diff --git a/ecoli/composites/ecoli_configs/fba_redux_div.json b/ecoli/composites/ecoli_configs/fba_redux_div.json
deleted file mode 100644
index ae43a7bd3..000000000
--- a/ecoli/composites/ecoli_configs/fba_redux_div.json
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-    "experiment_id" : "fba_redux",
-    "total_time" : 10,
-    "swap_processes" : {
-        "ecoli-metabolism" : "ecoli-metabolism-redux"
-    },
-    "exclude_processes": ["exchange_data"],
-    "flow": {
-        "ecoli-metabolism-redux": [["ecoli-chromosome-structure"]],
-        "ecoli-mass-listener": [["ecoli-metabolism-redux"]],
-        "RNA_counts_listener": [["ecoli-metabolism-redux"]],
-        "rna_synth_prob_listener": [["ecoli-metabolism-redux"]],
-        "monomer_counts_listener": [["ecoli-metabolism-redux"]],
-        "dna_supercoiling_listener": [["ecoli-metabolism-redux"]],
-        "replication_data_listener": [["ecoli-metabolism-redux"]],
-        "rnap_data_listener": [["ecoli-metabolism-redux"]],
-        "unique_molecule_counts": [["ecoli-metabolism-redux"]],
-        "ribosome_data_listener": [["ecoli-metabolism-redux"]]
-    },
-    "raw_output" : false,
-    "divide" : false
-}
diff --git a/ecoli/composites/ecoli_configs/fba_redux.json b/ecoli/composites/ecoli_configs/metabolism_redux.json
similarity index 100%
rename from ecoli/composites/ecoli_configs/fba_redux.json
rename to ecoli/composites/ecoli_configs/metabolism_redux.json
diff --git a/ecoli/composites/ecoli_configs/fba_redux_classic.json b/ecoli/composites/ecoli_configs/metabolism_redux_classic.json
similarity index 55%
rename from ecoli/composites/ecoli_configs/fba_redux_classic.json
rename to ecoli/composites/ecoli_configs/metabolism_redux_classic.json
index 853723d17..d45c5563a 100644
--- a/ecoli/composites/ecoli_configs/fba_redux_classic.json
+++ b/ecoli/composites/ecoli_configs/metabolism_redux_classic.json
@@ -7,15 +7,15 @@
     "exclude_processes": ["exchange_data"],
     "flow": {
         "ecoli-metabolism-redux": [["ecoli-chromosome-structure"]],
-        "ecoli-mass-listener": [["ecoli-metabolism-redux"]],
-        "RNA_counts_listener": [["ecoli-metabolism-redux"]],
-        "rna_synth_prob_listener": [["ecoli-metabolism-redux"]],
-        "monomer_counts_listener": [["ecoli-metabolism-redux"]],
-        "dna_supercoiling_listener": [["ecoli-metabolism-redux"]],
-        "replication_data_listener": [["ecoli-metabolism-redux"]],
-        "rnap_data_listener": [["ecoli-metabolism-redux"]],
-        "unique_molecule_counts": [["ecoli-metabolism-redux"]],
-        "ribosome_data_listener": [["ecoli-metabolism-redux"]]
+        "ecoli-mass-listener": [["ecoli-metabolism-redux-classic"]],
+        "RNA_counts_listener": [["ecoli-metabolism-redux-classic"]],
+        "rna_synth_prob_listener": [["ecoli-metabolism-redux-classic"]],
+        "monomer_counts_listener": [["ecoli-metabolism-redux-classic"]],
+        "dna_supercoiling_listener": [["ecoli-metabolism-redux-classic"]],
+        "replication_data_listener": [["ecoli-metabolism-redux-classic"]],
+        "rnap_data_listener": [["ecoli-metabolism-redux-classic"]],
+        "unique_molecule_counts": [["ecoli-metabolism-redux-classic"]],
+        "ribosome_data_listener": [["ecoli-metabolism-redux-classic"]]
     },
     "raw_output": false,
     "operons": true,
diff --git a/ecoli/experiments/metabolism_exchanger.py b/ecoli/experiments/metabolism_exchanger.py
new file mode 100644
index 000000000..52c2e3467
--- /dev/null
+++ b/ecoli/experiments/metabolism_exchanger.py
@@ -0,0 +1,340 @@
+"""
+==================================
+Metabolism using user-friendly FBA
+==================================
+"""
+import argparse
+
+# vivarium-core imports
+import pytest
+from vivarium.core.engine import Engine
+from vivarium.core.composer import Composer
+from vivarium.library.dict_utils import deep_merge
+
+# vivarium-ecoli imports
+from ecoli.experiments.ecoli_master_sim import EcoliSim, CONFIG_DIR_PATH
+from ecoli.library.sim_data import LoadSimData
+from ecoli.states.wcecoli_state import get_state_from_file
+from ecoli.composites.ecoli_master import SIM_DATA_PATH
+from ecoli.processes.metabolism_redux import MetabolismRedux
+from ecoli.processes.stubs.exchange_stub import Exchange
+from ecoli.processes.registries import topology_registry
+
+from wholecell.utils import units
+
+import numpy as np
+import pathlib, datetime
+import dill
+
+# get topology from ecoli_master
+metabolism_topology = topology_registry.access('ecoli-metabolism')
+
+
+# make a composite with Exchange
+class MetabolismExchange(Composer):
+    defaults = {
+        'metabolism': {
+            'kinetic_rates': [],
+        },
+        'exchanger': {},
+        'sim_data_path': SIM_DATA_PATH,
+        'seed': 0,
+    }
+
+    def __init__(self, config=None):
+        super().__init__(config)
+        self.load_sim_data = LoadSimData(
+            sim_data_path=self.config['sim_data_path'],
+            seed=self.config['seed'])
+
+    def generate_processes(self, config):
+        # configure metabolism
+        metabolism_config = self.load_sim_data.get_metabolism_redux_config()
+        metabolism_config = deep_merge(metabolism_config, config['metabolism'])
+        metabolism_process = MetabolismRedux(metabolism_config)
+
+        example_update = {'ATP[c]': 9064, 'DATP[c]': 2222, 'DCTP[c]': 1649, 'DGTP[c]': 1647, 'FAD[c]': 171,
+                          'GTP[c]': 20122, 'LEU[c]': 325, 'METHYLENE-THF[c]': 223, 'NAD[c]': 769,
+                          'PHENYL-PYRUVATE[c]': 996, 'REDUCED-MENAQUINONE[c]': 240, 'UTP[c]': 14648}
+
+        # configure exchanger stub process
+        # TODO -- this needs a dictionary with {mol_id: exchanged counts/sec}
+        exchanger_config = {'exchanges': example_update, 'time_step': metabolism_config['time_step']}
+        exchanger_process = Exchange(exchanger_config)
+
+        return {
+            'metabolism': metabolism_process,
+            'exchanger': exchanger_process,
+        }
+
+    def generate_topology(self, config):
+        return {
+            'metabolism': metabolism_topology,
+            'exchanger': {
+                'bulk': ('bulk',),
+            }
+        }
+
+
+def run_metabolism():
+    # load the sim data
+    load_sim_data = LoadSimData(
+        sim_data_path=SIM_DATA_PATH,
+        seed=0)
+
+    # Create process, experiment, loading in initial state from file.
+    config = load_sim_data.get_metabolism_redux_config()
+    metabolism_process = MetabolismRedux(config)
+
+    initial_state = get_state_from_file(
+        path=f'data/wcecoli_t0.json')
+
+    metabolism_composite = metabolism_process.generate()
+    metabolism_composite['topology']['ecoli-metabolism-redux'][
+        'bulk_total'] = ('bulk',)
+    experiment = Engine(
+        steps=metabolism_composite['steps'],
+        topology=metabolism_composite['topology'],
+        initial_state=initial_state
+    )
+
+    experiment.update(10)
+
+    data = experiment.emitter.get_timeseries()
+
+
+def run_metabolism_composite():
+    composer = MetabolismExchange()
+    metabolism_composite = composer.generate()
+    metabolism_composite['topology']['metabolism'][
+        'bulk_total'] = ('bulk',)
+
+    initial_state = get_state_from_file(
+        path=f'data/wcecoli_t0.json')
+    initial_state['process_state'] = {
+        'polypeptide_elongation': {
+            'aa_exchange_rates': units.mol / (units.L * units.s) * np.array([
+            -4.520e-07, -3.786e-07, -5.700e-09, -8.880e-08,  0.000e+00,
+            -6.600e-09, -1.200e-09, -6.670e-08, -3.200e-09, -4.800e-09,
+            -1.251e-07, -7.870e-08, -2.200e-09, -3.860e-08, -4.600e-09,
+            -1.486e-07, -8.400e-09, -1.560e-08, -3.800e-08,  0.000e+00,
+            -8.300e-09]),
+            'gtp_to_hydrolyze': 1009121.4
+        }}
+
+    experiment = Engine(
+        processes=metabolism_composite['processes'],
+        topology=metabolism_composite['topology'],
+        initial_state=initial_state
+    )
+
+    experiment.update(10)
+
+    data = experiment.emitter.get_data()
+
+
+def run_ecoli_with_metabolism_redux(
+        filename='fba_redux',
+        total_time=50,
+        divide=True,
+        initial_state_file='wcecoli_t0',
+        progress_bar=True,
+        log_updates=False,
+        emitter='timeseries',
+        name='fba-redux',
+        raw_output=False,
+        save=False,
+        # save_times=4,
+):
+    # filename = 'default'
+    sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + '.json')
+    sim.total_time = total_time
+    sim.divide = divide
+    sim.progress_bar = progress_bar
+    sim.log_updates = log_updates
+    sim.emitter = emitter
+    sim.initial_state = get_state_from_file(path=f'data/{initial_state_file}.json')
+    sim.raw_output = raw_output
+    sim.save = save
+
+
+    sim.build_ecoli()
+    sim.run()
+
+    query = []
+    folder = f'out/fbagd/{name}_{total_time}_{datetime.date.today()}/'
+    # save_sim_output(folder, query, sim, save_model=True)
+
+
+def run_ecoli_with_metabolism_redux_classic(
+        filename='fba_redux_classic',
+        total_time=4,
+        divide=True,
+        initial_state_file='wcecoli_t0',
+        progress_bar=True,
+        log_updates=False,
+        emitter='timeseries',
+        name='fba-redux',
+        raw_output=False,
+        save=False,
+        # save_times=4,
+):
+    # filename = 'default'
+    sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + '.json')
+    sim.total_time = total_time
+    sim.divide = divide
+    sim.progress_bar = progress_bar
+    sim.log_updates = log_updates
+    sim.emitter = emitter
+    sim.initial_state = get_state_from_file(path=f'data/{initial_state_file}.json')
+    sim.raw_output = raw_output
+    sim.save = save
+    # sim.save_times = [4]
+
+    # # simplify working with uptake
+    # sim.initial_state['environment']['exchange_data']['constrained'] = {}
+    # sim.initial_state['environment']['exchange_data']['unconstrained'].add('GLC[p]')
+    #
+    # # in sim.initial_state['environment']['exchange_data']['unconstrained'], edit the set of molecules to be exchanged
+    # sim.initial_state['environment']['exchange_data']['unconstrained'].remove('GLC[p]')
+    # sim.initial_state['environment']['exchange_data']['unconstrained'].add('FRU[p]')
+
+
+    sim.build_ecoli()
+    sim.run()
+
+    query = []
+    folder = f'out/fbagd/{name}_{total_time}_{datetime.date.today()}/'
+    # save_sim_output(folder, query, sim, save_model=True)
+
+
+@pytest.mark.slow
+def test_ecoli_with_metabolism_redux(
+        filename='fba_redux',
+        total_time=4,
+        divide=False,
+        progress_bar=True,
+        log_updates=False,
+        emitter='timeseries',
+):
+    sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + '.json')
+    sim.total_time = total_time
+    sim.divide = divide
+    sim.progress_bar = progress_bar
+    sim.log_updates = log_updates
+    sim.emitter = emitter
+    sim.build_ecoli()
+
+    # run simulation and add asserts to output
+    sim.run()
+
+    # assert 'ecoli-metabolism-gradient-descent' in sim.ecoli['processes']
+    # assert 'ecoli-metabolism' not in sim.ecoli['processes']
+    # assert 'ecoli-metabolism-gradient-descent' in sim.ecoli['topology']
+    # assert 'ecoli-metabolism' not in sim.ecoli['topology']
+
+
+
+@pytest.mark.slow
+def test_ecoli_with_metabolism_redux_div(
+        filename='fba_redux_div',
+        total_time=4,
+        divide=True,
+        emitter='timeseries',
+):
+    # TODO (Cyrus) - Add test that affirms structure of output query.
+    sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + '.json')
+    sim.total_time = total_time
+    sim.divide = divide
+    sim.emitter = emitter
+    sim.build_ecoli()
+
+    sim.run()
+    
+    # # assert that the processes were swapped
+    # assert 'ecoli-metabolism-gradient-descent' in sim.processes
+    # assert 'ecoli-metabolism' not in sim.processes
+    # assert 'ecoli-metabolism-gradient-descent' in sim.processes
+    # assert 'ecoli-metabolism' not in sim.processes
+
+    query = []
+    agents = sim.query()['agents'].keys()
+    for agent in agents:
+        query.extend([('agents', agent, 'listeners', 'fba_results'),
+                      ('agents', agent, 'listeners', 'mass'),
+                      ('agents', agent, 'bulk')])
+    output = sim.query(query)
+
+    # test that water is being used (model is running)
+    assert sum(output['agents'][agent]['listeners']['fba_results']['estimated_exchange_dmdt']['WATER']) != 0
+
+def run_ecoli_with_default_metabolism(
+        filename='default',
+        total_time=10,
+        divide=False,
+        progress_bar=True,
+        log_updates=False,
+        emitter='timeseries',
+):
+    sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + '.json')
+    sim.total_time = total_time
+    sim.divide = divide
+    sim.progress_bar = progress_bar
+    sim.log_updates = log_updates
+    sim.emitter = emitter
+    sim.build_ecoli()
+
+    sim.run()
+    # output = sim.query()
+    output = sim.ecoli_experiment.emitter.get_timeseries()
+
+
+    folder = f'out/fbagd/{total_time}/{datetime.datetime.now()}/'
+    pathlib.Path(folder).mkdir(parents=True, exist_ok=True)
+    np.save(folder + 'fba_results.npy', output['listeners']['fba_results'])
+    np.save(folder + 'mass.npy', output['listeners']['mass'])
+    np.save(folder + 'bulk.npy', output['bulk'])
+    np.save(folder + 'stoichiometry.npy', sim.ecoli_experiment.steps['ecoli-metabolism'].model.stoichiometry)
+
+experiment_library = {
+    '0': run_metabolism,
+    '1': run_metabolism_composite,
+    '2': run_ecoli_with_metabolism_redux,
+    '2a': run_ecoli_with_metabolism_redux_classic,
+    '3': test_ecoli_with_metabolism_redux,
+    '4': test_ecoli_with_metabolism_redux_div,
+    '5': run_ecoli_with_default_metabolism,
+}
+
+
+def save_sim_output(folder, query, sim, save_model=False):
+    agents = sim.query()['agents'].keys()
+    for agent in agents:
+        query.extend([('agents', agent, 'listeners', 'fba_results'),
+                      ('agents', agent, 'listeners', 'mass'),
+                      ('agents', agent, 'bulk')])
+    output = sim.query(query)
+    pathlib.Path(folder).mkdir(parents=True, exist_ok=True)
+    np.save(folder + 'output.npy', output)
+
+    if save_model:
+        f = open(folder + 'agent_processes.pkl', 'wb')
+        dill.dump(sim.ecoli['processes']['agents'][agent], f)
+        f.close()
+
+        f = open(folder + 'agent_steps.pkl', 'wb')
+        dill.dump(sim.ecoli['steps']['agents'][agent], f)
+        f.close()
+
+# run experiments with command line arguments: python ecoli/experiments/metabolism_redux_sim.py -n exp_id
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='user-friendly metabolism')
+    parser.add_argument('--name', '-n', default=[], nargs='+', help='test ids to run')
+    args = parser.parse_args()
+    run_all = not args.name
+
+    for name in args.name:
+        experiment_library[name]()
+    if run_all:
+        for name, test in experiment_library.items():
+            test()
diff --git a/ecoli/experiments/metabolism_redux_sim.py b/ecoli/experiments/metabolism_redux_sim.py
index 52c2e3467..cc9506a74 100644
--- a/ecoli/experiments/metabolism_redux_sim.py
+++ b/ecoli/experiments/metabolism_redux_sim.py
@@ -7,18 +7,10 @@
 
 # vivarium-core imports
 import pytest
-from vivarium.core.engine import Engine
-from vivarium.core.composer import Composer
-from vivarium.library.dict_utils import deep_merge
 
 # vivarium-ecoli imports
 from ecoli.experiments.ecoli_master_sim import EcoliSim, CONFIG_DIR_PATH
-from ecoli.library.sim_data import LoadSimData
 from ecoli.states.wcecoli_state import get_state_from_file
-from ecoli.composites.ecoli_master import SIM_DATA_PATH
-from ecoli.processes.metabolism_redux import MetabolismRedux
-from ecoli.processes.stubs.exchange_stub import Exchange
-from ecoli.processes.registries import topology_registry
 
 from wholecell.utils import units
 
@@ -26,115 +18,8 @@
 import pathlib, datetime
 import dill
 
-# get topology from ecoli_master
-metabolism_topology = topology_registry.access('ecoli-metabolism')
-
-
-# make a composite with Exchange
-class MetabolismExchange(Composer):
-    defaults = {
-        'metabolism': {
-            'kinetic_rates': [],
-        },
-        'exchanger': {},
-        'sim_data_path': SIM_DATA_PATH,
-        'seed': 0,
-    }
-
-    def __init__(self, config=None):
-        super().__init__(config)
-        self.load_sim_data = LoadSimData(
-            sim_data_path=self.config['sim_data_path'],
-            seed=self.config['seed'])
-
-    def generate_processes(self, config):
-        # configure metabolism
-        metabolism_config = self.load_sim_data.get_metabolism_redux_config()
-        metabolism_config = deep_merge(metabolism_config, config['metabolism'])
-        metabolism_process = MetabolismRedux(metabolism_config)
-
-        example_update = {'ATP[c]': 9064, 'DATP[c]': 2222, 'DCTP[c]': 1649, 'DGTP[c]': 1647, 'FAD[c]': 171,
-                          'GTP[c]': 20122, 'LEU[c]': 325, 'METHYLENE-THF[c]': 223, 'NAD[c]': 769,
-                          'PHENYL-PYRUVATE[c]': 996, 'REDUCED-MENAQUINONE[c]': 240, 'UTP[c]': 14648}
-
-        # configure exchanger stub process
-        # TODO -- this needs a dictionary with {mol_id: exchanged counts/sec}
-        exchanger_config = {'exchanges': example_update, 'time_step': metabolism_config['time_step']}
-        exchanger_process = Exchange(exchanger_config)
-
-        return {
-            'metabolism': metabolism_process,
-            'exchanger': exchanger_process,
-        }
-
-    def generate_topology(self, config):
-        return {
-            'metabolism': metabolism_topology,
-            'exchanger': {
-                'bulk': ('bulk',),
-            }
-        }
-
-
-def run_metabolism():
-    # load the sim data
-    load_sim_data = LoadSimData(
-        sim_data_path=SIM_DATA_PATH,
-        seed=0)
-
-    # Create process, experiment, loading in initial state from file.
-    config = load_sim_data.get_metabolism_redux_config()
-    metabolism_process = MetabolismRedux(config)
-
-    initial_state = get_state_from_file(
-        path=f'data/wcecoli_t0.json')
-
-    metabolism_composite = metabolism_process.generate()
-    metabolism_composite['topology']['ecoli-metabolism-redux'][
-        'bulk_total'] = ('bulk',)
-    experiment = Engine(
-        steps=metabolism_composite['steps'],
-        topology=metabolism_composite['topology'],
-        initial_state=initial_state
-    )
-
-    experiment.update(10)
-
-    data = experiment.emitter.get_timeseries()
-
-
-def run_metabolism_composite():
-    composer = MetabolismExchange()
-    metabolism_composite = composer.generate()
-    metabolism_composite['topology']['metabolism'][
-        'bulk_total'] = ('bulk',)
-
-    initial_state = get_state_from_file(
-        path=f'data/wcecoli_t0.json')
-    initial_state['process_state'] = {
-        'polypeptide_elongation': {
-            'aa_exchange_rates': units.mol / (units.L * units.s) * np.array([
-            -4.520e-07, -3.786e-07, -5.700e-09, -8.880e-08,  0.000e+00,
-            -6.600e-09, -1.200e-09, -6.670e-08, -3.200e-09, -4.800e-09,
-            -1.251e-07, -7.870e-08, -2.200e-09, -3.860e-08, -4.600e-09,
-            -1.486e-07, -8.400e-09, -1.560e-08, -3.800e-08,  0.000e+00,
-            -8.300e-09]),
-            'gtp_to_hydrolyze': 1009121.4
-        }}
-
-    experiment = Engine(
-        processes=metabolism_composite['processes'],
-        topology=metabolism_composite['topology'],
-        initial_state=initial_state
-    )
-
-    experiment.update(10)
-
-    data = experiment.emitter.get_data()
-
-
 def run_ecoli_with_metabolism_redux(
-        filename='fba_redux',
+        filename='metabolism_redux',
         total_time=50,
         divide=True,
         initial_state_file='wcecoli_t0',
@@ -167,14 +52,14 @@ def run_ecoli_with_metabolism_redux(
 
 
 def run_ecoli_with_metabolism_redux_classic(
-        filename='fba_redux_classic',
+        filename='metabolism_redux_classic',
         total_time=4,
         divide=True,
         initial_state_file='wcecoli_t0',
         progress_bar=True,
         log_updates=False,
         emitter='timeseries',
-        name='fba-redux',
+        name='metabolism-redux-classic',
         raw_output=False,
         save=False,
         # save_times=4,
@@ -210,7 +95,7 @@ def run_ecoli_with_metabolism_redux_classic(
 
 @pytest.mark.slow
 def test_ecoli_with_metabolism_redux(
-        filename='fba_redux',
+        filename='metabolism_redux',
         total_time=4,
         divide=False,
         progress_bar=True,
@@ -237,7 +122,7 @@ def test_ecoli_with_metabolism_redux(
 
 @pytest.mark.slow
 def test_ecoli_with_metabolism_redux_div(
-        filename='fba_redux_div',
+        filename='metabolism_redux',
         total_time=4,
         divide=True,
         emitter='timeseries',
@@ -268,6 +153,66 @@ def test_ecoli_with_metabolism_redux_div(
     # test that water is being used (model is running)
     assert sum(output['agents'][agent]['listeners']['fba_results']['estimated_exchange_dmdt']['WATER']) != 0
 
+
+@pytest.mark.slow
+def test_ecoli_with_metabolism_classic(
+        filename='metabolism_redux_classic',
+        total_time=4,
+        divide=False,
+        progress_bar=True,
+        log_updates=False,
+        emitter='timeseries',
+):
+    sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + '.json')
+    sim.total_time = total_time
+    sim.divide = divide
+    sim.progress_bar = progress_bar
+    sim.log_updates = log_updates
+    sim.emitter = emitter
+    sim.build_ecoli()
+
+    # run simulation and add asserts to output
+    sim.run()
+
+    # assert 'ecoli-metabolism-gradient-descent' in sim.ecoli['processes']
+    # assert 'ecoli-metabolism' not in sim.ecoli['processes']
+    # assert 'ecoli-metabolism-gradient-descent' in sim.ecoli['topology']
+    # assert 'ecoli-metabolism' not in sim.ecoli['topology']
+
+
+@pytest.mark.slow
+def test_ecoli_with_metabolism_classic_div(
+        filename='metabolism_redux_classic',
+        total_time=4,
+        divide=True,
+        emitter='timeseries',
+):
+    # TODO (Cyrus) - Add test that affirms structure of output query.
+    sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + '.json')
+    sim.total_time = total_time
+    sim.divide = divide
+    sim.emitter = emitter
+    sim.build_ecoli()
+
+    sim.run()
+
+    # # assert that the processes were swapped
+    # assert 'ecoli-metabolism-gradient-descent' in sim.processes
+    # assert 'ecoli-metabolism' not in sim.processes
+    # assert 'ecoli-metabolism-gradient-descent' in sim.processes
+    # assert 'ecoli-metabolism' not in sim.processes
+
+    query = []
+    agents = sim.query()['agents'].keys()
+    for agent in agents:
+        query.extend([('agents', agent, 'listeners', 'fba_results'),
+                      ('agents', agent, 'listeners', 'mass'),
+                      ('agents', agent, 'bulk')])
+    output = sim.query(query)
+
+    # test that water is being used (model is running)
+    assert sum(output['agents'][agent]['listeners']['fba_results']['estimated_exchange_dmdt']['WATER']) != 0
+
 def run_ecoli_with_default_metabolism(
         filename='default',
         total_time=10,
@@ -297,8 +242,6 @@ def run_ecoli_with_default_metabolism(
     np.save(folder + 'stoichiometry.npy', sim.ecoli_experiment.steps['ecoli-metabolism'].model.stoichiometry)
 
 experiment_library = {
-    '0': run_metabolism,
-    '1': run_metabolism_composite,
     '2': run_ecoli_with_metabolism_redux,
     '2a': run_ecoli_with_metabolism_redux_classic,
     '3': test_ecoli_with_metabolism_redux,
diff --git a/ecoli/processes/metabolism_redux_classic.py b/ecoli/processes/metabolism_redux_classic.py
index 0b009a23d..76a71cdd0 100644
--- a/ecoli/processes/metabolism_redux_classic.py
+++ b/ecoli/processes/metabolism_redux_classic.py
@@ -427,8 +427,9 @@ def __init__(self,
                  reactions: Iterable[list],
                  homeostatic_metabolites: Iterable[str],
                  kinetic_reactions: Iterable[str],
-                 free_reactions: Iterable[str],
+                 free_reactions: Iterable[str] = None, # TODO Use free reactions
     ):
+
         self.S_orig = csr_matrix(stoich_arr.astype(np.int64))
         self.S_exch = None
         self.n_mets, self.n_orig_rxns = self.S_orig.shape