+    switch_conn_pin(BASEBD_J3_PIN2, LOW); //Experiment 1 preservativeThree V3
+    Serial.println("open preservativeThree bag");
+    saveExperimentalLog("E1_open preservativeThree bag");
+  }
+    if (experiment == 1 && bag == 4)
+  {
+    switch_conn_pin(BASEBD_J5_PIN4, HIGH); //NOT V6
+    switch_conn_pin(BASEBD_J5_PIN2, HIGH); //NOT V5
+    switch_conn_pin(BASEBD_J3_PIN4, HIGH); //NOT V4
+    switch_conn_pin(BASEBD_J3_PIN2, HIGH); //NOT V3
+    switch_conn_pin(BASEBD_J1_PIN4, LOW); //Experiment 1 preservativeFour V2
+    Serial.println("E1_open preservativeFour bag");
+    }
+
+  //experiment two collection
+
+  if (experiment == 2 && bag == 0)
+  {
+    switch_conn_pin(BASEBD_J2_PIN2, LOW); //Experiment 2 waste V7
+    Serial.println("E2 open waste bag");
+    saveExperimentalLog("E2_opem waste bag");
+  }
+  if (experiment == 2 && bag == 1)
+  {
+    switch_conn_pin(BASEBD_J2_PIN2, HIGH); //NOT V7
+    switch_conn_pin(BASEBD_J2_PIN4, LOW); //Experiment 2 preservativeOne V8
+    Serial.println("E2 open preservativeOne bag");
+    saveExperimentalLog("E2_open preservativeOne bag");
+  }
+  if (experiment == 2 && bag == 2)
+  {
+    switch_conn_pin(BASEBD_J2_PIN2, HIGH); //NOT V7
+    switch_conn_pin(BASEBD_J2_PIN4, HIGH); //NOT V8
+    switch_conn_pin(BASEBD_J4_PIN2, LOW); ////Experiment 2 preservativeTwo V9
+    Serial.println("E2 open preservativeTwo bag");
+    saveExperimentalLog("E2_open preservativeTwo bag");
+  }
+  if (experiment == 2 && bag == 3)
+  {
+  switch_conn_pin(BASEBD_J2_PIN2, HIGH); //NOT V7
+  switch_conn_pin(BASEBD_J2_PIN4, HIGH); //NOT V8
+  switch_conn_pin(BASEBD_J4_PIN2, HIGH); //NOT V9
+  switch_conn_pin(BASEBD_J4_PIN4, LOW); //Experiment 2 preservativeThree V10
+  Serial.println("E2_open preservativeThree bag");
+  saveExperimentalLog("E2_open preservativeThree bag");
+  }
+if (experiment == 2 && bag == 4)
+{
+  switch_conn_pin(BASEBD_J2_PIN2, HIGH); //NOT V7
+  switch_conn_pin(BASEBD_J2_PIN4, HIGH); //NOT V8
+  switch_conn_pin(BASEBD_J4_PIN2, HIGH); //NOT V9
+  switch_conn_pin(BASEBD_J4_PIN4, HIGH); //NOT V10
+  switch_conn_pin(BASEBD_J6_PIN2, LOW); //Experiment 2 preservativeFour V11
+  Serial.println("E2_open preservativeFour bag");
+  saveExperimentalLog("E2_open preservativeFour bag");
+}
+}
+
+void Taking_Sensor_Data() {
+  Serial.println("Taking Sensor Data");
+  Serial.print("Time is now: ");
+  Serial.println(now());
+  float temp1, temp2;
+  uint16_t as1_sensorValues[AS726x_NUM_CHANNELS], as2_sensorValues[AS726x_NUM_CHANNELS];
+
+// Select the first BME280 and AS726xread some data
+  tcaselect(BME280_SENSOR1);
+  Serial.println("Sensor Data Experiment One");
+  whichsensor = 1;
+  delay(100);
+  get_data();
+  delay(2000);
+// Select the second BME280 and AS726xread some data
+  tcaselect(BME280_SENSOR2);
+  Serial.println("Sensor Data Experiment Two");
+  whichsensor = 2;
+  delay(100);
+  get_data();
+  delay(2000);
+}
+
+
+void digitalClockDisplay()
+{
+  // digital clock display of the time
+  Serial.print(now());
+  Serial.print(hour());
+  printDigits(minute());
+  printDigits(second());
+  Serial.println();
+}
+
+void printDigits(int digits)
+{
+  Serial.print(":");
+  if (digits < 10)
+    Serial.print('0');
+  Serial.print(digits);
+}
+
+
+time_t tmConvert_t(int YYYY, byte MM, byte DD, byte hh, byte mm, byte ss)
+{
+  tmElements_t tmSet;
+  tmSet.Year = YYYY - 1970;
+  tmSet.Month = MM;
+  tmSet.Day = DD;
+  tmSet.Hour = hh;
+  tmSet.Minute = mm;
+  tmSet.Second = ss;
+  return makeTime(tmSet);
+}
+
+
+
+
+void get_data() {
+  //AMS
+  //read the device temperature
+  uint8_t temp = ams.readTemperature();
+
+  ams.drvOn(); //uncomment this if you want to use the driver LED for readings
+  ams.startMeasurement(); //begin a measurement
+
+  //wait till data is available
+  bool rdy = false;
+  while (!rdy) {
+    delay(5);
+    rdy = ams.dataReady();
+  }
+
+
+  //read the values!
+  ams.readRawValues(sensorValues);
+  //ams.readCalibratedValues(calibratedValues);
+
+  Serial.print("Temp: "); Serial.print(temp);
+  Serial.print(" Violet: "); Serial.print(sensorValues[AS726x_VIOLET]);
+  Serial.print(" Blue: "); Serial.print(sensorValues[AS726x_BLUE]);
+  Serial.print(" Green: "); Serial.print(sensorValues[AS726x_GREEN]);
+  Serial.print(" Yellow: "); Serial.print(sensorValues[AS726x_YELLOW]);
+  Serial.print(" Orange: "); Serial.print(sensorValues[AS726x_ORANGE]);
+  Serial.print(" Red: "); Serial.print(sensorValues[AS726x_RED]);
+  Serial.println();
+
+  ams.drvOff();
+
+  //BME
+  Serial.print("Temperature = ");
+  Serial.print(bme.readTemperature());
+  Serial.println(" °C");
+  Serial.print("Pressure = ");
+  Serial.print(bme.readPressure() / 100.0F);
+  Serial.println(" hPa");
+  Serial.print("Approx. Altitude = ");
+  Serial.print(bme.readAltitude(SEALEVELPRESSURE_HPA));
+  Serial.println(" m");
+  Serial.print("Humidity = ");
+  Serial.print(bme.readHumidity());
+  Serial.println(" %");
+
+
+
+  //SAVING
+  // open the file.
+  myFile = SD.open("savefile.csv", FILE_WRITE);
+  if (myFile)
+  {
+    Serial.print("Writing to file...");
+    //myFile.println();
+
+    //DT
+    myFile.print(now());
+    myFile.print(',');
+
+    //millis
+    myFile.print(millis());
+    myFile.print(',');
+
+   //whichsensor
+    myFile.print(whichsensor);
+    myFile.print(',');
+
+    //Temp
+    myFile.print(bme.readTemperature());
+    myFile.print(',');
+
+    //Pressure
+    myFile.print(bme.readPressure() / 100.0F);
+    myFile.print(',');
+
+    //Attitude
+    myFile.print(bme.readAltitude(SEALEVELPRESSURE_HPA));
+    myFile.print(',');
+
+    //Humidity
+    myFile.print(bme.readHumidity());
+    myFile.print(',');
+
+    //Temp2
+    myFile.print(temp);
+    myFile.print(',');
+
+    //Spectral_Violet
+    myFile.print(sensorValues[AS726x_VIOLET]);
+    myFile.print(',');
+
+    //Spectral_Blue
+    myFile.print(sensorValues[AS726x_VIOLET]);
+    myFile.print(',');
+
+    //Spectral_Green
+    myFile.print(sensorValues[AS726x_GREEN]);
+    myFile.print(',');
+
+    //Spectral_Yellow
+    myFile.print(sensorValues[AS726x_YELLOW]);
+    myFile.print(',');
+
+    //Spectral_Orange
+    myFile.print(sensorValues[AS726x_ORANGE]);
+    myFile.print(',');
+
+    //Spectral_Red
+    myFile.print(sensorValues[AS726x_RED]);
+//    myFile.print(',');
+//
+//    //EXP Log
+//    myFile.print(experimenta_log);
+
+    myFile.println();
+    myFile.close();
+    Serial.println("done.");
+    digitalWrite(ledPin, HIGH);   // set the LED on
+    delay(300);                  // wait for a second
+    digitalWrite(ledPin, LOW);    // set the LED off
+    delay(300);                  // wait for a second
+  }
+  else {
+    Serial.println("error opening file");
+  }
+
+}
+
+void saveExperimentalLog(String logmessage){
+  expLogFile = SD.open("explog.csv", FILE_WRITE);
+  if(expLogFile){
+     expLogFile.print(now());
+     expLogFile.print(',');
+     expLogFile.print(logmessage);
+     expLogFile.println();
+     expLogFile.close();
+  }
+}
+
+void init_card() {
+
+  Serial.print("Initializing SD card...");
+
+  if (!SD.begin(chipSelect)) {
+    Serial.println("initialization failed!");
+    return;
+  }
+  Serial.println("initialization done.");
+
+
+  // open the file.
+  myFile = SD.open("savefile.csv", FILE_WRITE);
+  if (myFile) {
+    Serial.print("Init header to file...");
+    digitalWrite(ledPin, HIGH);   // set the LED on
+    delay(1000);                  // wait for a second
+    digitalWrite(ledPin, LOW);    // set the LED off
+    delay(1000);                  // wait for a second
+
+    //Content
+    myFile.println("DT, millis, Sensorline, Temp, Pressure, Attitude, Humidity, Temp2, Spectral_Violet, Spectral_Blue, Spectral_Green, Spectral_Yellow, Spectral_Orange, Spectral_Red");
+    myFile.close();
+    Serial.println("done.");
+  } else {
+    Serial.println("error opening file");
+  }
+  //Close the file
+}
+
+void initExpLogFile(){
+  expLogFile = SD.open("explog.csv", FILE_WRITE);
+  if (expLogFile) {
+    expLogFile.print("timestamp");
+     expLogFile.print(',');
+     expLogFile.print("log_message");
+     expLogFile.println();
+     expLogFile.close();
+  }
+}
+
+/* Function to control motors on sensor board */
+/* Input: (1) motor_num is either 1 or 3
+ *        (2) dir is either forward, reverse, or halt
+ */
+void motorSensorBrdCtrl(uint8_t motor_num, motion dir){
+  if(motor_num == 1){
+    if(dir == forward){
+      mcp2.digitalWrite(PUMP1_A, HIGH);
+      mcp2.digitalWrite(PUMP1_B, LOW);
+    }else if(dir == reverse){
+      mcp2.digitalWrite(PUMP1_A, LOW);
+      mcp2.digitalWrite(PUMP1_B, HIGH);
+    }else if(dir == halt){
+      mcp2.digitalWrite(PUMP1_A, LOW);
+      mcp2.digitalWrite(PUMP1_B, LOW);
+    }
+  }else if(motor_num == 3){
+    if(dir == forward){
+      mcp2.digitalWrite(PUMP3_A, HIGH);
+      mcp2.digitalWrite(PUMP3_B, LOW);
+    }else if(dir == reverse){
+      mcp2.digitalWrite(PUMP3_A, LOW);
+      mcp2.digitalWrite(PUMP3_B, HIGH);
+    }else if(dir == halt){
+      mcp2.digitalWrite(PUMP3_A, LOW);
+      mcp2.digitalWrite(PUMP3_B, LOW);
+    }
+  }
+  delay (1000);
+}