diff --git a/.github/workflows/CI_Tests.yml b/.github/workflows/CI_Tests.yml
index 01bae148..b789a186 100644
--- a/.github/workflows/CI_Tests.yml
+++ b/.github/workflows/CI_Tests.yml
@@ -39,5 +39,8 @@ jobs:
     
     - name: Run the smoke tests
       run: |
-        music_box configFile=tests/configs/analytical_config/my_config.json outputDir=tests/configs/analytical_config
+        music_box -c src/acom_music_box/examples/configs/analytical/my_config.json -o output.csv
+        music_box -e Analytical -o output.csv
+        music_box -e Analytical -o output.csv -vv --color-output
+
 
diff --git a/examples/camp_examples/bright_chamber/use_case_7/camp_data/config.json b/examples/camp_examples/bright_chamber/use_case_7/camp_data/config.json
deleted file mode 100644
index 4629149f..00000000
--- a/examples/camp_examples/bright_chamber/use_case_7/camp_data/config.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-  "camp-files" : [
-    "camp_data/species.json",
-    "camp_data/mechanism.json"
-  ]
-}
diff --git a/examples/camp_examples/bright_chamber/use_case_7/camp_data/mechanism.json b/examples/camp_examples/bright_chamber/use_case_7/camp_data/mechanism.json
deleted file mode 100644
index bc6b69de..00000000
--- a/examples/camp_examples/bright_chamber/use_case_7/camp_data/mechanism.json
+++ /dev/null
@@ -1,135 +0,0 @@
-{
-  "camp-data" : [
-    {
-      "name" : "Chapman",
-      "type" : "MECHANISM",
-      "reactions" : [
-        {
-          "type" : "PHOTOLYSIS",
-          "reactants" : {
-            "O2" : { }
-          },
-          "products" : {
-            "O" : { "yield" : 2.0 }
-          },
-          "MUSICA name" : "O2_1"
-        },
-        {
-          "type" : "PHOTOLYSIS",
-          "reactants" : {
-            "O3" : { }
-          },
-          "products" : {
-            "O1D" : { },
-            "O2" : { }
-          },
-          "MUSICA name" : "O3_1"
-        },
-        {
-          "type" : "PHOTOLYSIS",
-          "reactants" : {
-            "O3" : { }
-          },
-          "products" : {
-            "O" : { },
-            "O2" : { }
-          },
-          "MUSICA name" : "O3_2"
-        },
-        {
-          "type" : "ARRHENIUS",
-          "reactants" : {
-            "O1D" : { },
-            "N2" : { }
-          },
-          "products" : {
-            "O" : { },
-            "N2" : { }
-          },
-          "A" : 2.15e-11,
-          "C" : 110.0
-        },
-        {
-          "type" : "ARRHENIUS",
-          "reactants" : {
-            "O1D" : { },
-            "O2" : { }
-          },
-          "products" : {
-            "O" : { },
-            "O2" : { }
-          },
-          "A" : 3.3e-11,
-          "C" : 55.0
-        },
-        {
-          "type" : "ARRHENIUS",
-          "reactants" : {
-            "O" : { },
-            "O3" : { }
-          },
-          "products" : {
-            "O2" : { "yield" : 2.0 }
-          },
-          "A" : 8.0e-12,
-          "C" : -2060.00
-        },
-        {
-          "type" : "ARRHENIUS",
-          "reactants" : {
-            "O" : { },
-            "O2" : { },
-            "M" : { }
-          },
-          "products" : {
-            "O3" : { },
-            "M" : { }
-          },
-          "A" : 6.0e-34,
-          "B" : 2.4
-        },
-        {
-          "type" : "EMISSION",
-          "species" : "O1D",
-          "MUSICA name" : "O1D"
-        },
-        {
-          "type" : "EMISSION",
-          "species" : "O",
-          "MUSICA name" : "O"
-        },
-        {
-          "type" : "EMISSION",
-          "species" : "O3",
-          "MUSICA name" : "O3"
-        },
-        {
-          "type" : "FIRST_ORDER_LOSS",
-          "species" : "N2",
-          "MUSICA name" : "N2"
-        },
-        {
-          "type" : "FIRST_ORDER_LOSS",
-          "species" : "O2",
-          "MUSICA name" : "O2"
-        },
-        {
-          "type" : "FIRST_ORDER_LOSS",
-          "species" : "CO2",
-          "MUSICA name" : "CO2"
-        },
-        {
-          "type" : "FIRST_ORDER_LOSS",
-          "species" : "Ar",
-          "MUSICA name" : "Ar"
-        },
-        {
-          "type" : "FIRST_ORDER_LOSS",
-          "species" : "H2O",
-          "MUSICA name" : "H2O"
-        }
-      ]
-    }
-  ]
-}
-
diff --git a/examples/camp_examples/bright_chamber/use_case_7/camp_data/species.json b/examples/camp_examples/bright_chamber/use_case_7/camp_data/species.json
deleted file mode 100644
index 948aca00..00000000
--- a/examples/camp_examples/bright_chamber/use_case_7/camp_data/species.json
+++ /dev/null
@@ -1,54 +0,0 @@
-{
-  "camp-data" : [
-    {
-      "type" : "RELATIVE_TOLERANCE",
-      "value" : 1.0e-4
-    },
-    {
-      "name" : "M",
-      "type" : "CHEM_SPEC",
-      "tracer type" : "CONSTANT"
-    },
-    {
-      "name" : "Ar",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "CO2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "H2O",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "N2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O1D",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O3",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    }
-  ]
-}
-
diff --git a/examples/camp_examples/bright_chamber/use_case_7/emissions.csv b/examples/camp_examples/bright_chamber/use_case_7/emissions.csv
deleted file mode 100644
index 2553005b..00000000
--- a/examples/camp_examples/bright_chamber/use_case_7/emissions.csv
+++ /dev/null
@@ -1,5 +0,0 @@
-time.hr, EMIS.O1D, EMIS.O, EMIS.O3
-0.0, 0.0, 0.0, 0.0
-0.2, 0.1, 0.05, 0.05
-1.0, 0.2, 0.1, 0.1
-1.5, 0.0, 0.0, 0.0
diff --git a/examples/camp_examples/bright_chamber/use_case_7/initial.csv b/examples/camp_examples/bright_chamber/use_case_7/initial.csv
deleted file mode 100644
index 2af07f8d..00000000
--- a/examples/camp_examples/bright_chamber/use_case_7/initial.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-CONC.N2& CONC.O2& CONC.Ar& CONC.CO2& ENV.temperature& ENV.pressure.atm
-3.29e1& 8.84& 3.92e-1& 1.69e-2& 298.0& 1.0
diff --git a/examples/camp_examples/bright_chamber/use_case_7/parking_lot_photo_rates.nc b/examples/camp_examples/bright_chamber/use_case_7/parking_lot_photo_rates.nc
deleted file mode 100644
index fd3ba0f2..00000000
Binary files a/examples/camp_examples/bright_chamber/use_case_7/parking_lot_photo_rates.nc and /dev/null differ
diff --git a/examples/camp_examples/bright_chamber/use_case_7/use_case_7_config.json b/examples/camp_examples/bright_chamber/use_case_7/use_case_7_config.json
deleted file mode 100644
index 6cd6ef43..00000000
--- a/examples/camp_examples/bright_chamber/use_case_7/use_case_7_config.json
+++ /dev/null
@@ -1,83 +0,0 @@
-{
-  "box model options" : {
-    "grid"                      : "box",
-    "chemistry time step [min]" : 5.0,
-    "output time step [hr]"     : 1.0,
-    "simulation length [hr]"    : 2.5,
-    "simulation start" : {
-      "time zone" : "UTC-8",
-      "year" : 2020,
-      "month" : 6,
-      "day" : 10,
-      "hour" : 13
-    }
-  },
-  "initial conditions" : {
-    "initial.csv" : {
-      "delimiter" : "&"
-    }
-  },
-  "evolving conditions" : {
-    "emissions.csv" : {
-      "properties" : {
-        "time.hr" : {
-          "shift first entry to" :{
-            "time zone" : "UTC-8",
-            "year" : 2020,
-            "month" : 6,
-            "day" : 10,
-            "hour" : 13
-          }
-        }
-      }
-    },
-    "wall_loss_rates_011519.txt" : {
-      "delimiter" : ";",
-      "time axis" : "columns",
-      "properties" : {
-        "simtime" : {
-          "MusicBox name" : "time",
-          "units" : "hr",
-          "shift first entry to" :{
-            "time zone" : "UTC-8",
-            "year" : 2020,
-            "month" : 6,
-            "day" : 10,
-            "hour" : 13
-          }
-        },
-        "*" : {
-          "MusicBox name" : "LOSS.*",
-          "units" : "min-1"
-        }
-      }
-    },
-    "parking_lot_photo_rates.nc" : {
-      "time offset" : { "years" : 15 },
-      "properties" : {
-        "*" : { "MusicBox name" : "PHOT.*" },
-        "time" : {
-          "MusicBox name" : "time",
-          "shift first entry to" : {
-            "year" : 2020,
-            "month" : 1,
-            "day" : 1,
-            "time zone" : "UTC-8"
-          }
-        }
-      }
-    }
-  },
-  "model components" : [
-    {
-      "type" : "CAMP",
-      "configuration file" : "camp_data/config.json",
-      "override species" : {
-        "M" : { "mixing ratio mol mol-1" : 1.0 }
-      },
-      "suppress output" : {
-        "M" : { }
-      }
-    }
-  ]
-}
diff --git a/examples/camp_examples/bright_chamber/use_case_7/wall_loss_rates_011519.txt b/examples/camp_examples/bright_chamber/use_case_7/wall_loss_rates_011519.txt
deleted file mode 100644
index fa5182fa..00000000
--- a/examples/camp_examples/bright_chamber/use_case_7/wall_loss_rates_011519.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-simtime; 0.0; 0.3; 0.6; 0.9; 1.2
-N2; 0.010; 0.012; 0.013; 0.014; 0.015
-O2; 0.015; 0.016; 0.017; 0.018; 0.019
-Ar; 0.015; 0.016; 0.017; 0.018; 0.019
-CO2; 0.010; 0.012; 0.013; 0.014; 0.015
-H2O; 0.010; 0.012; 0.013; 0.014; 0.015
diff --git a/examples/camp_examples/bright_chamber/use_case_8/camp_data/config.json b/examples/camp_examples/bright_chamber/use_case_8/camp_data/config.json
deleted file mode 100644
index 4629149f..00000000
--- a/examples/camp_examples/bright_chamber/use_case_8/camp_data/config.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-  "camp-files" : [
-    "camp_data/species.json",
-    "camp_data/mechanism.json"
-  ]
-}
diff --git a/examples/camp_examples/bright_chamber/use_case_8/camp_data/mechanism.json b/examples/camp_examples/bright_chamber/use_case_8/camp_data/mechanism.json
deleted file mode 100644
index d3a78ae3..00000000
--- a/examples/camp_examples/bright_chamber/use_case_8/camp_data/mechanism.json
+++ /dev/null
@@ -1,66 +0,0 @@
-{
-  "camp-data" : [
-    {
-      "name" : "Chapman",
-      "type" : "MECHANISM",
-      "reactions" : [
-        {
-          "type" : "EMISSION",
-          "species" : "O1D",
-          "MUSICA name" : "O1D"
-        },
-        {
-          "type" : "EMISSION",
-          "species" : "O",
-          "MUSICA name" : "O"
-        },
-        {
-          "type" : "EMISSION",
-          "species" : "O3",
-          "MUSICA name" : "O3"
-        },
-        {
-          "type" : "EMISSION",
-          "species" : "N2",
-          "MUSICA name" : "N2"
-        },
-        {
-          "type" : "EMISSION",
-          "species" : "Ar",
-          "MUSICA name" : "Ar"
-        },
-        {
-          "type" : "EMISSION",
-          "species" : "O2",
-          "MUSICA name" : "O2"
-        },
-        {
-          "type" : "FIRST_ORDER_LOSS",
-          "species" : "N2",
-          "MUSICA name" : "N2"
-        },
-        {
-          "type" : "FIRST_ORDER_LOSS",
-          "species" : "O2",
-          "MUSICA name" : "O2"
-        },
-        {
-          "type" : "FIRST_ORDER_LOSS",
-          "species" : "CO2",
-          "MUSICA name" : "CO2"
-        },
-        {
-          "type" : "FIRST_ORDER_LOSS",
-          "species" : "Ar",
-          "MUSICA name" : "Ar"
-        },
-        {
-          "type" : "FIRST_ORDER_LOSS",
-          "species" : "H2O",
-          "MUSICA name" : "H2O"
-        }
-      ]
-    }
-  ]
-}
-
diff --git a/examples/camp_examples/bright_chamber/use_case_8/camp_data/species.json b/examples/camp_examples/bright_chamber/use_case_8/camp_data/species.json
deleted file mode 100644
index 948aca00..00000000
--- a/examples/camp_examples/bright_chamber/use_case_8/camp_data/species.json
+++ /dev/null
@@ -1,54 +0,0 @@
-{
-  "camp-data" : [
-    {
-      "type" : "RELATIVE_TOLERANCE",
-      "value" : 1.0e-4
-    },
-    {
-      "name" : "M",
-      "type" : "CHEM_SPEC",
-      "tracer type" : "CONSTANT"
-    },
-    {
-      "name" : "Ar",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "CO2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "H2O",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "N2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O1D",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O3",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    }
-  ]
-}
-
diff --git a/examples/camp_examples/bright_chamber/use_case_8/emissions.csv b/examples/camp_examples/bright_chamber/use_case_8/emissions.csv
deleted file mode 100644
index 2553005b..00000000
--- a/examples/camp_examples/bright_chamber/use_case_8/emissions.csv
+++ /dev/null
@@ -1,5 +0,0 @@
-time.hr, EMIS.O1D, EMIS.O, EMIS.O3
-0.0, 0.0, 0.0, 0.0
-0.2, 0.1, 0.05, 0.05
-1.0, 0.2, 0.1, 0.1
-1.5, 0.0, 0.0, 0.0
diff --git a/examples/camp_examples/bright_chamber/use_case_8/emit_all.csv b/examples/camp_examples/bright_chamber/use_case_8/emit_all.csv
deleted file mode 100644
index 0f4445c6..00000000
--- a/examples/camp_examples/bright_chamber/use_case_8/emit_all.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-time, EMIS.O, EMIS.O1D, EMIS.O3, EMIS.N2, EMIS.Ar, EMIS.O2
-0, 1.0, 2.0, 3.0, 1.0, 2.0, 3.0
-20.0, 2.0, 1.0, 1.0, 2.0, 1.0, 1.0
-30.0, 1.0, 2.0, 3.0, 1.0, 2.0, 3.0
diff --git a/examples/camp_examples/bright_chamber/use_case_8/initial.csv b/examples/camp_examples/bright_chamber/use_case_8/initial.csv
deleted file mode 100644
index 98cf0ff3..00000000
--- a/examples/camp_examples/bright_chamber/use_case_8/initial.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-CONC.O& CONC.O1D& CONC.O3 &CONC.N2& CONC.O2& CONC.Ar& CONC.CO2& ENV.temperature& ENV.pressure.atm
-1.0e-7& 1.0e-6& 1.0e-4& 3.29e1& 8.84& 3.92e-1& 1.69e-2& 298.0& 1.0
diff --git a/examples/camp_examples/bright_chamber/use_case_8/parking_lot_photo_rates.nc b/examples/camp_examples/bright_chamber/use_case_8/parking_lot_photo_rates.nc
deleted file mode 100644
index fd3ba0f2..00000000
Binary files a/examples/camp_examples/bright_chamber/use_case_8/parking_lot_photo_rates.nc and /dev/null differ
diff --git a/examples/camp_examples/bright_chamber/use_case_8/use_case_8_config.json b/examples/camp_examples/bright_chamber/use_case_8/use_case_8_config.json
deleted file mode 100644
index 77c4a885..00000000
--- a/examples/camp_examples/bright_chamber/use_case_8/use_case_8_config.json
+++ /dev/null
@@ -1,95 +0,0 @@
-{
-  "box model options" : {
-    "grid"                      : "box",
-    "chemistry time step [min]" : 5.0,
-    "output time step [hr]"     : 1.0,
-    "simulation length [hr]"    : 2.5,
-    "simulation start" : {
-      "time zone" : "UTC-8",
-      "year" : 2020,
-      "month" : 6,
-      "day" : 10,
-      "hour" : 13
-    }
-  },
-  "initial conditions" : {
-    "initial.csv" : {
-      "delimiter" : "&",
-      "properties" : {
-        "CONC.O3" : { "variability" : "tethered" }
-      },
-      "linear combinations" : {
-        "atomic oxygen" : {
-          "properties" : {
-            "CONC.O" : { },
-            "CONC.O1D" : { }
-          },
-          "scale factor" : 1.2
-        }
-      }
-    }
-  },
-  "evolving conditions" : {
-    "emissions.csv" : {
-      "properties" : {
-        "time.hr" : {
-          "shift first entry to" :{
-            "time zone" : "UTC-8",
-            "year" : 2020,
-            "month" : 6,
-            "day" : 10,
-            "hour" : 13
-          }
-        }
-      }
-    },
-    "wall_loss_rates_011519.txt" : {
-      "delimiter" : ";",
-      "time axis" : "columns",
-      "properties" : {
-        "simtime" : {
-          "MusicBox name" : "time",
-          "units" : "hr",
-          "shift first entry to" :{
-            "time zone" : "UTC-8",
-            "year" : 2020,
-            "month" : 6,
-            "day" : 10,
-            "hour" : 13
-          }
-        },
-        "*" : {
-          "MusicBox name" : "LOSS.*",
-          "units" : "min-1"
-        }
-      }
-    },
-    "parking_lot_photo_rates.nc" : {
-      "time offset" : { "years" : 15 },
-      "properties" : {
-        "*" : { "MusicBox name" : "PHOT.*" },
-        "time" : {
-          "MusicBox name" : "time",
-          "shift first entry to" : {
-            "year" : 2020,
-            "month" : 1,
-            "day" : 1,
-            "time zone" : "UTC-8"
-          }
-        }
-      }
-    }
-  },
-  "model components" : [
-    {
-      "type" : "CAMP",
-      "configuration file" : "camp_data/config.json",
-      "override species" : {
-        "M" : { "mixing ratio mol mol-1" : 1.0 }
-      },
-      "suppress output" : {
-        "M" : { }
-      }
-    }
-  ]
-}
diff --git a/examples/camp_examples/bright_chamber/use_case_8/wall_loss_rates_011519.txt b/examples/camp_examples/bright_chamber/use_case_8/wall_loss_rates_011519.txt
deleted file mode 100644
index fa5182fa..00000000
--- a/examples/camp_examples/bright_chamber/use_case_8/wall_loss_rates_011519.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-simtime; 0.0; 0.3; 0.6; 0.9; 1.2
-N2; 0.010; 0.012; 0.013; 0.014; 0.015
-O2; 0.015; 0.016; 0.017; 0.018; 0.019
-Ar; 0.015; 0.016; 0.017; 0.018; 0.019
-CO2; 0.010; 0.012; 0.013; 0.014; 0.015
-H2O; 0.010; 0.012; 0.013; 0.014; 0.015
diff --git a/examples/camp_examples/dark_chamber/use_case_1/camp_data/config.json b/examples/camp_examples/dark_chamber/use_case_1/camp_data/config.json
deleted file mode 100644
index af4e8619..00000000
--- a/examples/camp_examples/dark_chamber/use_case_1/camp_data/config.json
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-  "camp-files" : [
-    "camp_data/species.json"
-  ]
-}
diff --git a/examples/camp_examples/dark_chamber/use_case_1/camp_data/species.json b/examples/camp_examples/dark_chamber/use_case_1/camp_data/species.json
deleted file mode 100644
index 948aca00..00000000
--- a/examples/camp_examples/dark_chamber/use_case_1/camp_data/species.json
+++ /dev/null
@@ -1,54 +0,0 @@
-{
-  "camp-data" : [
-    {
-      "type" : "RELATIVE_TOLERANCE",
-      "value" : 1.0e-4
-    },
-    {
-      "name" : "M",
-      "type" : "CHEM_SPEC",
-      "tracer type" : "CONSTANT"
-    },
-    {
-      "name" : "Ar",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "CO2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "H2O",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "N2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O1D",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O3",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    }
-  ]
-}
-
diff --git a/examples/camp_examples/dark_chamber/use_case_1/use_case_1_config.json b/examples/camp_examples/dark_chamber/use_case_1/use_case_1_config.json
deleted file mode 100644
index b1ae76a7..00000000
--- a/examples/camp_examples/dark_chamber/use_case_1/use_case_1_config.json
+++ /dev/null
@@ -1,32 +0,0 @@
-{
-  "box model options" : {
-    "grid"                      : "box",
-    "chemistry time step [min]" : 5.0,
-    "output time step [hr]"     : 1.0,
-    "simulation length [hr]"    : 2.5
-  },
-  "chemical species" : {
-    "N2"   : { "initial value [mol m-3]" : 3.29e1  },
-    "O2"   : { "initial value [mol m-3]" : 8.84e0  },
-    "Ar"   : { "initial value [mol m-3]" : 3.92e-1 },
-    "CO2"  : { "initial value [mol m-3]" : 1.69e-2 },
-    "O"    : { "initial value [mol m-3]" : 1.0e-5 }
-  },
-  "environmental conditions" : {
-    "temperature" : { "initial value [K]"   : 298.0 },
-    "pressure"    : { "initial value [atm]" : 1.0   }
-  },
-  "model components" : [
-    {
-      "type" : "CAMP",
-      "configuration file" : "camp_data/config.json",
-      "override species" : {
-        "M" : { "mixing ratio mol mol-1" : 1.0 }
-      },
-      "suppress output" : {
-        "M" : { }
-      }
-    }
-  ]
-}
-
diff --git a/examples/camp_examples/dark_chamber/use_case_2/camp_data/config.json b/examples/camp_examples/dark_chamber/use_case_2/camp_data/config.json
deleted file mode 100644
index af4e8619..00000000
--- a/examples/camp_examples/dark_chamber/use_case_2/camp_data/config.json
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-  "camp-files" : [
-    "camp_data/species.json"
-  ]
-}
diff --git a/examples/camp_examples/dark_chamber/use_case_2/camp_data/species.json b/examples/camp_examples/dark_chamber/use_case_2/camp_data/species.json
deleted file mode 100644
index 948aca00..00000000
--- a/examples/camp_examples/dark_chamber/use_case_2/camp_data/species.json
+++ /dev/null
@@ -1,54 +0,0 @@
-{
-  "camp-data" : [
-    {
-      "type" : "RELATIVE_TOLERANCE",
-      "value" : 1.0e-4
-    },
-    {
-      "name" : "M",
-      "type" : "CHEM_SPEC",
-      "tracer type" : "CONSTANT"
-    },
-    {
-      "name" : "Ar",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "CO2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "H2O",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "N2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O1D",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O3",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    }
-  ]
-}
-
diff --git a/examples/camp_examples/dark_chamber/use_case_2/initial.csv b/examples/camp_examples/dark_chamber/use_case_2/initial.csv
deleted file mode 100644
index f422d6fa..00000000
--- a/examples/camp_examples/dark_chamber/use_case_2/initial.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-CONC.N2, CONC.O2, CONC.Ar, CONC.CO2, CONC.O, ENV.temperature, ENV.pressure
-3.29e1, 8.84, 3.92e-1, 1.69e-2, 1.0e-5, 298.0, 1.0
diff --git a/examples/camp_examples/dark_chamber/use_case_2/use_case_2_config.json b/examples/camp_examples/dark_chamber/use_case_2/use_case_2_config.json
deleted file mode 100644
index d6f6ed3d..00000000
--- a/examples/camp_examples/dark_chamber/use_case_2/use_case_2_config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
-  "box model options" : {
-    "grid"                      : "box",
-    "chemistry time step [min]" : 5.0,
-    "output time step [hr]"     : 1.0,
-    "simulation length [hr]"    : 2.5
-  },
-  "initial conditions" : {
-    "initial.csv" : {
-      "properties" : {
-        "ENV.pressure" : { "units" : "atm" }
-      }
-    }
-  },
-  "model components" : [
-    {
-      "type" : "CAMP",
-      "configuration file" : "camp_data/config.json",
-      "override species" : {
-        "M" : { "mixing ratio mol mol-1" : 1.0 }
-      },
-      "suppress output" : {
-        "M" : { }
-      }
-    }
-  ]
-}
diff --git a/examples/camp_examples/dark_chamber/use_case_3/camp_data/config.json b/examples/camp_examples/dark_chamber/use_case_3/camp_data/config.json
deleted file mode 100644
index af4e8619..00000000
--- a/examples/camp_examples/dark_chamber/use_case_3/camp_data/config.json
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-  "camp-files" : [
-    "camp_data/species.json"
-  ]
-}
diff --git a/examples/camp_examples/dark_chamber/use_case_3/camp_data/species.json b/examples/camp_examples/dark_chamber/use_case_3/camp_data/species.json
deleted file mode 100644
index 948aca00..00000000
--- a/examples/camp_examples/dark_chamber/use_case_3/camp_data/species.json
+++ /dev/null
@@ -1,54 +0,0 @@
-{
-  "camp-data" : [
-    {
-      "type" : "RELATIVE_TOLERANCE",
-      "value" : 1.0e-4
-    },
-    {
-      "name" : "M",
-      "type" : "CHEM_SPEC",
-      "tracer type" : "CONSTANT"
-    },
-    {
-      "name" : "Ar",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "CO2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "H2O",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "N2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O1D",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O2",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    },
-    {
-      "name" : "O3",
-      "type" : "CHEM_SPEC",
-      "absolute tolerance" : 1.0e-12
-    }
-  ]
-}
-
diff --git a/examples/camp_examples/dark_chamber/use_case_3/initial.csv b/examples/camp_examples/dark_chamber/use_case_3/initial.csv
deleted file mode 100644
index d53e9b6d..00000000
--- a/examples/camp_examples/dark_chamber/use_case_3/initial.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-CONC.N2& CONC.O2& CONC.Ar& CONC.CO2& CONC.O& ENV.temperature& ENV.pressure.atm
-3.29e1& 8.84& 3.92e-1& 1.69e-2& 1.0e-5& 298.0& 1.0
diff --git a/examples/camp_examples/dark_chamber/use_case_3/use_case_3_config.json b/examples/camp_examples/dark_chamber/use_case_3/use_case_3_config.json
deleted file mode 100644
index 26285c60..00000000
--- a/examples/camp_examples/dark_chamber/use_case_3/use_case_3_config.json
+++ /dev/null
@@ -1,25 +0,0 @@
-{
-  "box model options" : {
-    "grid"                      : "box",
-    "chemistry time step [min]" : 5.0,
-    "output time step [hr]"     : 1.0,
-    "simulation length [hr]"    : 2.5
-  },
-  "initial conditions" : {
-    "initial.csv" : {
-      "delimiter" : "&"
-    }
-  },
-  "model components" : [
-    {
-      "type" : "CAMP",
-      "configuration file" : "camp_data/config.json",
-      "override species" : {
-        "M" : { "mixing ratio mol mol-1" : 1.0 }
-      },
-      "suppress output" : {
-        "M" : { }
-      }
-    }
-  ]
-}
diff --git a/pyproject.toml b/pyproject.toml
index bb75bd54..9732f59a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,7 +21,9 @@ classifiers = ["License :: OSI Approved :: Apache Software License"]
 dynamic = ["version", "description"]
 
 dependencies = [
-  "musica==0.7.3"
+  "musica==0.7.3",
+  "colorlog",
+  "pandas"
 ]
 
 [project.urls]
diff --git a/src/acom_music_box/__init__.py b/src/acom_music_box/__init__.py
index dec1591c..f7274688 100644
--- a/src/acom_music_box/__init__.py
+++ b/src/acom_music_box/__init__.py
@@ -19,3 +19,4 @@
 
 from .evolving_conditions import EvolvingConditions
 from .music_box import MusicBox
+from .examples import Examples
\ No newline at end of file
diff --git a/src/acom_music_box/examples/__init__.py b/src/acom_music_box/examples/__init__.py
new file mode 100644
index 00000000..cccf6e33
--- /dev/null
+++ b/src/acom_music_box/examples/__init__.py
@@ -0,0 +1 @@
+from .examples import Examples
\ No newline at end of file
diff --git a/tests/configs/analytical_config/camp_data/config.json b/src/acom_music_box/examples/configs/analytical/camp_data/config.json
similarity index 100%
rename from tests/configs/analytical_config/camp_data/config.json
rename to src/acom_music_box/examples/configs/analytical/camp_data/config.json
diff --git a/tests/configs/analytical_config/camp_data/reactions.json b/src/acom_music_box/examples/configs/analytical/camp_data/reactions.json
similarity index 100%
rename from tests/configs/analytical_config/camp_data/reactions.json
rename to src/acom_music_box/examples/configs/analytical/camp_data/reactions.json
diff --git a/tests/configs/analytical_config/camp_data/species.json b/src/acom_music_box/examples/configs/analytical/camp_data/species.json
similarity index 100%
rename from tests/configs/analytical_config/camp_data/species.json
rename to src/acom_music_box/examples/configs/analytical/camp_data/species.json
diff --git a/tests/configs/analytical_config/evolving_conditions.csv b/src/acom_music_box/examples/configs/analytical/evolving_conditions.csv
similarity index 100%
rename from tests/configs/analytical_config/evolving_conditions.csv
rename to src/acom_music_box/examples/configs/analytical/evolving_conditions.csv
diff --git a/tests/configs/analytical_config/my_config.json b/src/acom_music_box/examples/configs/analytical/my_config.json
similarity index 100%
rename from tests/configs/analytical_config/my_config.json
rename to src/acom_music_box/examples/configs/analytical/my_config.json
diff --git a/tests/configs/chapman_config/camp_data/config.json b/src/acom_music_box/examples/configs/carbon_bond_5/camp_data/config.json
similarity index 100%
rename from tests/configs/chapman_config/camp_data/config.json
rename to src/acom_music_box/examples/configs/carbon_bond_5/camp_data/config.json
diff --git a/tests/configs/full_gas_phase_mechanism_config/camp_data/reactions.json b/src/acom_music_box/examples/configs/carbon_bond_5/camp_data/reactions.json
similarity index 100%
rename from tests/configs/full_gas_phase_mechanism_config/camp_data/reactions.json
rename to src/acom_music_box/examples/configs/carbon_bond_5/camp_data/reactions.json
diff --git a/tests/configs/full_gas_phase_mechanism_config/camp_data/species.json b/src/acom_music_box/examples/configs/carbon_bond_5/camp_data/species.json
similarity index 100%
rename from tests/configs/full_gas_phase_mechanism_config/camp_data/species.json
rename to src/acom_music_box/examples/configs/carbon_bond_5/camp_data/species.json
diff --git a/tests/configs/full_gas_phase_mechanism_config/initial_conditions.csv b/src/acom_music_box/examples/configs/carbon_bond_5/initial_conditions.csv
similarity index 100%
rename from tests/configs/full_gas_phase_mechanism_config/initial_conditions.csv
rename to src/acom_music_box/examples/configs/carbon_bond_5/initial_conditions.csv
diff --git a/tests/configs/full_gas_phase_mechanism_config/my_config.json b/src/acom_music_box/examples/configs/carbon_bond_5/my_config.json
similarity index 100%
rename from tests/configs/full_gas_phase_mechanism_config/my_config.json
rename to src/acom_music_box/examples/configs/carbon_bond_5/my_config.json
diff --git a/tests/configs/full_gas_phase_mechanism_config/camp_data/config.json b/src/acom_music_box/examples/configs/chapman/camp_data/config.json
similarity index 100%
rename from tests/configs/full_gas_phase_mechanism_config/camp_data/config.json
rename to src/acom_music_box/examples/configs/chapman/camp_data/config.json
diff --git a/tests/configs/chapman_config/camp_data/reactions.json b/src/acom_music_box/examples/configs/chapman/camp_data/reactions.json
similarity index 100%
rename from tests/configs/chapman_config/camp_data/reactions.json
rename to src/acom_music_box/examples/configs/chapman/camp_data/reactions.json
diff --git a/tests/configs/chapman_config/camp_data/species.json b/src/acom_music_box/examples/configs/chapman/camp_data/species.json
similarity index 100%
rename from tests/configs/chapman_config/camp_data/species.json
rename to src/acom_music_box/examples/configs/chapman/camp_data/species.json
diff --git a/tests/configs/chapman_config/evolving_conditions.csv b/src/acom_music_box/examples/configs/chapman/evolving_conditions.csv
similarity index 100%
rename from tests/configs/chapman_config/evolving_conditions.csv
rename to src/acom_music_box/examples/configs/chapman/evolving_conditions.csv
diff --git a/tests/configs/chapman_config/my_config.json b/src/acom_music_box/examples/configs/chapman/my_config.json
similarity index 100%
rename from tests/configs/chapman_config/my_config.json
rename to src/acom_music_box/examples/configs/chapman/my_config.json
diff --git a/tests/configs/wall_loss_config/camp_data/config.json b/src/acom_music_box/examples/configs/flow_tube/camp_data/config.json
similarity index 100%
rename from tests/configs/wall_loss_config/camp_data/config.json
rename to src/acom_music_box/examples/configs/flow_tube/camp_data/config.json
diff --git a/tests/configs/wall_loss_config/camp_data/reactions.json b/src/acom_music_box/examples/configs/flow_tube/camp_data/reactions.json
similarity index 100%
rename from tests/configs/wall_loss_config/camp_data/reactions.json
rename to src/acom_music_box/examples/configs/flow_tube/camp_data/reactions.json
diff --git a/tests/configs/wall_loss_config/camp_data/species.json b/src/acom_music_box/examples/configs/flow_tube/camp_data/species.json
similarity index 100%
rename from tests/configs/wall_loss_config/camp_data/species.json
rename to src/acom_music_box/examples/configs/flow_tube/camp_data/species.json
diff --git a/tests/configs/wall_loss_config/evolving_conditions.csv b/src/acom_music_box/examples/configs/flow_tube/evolving_conditions.csv
similarity index 100%
rename from tests/configs/wall_loss_config/evolving_conditions.csv
rename to src/acom_music_box/examples/configs/flow_tube/evolving_conditions.csv
diff --git a/tests/configs/wall_loss_config/initial_conditions.csv b/src/acom_music_box/examples/configs/flow_tube/initial_conditions.csv
similarity index 100%
rename from tests/configs/wall_loss_config/initial_conditions.csv
rename to src/acom_music_box/examples/configs/flow_tube/initial_conditions.csv
diff --git a/tests/configs/wall_loss_config/my_config.json b/src/acom_music_box/examples/configs/flow_tube/my_config.json
similarity index 100%
rename from tests/configs/wall_loss_config/my_config.json
rename to src/acom_music_box/examples/configs/flow_tube/my_config.json
diff --git a/src/acom_music_box/examples/examples.py b/src/acom_music_box/examples/examples.py
new file mode 100644
index 00000000..b6e1a3db
--- /dev/null
+++ b/src/acom_music_box/examples/examples.py
@@ -0,0 +1,55 @@
+import os
+
+class Example:
+    def __init__(self, name, short_name, description, path):
+        self.name = name
+        self.short_name = short_name
+        self.description = description
+        self.path = path
+    
+    def __str__(self):
+        return f'{self.name}: {self.description}'
+    
+    def __repr__(self):
+        return f'{self.name}: {self.description}'
+
+    @classmethod
+    def from_config(cls, display_name, folder_name, short_name, description):
+        path = os.path.join(os.path.dirname(__file__), 'configs', folder_name, 'my_config.json')
+        return cls(name=display_name, short_name = short_name, description=description, path=path)
+
+class _Examples:
+    CarbonBond5 = Example.from_config(
+        display_name='Carbon Bond IV', 
+        short_name='CB5',
+        folder_name='carbon_bond_5',
+        description='Carbon bond 5')
+    Chapman = Example.from_config(
+        display_name='Chapman', 
+        short_name='Chapman',
+        folder_name='chapman',
+        description='The Chapman cycle with conditions over Boulder, Colorado')
+    FlowTube = Example.from_config(
+        display_name='Flow Tube', 
+        short_name='FlowTube',
+        folder_name='flow_tube',
+        description='A fictitious flow tube experiment')
+    Analytical = Example.from_config(
+        display_name='Analytical', 
+        short_name='Analytical',
+        folder_name='analytical',
+        description='An example of an analytical solution to a simple chemical system')
+
+    @classmethod
+    def get_all(cls):
+        return [cls.CarbonBond5, cls.Chapman, cls.FlowTube, cls.Analytical]
+
+    def __iter__(self):
+        return iter(self.get_all())
+
+    def __getattr__(self, item):
+        if hasattr(self, item):
+            return getattr(self, item)
+        raise AttributeError(f"'{self.__class__.__name__}' object has no attribute '{item}'")
+
+Examples = _Examples()
\ No newline at end of file
diff --git a/src/acom_music_box/main.py b/src/acom_music_box/main.py
index d3f1c01c..e1baa9f8 100644
--- a/src/acom_music_box/main.py
+++ b/src/acom_music_box/main.py
@@ -1,98 +1,156 @@
 import os
 import argparse
-from acom_music_box import MusicBox
-
-
-import math
+from acom_music_box import MusicBox, Examples
 import datetime
 import sys
-
 import logging
-logger = logging.getLogger(__name__)
-
-
-# configure argparse for key-value pairs
-class KeyValueAction(argparse.Action):
-    def __call__(self, parser, namespace, values, option_string=None):
-        for value in values:
-            key, val = value.split('=')
-            setattr(namespace, key, val)
-
-# Retrieve named arguments from the command line and
-# return in a dictionary of keywords.
-# argPairs = list of arguments, probably from sys.argv[1:]
-#       named arguments are formatted like this=3.14159
-# return dictionary of keywords and values
+import colorlog
+import subprocess
+import tempfile
 
+def format_examples_help(examples):
+    return '\n'.join(f"{e.short_name}: {e.description}" for e in examples)
 
-def getArgsDictionary(argPairs):
+def parse_arguments():
     parser = argparse.ArgumentParser(
-        description='Process some key=value pairs.')
+        description='MusicBox simulation runner.',
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+    parser.add_argument(
+        '-c', '--config',
+        type=str,
+        help='Path to the configuration file. If --example is provided, this argument is ignored.'
+    )
+    parser.add_argument(
+        '-e', '--example',
+        type=str,
+        choices=[e.short_name for e in Examples],
+        help=f'Name of the example to use. Overrides --config.\nAvailable examples:\n{format_examples_help(Examples)}'
+    )
+    parser.add_argument(
+        '-o', '--output',
+        type=str,
+        help='Path to save the output file, including the file name. If not provided, result will be printed to the console.'
+    )
+    parser.add_argument(
+        '-v', '--verbose',
+        action='count',
+        default=0,
+        help='Increase logging verbosity. Use -v for info, -vv for debug.'
+    )
     parser.add_argument(
-        'key_value_pairs',
-        nargs='+',  # This means one or more arguments are expected
-        action=KeyValueAction,
-        help="Arguments in key=value format. Example: configFile=my_config.json"
+        '--color-output',
+        action='store_true',
+        help='Enable color output for logs.'
     )
+    parser.add_argument(
+        '--plot',
+        type=str,
+        help='Plot a comma-separated list of species if gnuplot is available (e.g., CONC.A,CONC.B).'
+    )
+    return parser.parse_args()
+
+def setup_logging(verbosity, color_output):
+    if verbosity >= 2:
+        log_level = logging.DEBUG
+    elif verbosity == 1:
+        log_level = logging.INFO
+    else:
+        log_level = logging.CRITICAL
+
+    formatter = logging.Formatter('%(asctime)s - %(levelname)s - %(module)s.%(funcName)s - %(message)s', datefmt='%Y-%m-%d %H:%M:%S')
+    if color_output:
+        color_formatter = colorlog.ColoredFormatter('%(log_color)s%(asctime)s - %(levelname)s - %(module)s.%(funcName)s - %(message)s', datefmt='%Y-%m-%d %H:%M:%S', log_colors={'DEBUG': 'green', 'INFO': 'cyan', 'WARNING': 'yellow', 'ERROR': 'red', 'CRITICAL': 'bold_red'})
+        console_handler = logging.StreamHandler()
+        console_handler.setLevel(log_level)
+        console_handler.setFormatter(color_formatter)
+        logging.basicConfig(level=log_level, handlers=[console_handler])
+    else:
+        console_handler = logging.StreamHandler()
+        console_handler.setLevel(log_level)
+        console_handler.setFormatter(formatter)
+        logging.basicConfig(level=log_level, handlers=[console_handler])
+
+def plot_with_gnuplot(data, species_list):
+    # Prepare columns and data for plotting
+    columns = ['time'] + species_list
+    data_to_plot = data[columns]
+    
+    data_csv = data_to_plot.to_csv(index=False)
+    
+    try:
+        with tempfile.NamedTemporaryFile(delete=False, suffix='.csv') as data_file:
+            data_file.write(data_csv.encode())
+            data_file_path = data_file.name
+        
+        plot_commands = ',\n\t'.join(f"'{data_file_path}' using 1:{i+2} with lines title '{species}'" for i, species in enumerate(species_list))
+        
+        gnuplot_command = f"""
+        set datafile separator ",";
+        set terminal dumb size 120,25;
+        set xlabel 'Time';
+        set ylabel 'Value';
+        set title 'Time vs Species';
+        plot {plot_commands}
+        """
+        
+        subprocess.run(['gnuplot', '-e', gnuplot_command], check=True)
+    except FileNotFoundError:
+        logging.critical("gnuplot is not installed. Skipping plotting.")
+    except subprocess.CalledProcessError as e:
+        logging.error(f"Error occurred while plotting: {e}")
+    finally:
+        # Clean up the temporary file
+        if data_file_path:
+            os.remove(data_file_path)
+
+def main():
+    start = datetime.datetime.now()
 
-    argDict = vars(parser.parse_args(argPairs))      # return dictionary
+    args = parse_arguments()
+    setup_logging(args.verbose, args.color_output)
 
-    return (argDict)
+    logger = logging.getLogger(__name__)
 
+    logger.debug(f"{__file__}")
+    logger.info(f"Start time: {start}")
 
-def main():
-    logging.basicConfig(stream=sys.stdout, level=logging.INFO)
-    logger.info("{}".format(__file__))
-    logger.info("Start time: {}".format(datetime.datetime.now()))
-
-    logger.info("Hello, MusicBox World!")
-    logger.info("Working directory = {}".format(os.getcwd()))
-
-    # retrieve and parse the command-line arguments
-    myArgs = getArgsDictionary(sys.argv[1:])
-    logger.info("Command line = {}".format(myArgs))
-
-    # set up the home configuration file
-    musicBoxConfigFile = None
-    if ("configFile" in myArgs):
-        musicBoxConfigFile = myArgs.get("configFile")
-
-    # set up the output directory
-    musicBoxOutputDir = ".\\"      # default
-    if ("outputDir" in myArgs):
-        musicBoxOutputDir = myArgs.get("outputDir")
-
-    # check for required arguments and provide examples
-    if (musicBoxConfigFile is None):
-        errorString = "Error: The configFile parameter is required."
-        errorString += (
-            " Example: configFile={}" .format(
-                os.path.join(
-                    "tests",
-                    "configs",
-                    "analytical_config",
-                    "my_config.json")))
-        raise Exception(errorString)
-
-    # create and load a MusicBox object
+    logger.debug(f"Working directory = {os.getcwd()}")
+
+    if args.example:
+        example = next(e for e in Examples if e.short_name == args.example)
+        musicBoxConfigFile = example.path
+        logger.info(f"Using example: {example}")
+    else:
+        musicBoxConfigFile = args.config
+
+    musicBoxOutputPath = args.output
+    plot_species_list = args.plot.split(',') if args.plot else None
+
+    # Create and load a MusicBox object
     myBox = MusicBox()
-    logging.info("configuration file = {}".format(musicBoxConfigFile))
+    logger.debug(f"Configuration file = {musicBoxConfigFile}")
     myBox.readConditionsFromJson(musicBoxConfigFile)
-    logger.info("myBox = {}".format(myBox))
 
-    # create solver and solve, writing output to requested directory
-    campConfig = os.path.join(
+    # Create solver and solve
+    config_path = os.path.join(
         os.path.dirname(musicBoxConfigFile),
         myBox.config_file)
-    logger.info("CAMP config = {}".format(campConfig))
-    myBox.create_solver(campConfig)
-    logger.info("myBox.solver = {}".format(myBox.solver))
-    mySolution = myBox.solve(os.path.join(musicBoxOutputDir, "mySolution.csv"))
-    # logger.info("mySolution = {}".format(mySolution))
+    myBox.create_solver(config_path)
+    result = myBox.solve(musicBoxOutputPath)
+    
+    if musicBoxOutputPath is None:
+        print(result.to_csv(index=False))
+    
+    if plot_species_list:
+        # Prepare data for plotting
+        plot_with_gnuplot(result, plot_species_list)
+
+    end = datetime.datetime.now()
+    logger.info(f"End time: {end}")
+    logger.info(f"Elapsed time: {end - start} seconds")
 
-    logger.info("End time: {}".format(datetime.datetime.now()))
     sys.exit(0)
 
-
 if __name__ == "__main__":
     main()
diff --git a/src/acom_music_box/music_box.py b/src/acom_music_box/music_box.py
index 3eb0f922..14245bb7 100644
--- a/src/acom_music_box/music_box.py
+++ b/src/acom_music_box/music_box.py
@@ -8,9 +8,9 @@
 from .evolving_conditions import EvolvingConditions
 import json
 import os
+import pandas as pd
 
 import logging
-logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
 
 
@@ -552,16 +552,25 @@ def solve(self, output_path=None):
             # increments time
             curr_time += self.box_model_options.chem_step_time
 
+        df = pd.DataFrame(output_array[1:], columns=output_array[0])
         # outputs to file if output is present
-        if (output_path is not None):
-            logger.info("path_to_output = {}".format(output_path))
-            os.makedirs(os.path.dirname(output_path), exist_ok=True)
-            with open(output_path, 'w', newline='') as output:
-                writer = csv.writer(output)
-                writer.writerows(output_array)
-
-        # returns output_array
-        return output_array
+        if output_path is not None:
+
+            # Check if the output_path is a full path or just a file name
+            if os.path.dirname(output_path) == '':
+                # If output_path is just a filename, use the current directory
+                output_path = os.path.join(os.getcwd(), output_path)
+            elif not os.path.basename(output_path):
+                raise ValueError(f"Invalid output path: '{output_path}' does not contain a filename.")
+            
+            # Ensure the directory exists
+            dir_path = os.path.dirname(output_path)
+            if dir_path and not os.path.exists(dir_path):
+                os.makedirs(dir_path, exist_ok=True)
+
+            df.to_csv(output_path, index=False)
+
+        return df
 
     def readFromUIJson(self, path_to_json):
         """
diff --git a/tests/test_analytical.py b/tests/test_analytical.py
index c3eceb56..de0fd464 100644
--- a/tests/test_analytical.py
+++ b/tests/test_analytical.py
@@ -1,21 +1,25 @@
-from acom_music_box import MusicBox
+from acom_music_box import MusicBox, Examples
+import os
 
 import math
 
-
 class TestAnalytical:
     def test_run(self):
         box_model = MusicBox()
 
         # configures box model
-        conditions_path = "configs/analytical_config/my_config.json"
-        camp_path = "configs/analytical_config/camp_data"
-
+        conditions_path = Examples.Analytical.path
         box_model.readConditionsFromJson(conditions_path)
+
+        camp_path = os.path.join(
+            os.path.dirname(conditions_path),
+            box_model.config_file)
+
         box_model.create_solver(camp_path)
 
         # solves and saves output
-        output = box_model.solve()
+        df = box_model.solve()
+        output = [df.columns.values.tolist()] + df.values.tolist()
 
         conc_a_index = output[0].index("CONC.A")
         conc_b_index = output[0].index("CONC.B")
diff --git a/tests/test_full_gas_phase_mechanism.py b/tests/test_carbon_bond_5.py
similarity index 88%
rename from tests/test_full_gas_phase_mechanism.py
rename to tests/test_carbon_bond_5.py
index 2f104601..fdb82f01 100644
--- a/tests/test_full_gas_phase_mechanism.py
+++ b/tests/test_carbon_bond_5.py
@@ -1,22 +1,27 @@
-from acom_music_box import MusicBox
+from acom_music_box import MusicBox, Examples
+import os
 
 import csv
 import math
 
 
-class TestFullGassPhaseMechanism:
+class TestCarbonBond5:
     def test_run(self):
         box_model = MusicBox()
 
         # configures box model
-        conditions_path = "configs/full_gas_phase_mechanism_config/my_config.json"
-        camp_path = "configs/full_gas_phase_mechanism_config/camp_data"
-
+        conditions_path = Examples.CarbonBond5.path
         box_model.readConditionsFromJson(conditions_path)
+
+        camp_path = os.path.join(
+            os.path.dirname(conditions_path),
+            box_model.config_file)
+
         box_model.create_solver(camp_path)
 
         # solves and saves output
-        model_output = box_model.solve()
+        df = box_model.solve()
+        model_output = [df.columns.values.tolist()] + df.values.tolist()
 
         # read wall_loss_test.csv into test_output
         with open("expected_results/full_gas_phase_mechanism.csv", "r") as file:
@@ -116,5 +121,5 @@ def test_run(self):
 
 
 if __name__ == "__main__":
-    test = TestFullGassPhaseMechanism()
+    test = TestCarbonBond5()
     test.test_run()
diff --git a/tests/test_chapman.py b/tests/test_chapman.py
index 58e06175..765144da 100644
--- a/tests/test_chapman.py
+++ b/tests/test_chapman.py
@@ -1,4 +1,6 @@
-from acom_music_box import MusicBox
+from acom_music_box import MusicBox, Examples
+
+import os
 import csv
 import math
 
@@ -8,15 +10,18 @@ def test_run(self):
         box_model = MusicBox()
 
         # configures box model
-        conditions_path = "configs/chapman_config/my_config.json"
-        camp_path = "configs/chapman_config/camp_data"
-
+        conditions_path = Examples.Chapman.path
         box_model.readConditionsFromJson(conditions_path)
 
+        camp_path = os.path.join(
+            os.path.dirname(conditions_path),
+            box_model.config_file)
+
         box_model.create_solver(camp_path)
 
         # solves and saves output
-        model_output = box_model.solve()
+        df = box_model.solve()
+        model_output = [df.columns.values.tolist()] + df.values.tolist()
 
         # read chapman_test.csv into test_output
         with open("expected_results/chapman_test.csv", "r") as file:
diff --git a/tests/test_wall_loss.py b/tests/test_flow_tube.py
similarity index 82%
rename from tests/test_wall_loss.py
rename to tests/test_flow_tube.py
index f269054b..7fff3148 100644
--- a/tests/test_wall_loss.py
+++ b/tests/test_flow_tube.py
@@ -1,4 +1,5 @@
-from acom_music_box import MusicBox
+from acom_music_box import MusicBox, Examples
+import os
 
 import csv
 import math
@@ -9,14 +10,18 @@ def test_run(self):
         box_model = MusicBox()
 
         # configures box model
-        conditions_path = "configs/wall_loss_config/my_config.json"
-        camp_path = "configs/wall_loss_config/camp_data"
-
+        conditions_path = Examples.FlowTube.path
         box_model.readConditionsFromJson(conditions_path)
+
+        camp_path = os.path.join(
+            os.path.dirname(conditions_path),
+            box_model.config_file)
+
         box_model.create_solver(camp_path)
 
         # solves and saves output
-        model_output = box_model.solve()
+        df = box_model.solve()
+        model_output = [df.columns.values.tolist()] + df.values.tolist()
 
         # read wall_loss_test.csv into test_output
         with open("expected_results/wall_loss_test.csv", "r") as file: