Python MetabolicModel示例

示例#1

文件： test_randomsparse.py 项目： spikeliu/psamm

    def setUp(self):
        self._database = DictDatabase()
        self._database.set_reaction('rxn_1', parse_reaction('A[e] => B[e]'))
        self._database.set_reaction('rxn_2', parse_reaction('B[e] => C[e]'))
        self._database.set_reaction('rxn_3', parse_reaction('B[e] => D[e]'))
        self._database.set_reaction('rxn_4', parse_reaction('C[e] => E[e]'))
        self._database.set_reaction('rxn_5', parse_reaction('D[e] => E[e]'))
        self._database.set_reaction('rxn_6', parse_reaction('E[e] =>'))
        self._database.set_reaction('ex_A', parse_reaction('A[e] <=>'))

        self._mm = MetabolicModel.load_model(self._database,
                                             self._database.reactions)
        self._assoc = {
            'rxn_1': boolean.Expression('gene_1'),
            'rxn_2': boolean.Expression('gene_2 or gene_3'),
            'rxn_5': boolean.Expression('gene_3 and gene_4')
        }
        self._obj_reaction = 'rxn_6'

        try:
            self._solver = generic.Solver()
        except generic.RequirementsError:
            self.skipTest('Unable to find an LP solver for tests')

        self._prob = fluxanalysis.FluxBalanceProblem(self._mm, self._solver)

示例#2

文件： test_randomsparse.py 项目： spikeliu/psamm

    def setUp(self):
        self._database = DictDatabase()
        self._database.set_reaction('rxn_1', parse_reaction('A[e] => B[e]'))
        self._database.set_reaction('rxn_2', parse_reaction('B[e] => C[e]'))
        self._database.set_reaction('rxn_3', parse_reaction('B[e] => D[e]'))
        self._database.set_reaction('rxn_4', parse_reaction('C[e] => E[e]'))
        self._database.set_reaction('rxn_5', parse_reaction('D[e] => E[e]'))
        self._database.set_reaction('rxn_6', parse_reaction('E[e] =>'))
        self._database.set_reaction('ex_A', parse_reaction('A[e] <=>'))

        self._mm = MetabolicModel.load_model(
            self._database, self._database.reactions)
        self._assoc = {
            'rxn_1': boolean.Expression('gene_1'),
            'rxn_2': boolean.Expression('gene_2 or gene_3'),
            'rxn_5': boolean.Expression('gene_3 and gene_4')
        }
        self._obj_reaction = 'rxn_6'

        try:
            self._solver = generic.Solver()
        except generic.RequirementsError:
            self.skipTest('Unable to find an LP solver for tests')

        self._prob = fluxanalysis.FluxBalanceProblem(self._mm, self._solver)

示例#3

文件： test_fastcore.py 项目： gitter-badger/psamm

 def setUp(self):
     # TODO use mock model instead of actual model
     self.database = DictDatabase()
     self.database.set_reaction("rxn_1", parse_reaction("=> |A|"))
     self.database.set_reaction("rxn_2", parse_reaction("(0.000001) |A| =>"))
     self.model = MetabolicModel.load_model(self.database, self.database.reactions)
     self.solver = cplex.Solver()

示例#4

    def setUp(self):
        self._database = DictDatabase()
        self._database.set_reaction('rxn_1', parse_reaction('A[e] => B[e]'))
        self._database.set_reaction('rxn_2', parse_reaction('B[e] => C[e]'))
        self._database.set_reaction('rxn_3', parse_reaction('B[e] <=> D[e]'))
        self._database.set_reaction('rxn_4', parse_reaction('C[e] <=> E[e]'))
        self._database.set_reaction('rxn_5', parse_reaction('D[e] => E[e]'))
        self._database.set_reaction('rxn_6', parse_reaction('E[e] =>'))
        self._database.set_reaction('ex_A', parse_reaction('A[e] <=>'))

        self._mm = MetabolicModel.load_model(
            self._database, self._database.reactions)
        self._assoc = {
            'rxn_1': str('gene_1'),
            'rxn_2': str('gene_2'),
            'rxn_3': str('gene_5'),
            'rxn_4': str('gene_3 or gene_4'),
            'rxn_5': str('gene_5 and gene_6')
        }
        self._obj_reaction = 'rxn_6'

        try:
            self._solver = generic.Solver()
        except generic.RequirementsError:
            self.skipTest('Unable to find an LP solver for tests')
        try:
            self.solver = generic.Solver(integer=True)
        except generic.RequirementsError:
            self.skipTest('Needs and integer programming solver')

示例#5

文件： test_randomsparse.py 项目： spikeliu/psamm

 def setUp(self):
     self._database = DictDatabase()
     self._database.set_reaction('rxn_1', parse_reaction('|A| <=>'))
     self._database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
     self._database.set_reaction('rxn_3', parse_reaction('|C| <=> |B|'))
     self._database.set_reaction('rxn_4', parse_reaction('|C| <=>'))
     self._mm = MetabolicModel.load_model(self._database,
                                          self._database.reactions)

示例#6

文件： test_randomsparse.py 项目： spikeliu/psamm

 def setUp(self):
     self._database = DictDatabase()
     self._database.set_reaction('rxn_1', parse_reaction('|A| <=>'))
     self._database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
     self._database.set_reaction('rxn_3', parse_reaction('|C| <=> |B|'))
     self._database.set_reaction('rxn_4', parse_reaction('|C| <=>'))
     self._mm = MetabolicModel.load_model(
         self._database, self._database.reactions)

示例#7

文件： test_metabolicmodel.py 项目： amenge/psamm

    def test_load_model_with_reaction_subset(self):
        database = DictDatabase()
        database.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
        database.set_reaction('rxn_2', parse_reaction('|B| => |C|'))
        database.set_reaction('rxn_3', parse_reaction('|C| => |D|'))
        model = MetabolicModel.load_model(database, {'rxn_1'})

        self.assertEqual(set(model.reactions), {'rxn_1'})

示例#8

 def setUp(self):
     self.database = DictDatabase()
     self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
     self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
     self.database.set_reaction('rxn_3', parse_reaction('|A| => |D[e]|'))
     self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
     self.database.set_reaction('rxn_5', parse_reaction('|C| => |D[e]|'))
     self.database.set_reaction('rxn_6', parse_reaction('|D[e]| =>'))
     self.model = MetabolicModel.load_model(
         self.database, self.database.reactions)

示例#9

文件： test_randomsparse.py 项目： spikeliu/psamm

    def setUp(self):
        self._database = DictDatabase()
        self._database.set_reaction('rxn_1', parse_reaction('|A| <=>'))
        self._database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
        self._database.set_reaction('rxn_3', parse_reaction('|C| <=> |B|'))
        self._database.set_reaction('rxn_4', parse_reaction('|C| <=>'))
        self._mm = MetabolicModel.load_model(
            self._database, self._database.reactions)

        self._strategy = randomsparse.ReactionDeletionStrategy(self._mm)

示例#10

文件： test_randomsparse.py 项目： spikeliu/psamm

    def setUp(self):
        self._database = DictDatabase()
        self._database.set_reaction('rxn_1', parse_reaction('|A| <=>'))
        self._database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
        self._database.set_reaction('rxn_3', parse_reaction('|C| <=> |B|'))
        self._database.set_reaction('rxn_4', parse_reaction('|C| <=>'))
        self._mm = MetabolicModel.load_model(self._database,
                                             self._database.reactions)

        self._strategy = randomsparse.ReactionDeletionStrategy(self._mm)

示例#11

 def setUp(self):
     self.database = DictDatabase()
     self.database.set_reaction('rxn_1', parse_reaction('=> (2) A[c]'))
     self.database.set_reaction('rxn_2', parse_reaction('A[c] <=> B[c]'))
     self.database.set_reaction('rxn_3', parse_reaction('A[c] => D[e]'))
     self.database.set_reaction('rxn_4', parse_reaction('A[c] => C[c]'))
     self.database.set_reaction('rxn_5', parse_reaction('C[c] => D[e]'))
     self.database.set_reaction('rxn_6', parse_reaction('D[e] =>'))
     self.model = MetabolicModel.load_model(self.database,
                                            self.database.reactions)

示例#12

文件： test_metabolicmodel.py 项目： gitter-badger/psamm

 def setUp(self):
     # TODO use mock database instead of actual database
     self.database = DictDatabase()
     self.database.set_reaction("rxn_1", parse_reaction("=> (2) |A|"))
     self.database.set_reaction("rxn_2", parse_reaction("|A| <=> |B|"))
     self.database.set_reaction("rxn_3", parse_reaction("|A| => |D[e]|"))
     self.database.set_reaction("rxn_4", parse_reaction("|A| => |C|"))
     self.database.set_reaction("rxn_5", parse_reaction("|C| => |D[e]|"))
     self.database.set_reaction("rxn_6", parse_reaction("|D[e]| =>"))
     self.model = MetabolicModel.load_model(self.database, self.database.reactions)

示例#13

文件： test_gapfilling.py 项目： keitht547/psamm

 def setUp(self):
     self.database = DictDatabase()
     self.database.set_reaction('rxn_1', parse_reaction('=> (2) A[c]'))
     self.database.set_reaction('rxn_2', parse_reaction('A[c] <=> B[c]'))
     self.database.set_reaction('rxn_3', parse_reaction('A[c] => D[e]'))
     self.database.set_reaction('rxn_4', parse_reaction('A[c] => C[c]'))
     self.database.set_reaction('rxn_5', parse_reaction('C[c] => D[e]'))
     self.database.set_reaction('rxn_6', parse_reaction('D[e] =>'))
     self.model = MetabolicModel.load_model(
         self.database, self.database.reactions)

示例#14

文件： test_fastcore.py 项目： gitter-badger/psamm

 def setUp(self):
     # TODO use mock model instead of actual model
     self.database = DictDatabase()
     self.database.set_reaction("rxn_1", parse_reaction("=> (2) |A|"))
     self.database.set_reaction("rxn_2", parse_reaction("|A| <=> |B|"))
     self.database.set_reaction("rxn_3", parse_reaction("|A| => |D|"))
     self.database.set_reaction("rxn_4", parse_reaction("|A| => |C|"))
     self.database.set_reaction("rxn_5", parse_reaction("|C| => |D|"))
     self.database.set_reaction("rxn_6", parse_reaction("|D| =>"))
     self.model = MetabolicModel.load_model(self.database, self.database.reactions)
     self.solver = cplex.Solver()

示例#15

文件： test_metabolicmodel.py 项目： keitht547/psamm

    def setUp(self):
        self.database = DictDatabase()
        self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
        self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
        self.database.set_reaction('rxn_3', parse_reaction('|A| => |D|'))
        self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
        self.database.set_reaction('rxn_5', parse_reaction('|C| => |D|'))
        self.database.set_reaction('rxn_6', parse_reaction('|D| =>'))

        model = MetabolicModel.load_model(self.database, self.database.reactions)
        self.model = FlipableModelView(model)

示例#16

文件： test_fluxanalysis.py 项目： gitter-badger/psamm

 def setUp(self):
     self.database = DictDatabase()
     self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
     self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
     self.database.set_reaction('rxn_3', parse_reaction('|A| => |D|'))
     self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
     self.database.set_reaction('rxn_5', parse_reaction('|C| => |D|'))
     self.database.set_reaction('rxn_6', parse_reaction('|D| =>'))
     self.model = MetabolicModel.load_model(
         self.database, self.database.reactions)
     self.solver = cplex.Solver()

示例#17

文件： test_massconsistency.py 项目： gitter-badger/psamm

    def setUp(self):
        # TODO use mock model instead of actual model
        self.database = DictDatabase()
        self.database.set_reaction('rxn_1', parse_reaction(
            '|A| + |B| => |C|'))
        self.database.set_reaction('rxn_2', parse_reaction(
            '|C| + |Z| => |A| + |B|'))
        self.model = MetabolicModel.load_model(
            self.database, self.database.reactions)

        self.solver = cplex.Solver()

示例#18

文件： test_metabolicmodel.py 项目： amenge/psamm

 def setUp(self):
     # TODO use mock database instead of actual database
     self.database = DictDatabase()
     self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
     self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
     self.database.set_reaction('rxn_3', parse_reaction('|A| => |D[e]|'))
     self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
     self.database.set_reaction('rxn_5', parse_reaction('|C| => |D[e]|'))
     self.database.set_reaction('rxn_6', parse_reaction('|D[e]| =>'))
     self.model = MetabolicModel.load_model(
         self.database, self.database.reactions)

示例#19

文件： test_metabolicmodel.py 项目： amenge/psamm

    def setUp(self):
        # TODO use mock database instead of actual database
        self.database = DictDatabase()
        self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
        self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
        self.database.set_reaction('rxn_3', parse_reaction('|A| => |D|'))
        self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
        self.database.set_reaction('rxn_5', parse_reaction('|C| => |D|'))
        self.database.set_reaction('rxn_6', parse_reaction('|D| =>'))

        model = MetabolicModel.load_model(self.database, self.database.reactions)
        self.model = FlipableModelView(model)

示例#20

文件： test_randomsparse.py 项目： spikeliu/psamm

    def setUp(self):
        self._database = DictDatabase()
        self._database.set_reaction('rxn_1', parse_reaction('|A| <=>'))
        self._database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
        self._database.set_reaction('rxn_3', parse_reaction('|C| <=> |B|'))
        self._database.set_reaction('rxn_4', parse_reaction('|C| <=>'))
        self._mm = MetabolicModel.load_model(
            self._database, self._database.reactions)
        self._assoc = {'rxn_2': boolean.Expression('gene_1 or gene_2')}

        self._strategy = randomsparse.GeneDeletionStrategy(
            self._mm, self._assoc)

示例#21

    def setUp(self):
        self.database = DictDatabase()
        self.database.set_reaction('rxn_1', parse_reaction('|A| + |B| => |C|'))
        self.database.set_reaction('rxn_2',
                                   parse_reaction('|C| + |Z| => |A| + |B|'))
        self.model = MetabolicModel.load_model(self.database,
                                               self.database.reactions)

        try:
            self.solver = generic.Solver()
        except generic.RequirementsError:
            self.skipTest('Unable to find an LP solver for tests')

示例#22

文件： test_randomsparse.py 项目： spikeliu/psamm

    def setUp(self):
        self._database = DictDatabase()
        self._database.set_reaction('rxn_1', parse_reaction('|A| <=>'))
        self._database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
        self._database.set_reaction('rxn_3', parse_reaction('|C| <=> |B|'))
        self._database.set_reaction('rxn_4', parse_reaction('|C| <=>'))
        self._mm = MetabolicModel.load_model(self._database,
                                             self._database.reactions)
        self._assoc = {'rxn_2': boolean.Expression('gene_1 or gene_2')}

        self._strategy = randomsparse.GeneDeletionStrategy(
            self._mm, self._assoc)

示例#23

文件： test_fastcore.py 项目： keitht547/psamm

    def setUp(self):
        self.database = DictDatabase()
        self.database.set_reaction('rxn_1', parse_reaction('|A| <=>'))
        self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
        self.database.set_reaction('rxn_3', parse_reaction('|C| <=> |B|'))
        self.database.set_reaction('rxn_4', parse_reaction('|C| <=>'))
        self.model = MetabolicModel.load_model(
            self.database, self.database.reactions)

        try:
            self.solver = generic.Solver()
        except generic.RequirementsError:
            self.skipTest('Unable to find an LP solver for tests')

示例#24

    def setUp(self):
        # TODO use mock model instead of actual model
        self.database = DictDatabase()
        self.database.set_reaction('rxn_1', parse_reaction('=> |A|'))
        self.database.set_reaction('rxn_2',
                                   parse_reaction('(0.000001) |A| =>'))
        self.model = MetabolicModel.load_model(self.database,
                                               self.database.reactions)

        try:
            self.solver = generic.Solver()
        except generic.RequirementsError:
            self.skipTest('Unable to find an LP solver for tests')

示例#25

文件： test_fastcore.py 项目： amenge/psamm

    def setUp(self):
        # TODO use mock model instead of actual model
        self.database = DictDatabase()
        self.database.set_reaction('rxn_1', parse_reaction('=> |A|'))
        self.database.set_reaction('rxn_2',
            parse_reaction('(0.000001) |A| =>'))
        self.model = MetabolicModel.load_model(
            self.database, self.database.reactions)

        try:
            self.solver = generic.Solver()
        except generic.RequirementsError:
            self.skipTest('Unable to find an LP solver for tests')

示例#26

    def setUp(self):
        self.database = DictDatabase()
        self.database.set_reaction('rxn_1', parse_reaction('=> |A|'))
        self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
        self.database.set_reaction('rxn_3', parse_reaction('|A| => |C|'))
        self.database.set_reaction('rxn_4', parse_reaction('|C| => |D|'))
        self.database.set_reaction('rxn_5', parse_reaction('|D| <=> |E|'))
        self.model = MetabolicModel.load_model(
            self.database, self.database.reactions)

        try:
            self.solver = generic.Solver(integer=True)
        except generic.RequirementsError:
            self.skipTest('Unable to find an MILP solver for tests')

示例#27

    def setUp(self):
        self.database = DictDatabase()
        self.database.set_reaction('rxn_1', parse_reaction('=> |A|'))
        self.database.set_reaction('rxn_2',
            parse_reaction('(0.000001) |A| =>'))
        self.model = MetabolicModel.load_model(
            self.database, self.database.reactions)

        try:
            self.solver = generic.Solver()
        except generic.RequirementsError:
            self.skipTest('Unable to find an LP solver for tests')

        # Skip these tests with GLPK because of issue #61.
        if self.solver.properties['name'] == 'glpk':
            self.skipTest('Test has known issue with GLPK')

示例#28

文件： test_fluxanalysis.py 项目： gitter-badger/psamm

    def setUp(self):
        self.database = DictDatabase()
        self.database.set_reaction('ex_A', parse_reaction('|A| <=>'))
        self.database.set_reaction('ex_D', parse_reaction('|D| <=>'))
        self.database.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
        self.database.set_reaction('rxn_2', parse_reaction('|B| <=> |C|'))
        self.database.set_reaction('rxn_3', parse_reaction('|C| <=> |D|'))
        self.database.set_reaction('rxn_4', parse_reaction('|D| <=> |E|'))
        self.database.set_reaction('rxn_5', parse_reaction('|E| => |B|'))

        self.model = MetabolicModel.load_model(
            self.database, self.database.reactions)
        self.model.limits['ex_A'].lower = -10 # Low uptake
        self.model.limits['ex_D'].lower = 0 # No uptake

        self.solver = cplex.Solver()

示例#29

文件： test_fluxanalysis.py 项目： ForkBackups/psamm

    def setUp(self):
        self.database = DictDatabase()
        self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
        self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
        self.database.set_reaction('rxn_3', parse_reaction('|A| => |D|'))
        self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
        self.database.set_reaction('rxn_5', parse_reaction('|C| => |D|'))
        self.database.set_reaction('rxn_6', parse_reaction('|D| =>'))
        self.database.set_reaction('rxn_7', parse_reaction('|E| => |F|'))
        self.database.set_reaction('rxn_8', parse_reaction('|F| => |E|'))
        self.model = MetabolicModel.load_model(
            self.database, self.database.reactions)

        try:
            self.solver = generic.Solver(integer=True)
        except generic.RequirementsError:
            self.skipTest('Unable to find an MILP solver for tests')

示例#30

文件： test_fluxanalysis.py 项目： ForkBackups/psamm

    def setUp(self):
        self.database = DictDatabase()
        self.database.set_reaction('ex_A', parse_reaction('|A| <=>'))
        self.database.set_reaction('ex_D', parse_reaction('|D| <=>'))
        self.database.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
        self.database.set_reaction('rxn_2', parse_reaction('|B| <=> |C|'))
        self.database.set_reaction('rxn_3', parse_reaction('|C| <=> |D|'))
        self.database.set_reaction('rxn_4', parse_reaction('|D| <=> |E|'))
        self.database.set_reaction('rxn_5', parse_reaction('|E| => |B|'))

        self.model = MetabolicModel.load_model(
            self.database, self.database.reactions)
        self.model.limits['ex_A'].lower = -10 # Low uptake
        self.model.limits['ex_D'].lower = 0 # No uptake

        try:
            self.solver = generic.Solver(integer=True)
        except generic.RequirementsError:
            self.skipTest('Unable to find an MILP solver for tests')

示例#31

文件： test_fluxanalysis.py 项目： bishopbrian25/iMM904

    def setUp(self):
        self.database = DictDatabase()
        self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
        self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
        self.database.set_reaction('rxn_3', parse_reaction('|A| => |D|'))
        self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
        self.database.set_reaction('rxn_5', parse_reaction('|C| => |D|'))
        self.database.set_reaction('rxn_6', parse_reaction('|D| =>'))
        self.database.set_reaction('rxn_7', parse_reaction('|E| => |F|'))
        self.database.set_reaction('rxn_8', parse_reaction('|F| => |E|'))

        self.model = MetabolicModel.load_model(self.database,
                                               self.database.reactions)
        self.model.limits['rxn_5'].upper = 100

        try:
            self.solver = generic.Solver()
        except generic.RequirementsError:
            self.skipTest('Unable to find an LP solver for tests')

示例#32

文件： test_fluxanalysis.py 项目： bishopbrian25/iMM904

    def setUp(self):
        self.database = DictDatabase()
        self.database.set_reaction('ex_A', parse_reaction('|A| <=>'))
        self.database.set_reaction('ex_D', parse_reaction('|D| <=>'))
        self.database.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
        self.database.set_reaction('rxn_2', parse_reaction('|B| <=> |C|'))
        self.database.set_reaction('rxn_3', parse_reaction('|C| <=> |D|'))
        self.database.set_reaction('rxn_4', parse_reaction('|D| <=> |E|'))
        self.database.set_reaction('rxn_5', parse_reaction('|E| => |B|'))

        self.model = MetabolicModel.load_model(self.database,
                                               self.database.reactions)
        self.model.limits['ex_A'].lower = -10  # Low uptake
        self.model.limits['ex_D'].lower = 0  # No uptake

        try:
            self.solver = generic.Solver(integer=True)
        except generic.RequirementsError:
            self.skipTest('Unable to find an MILP solver for tests')

示例#33

文件： test_fluxcoupling.py 项目： bishopbrian25/iMM904

    def setUp(self):
        self.database = DictDatabase()
        self.database.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
        self.database.set_reaction('rxn_2', parse_reaction('|B| => |G|'))
        self.database.set_reaction('rxn_3', parse_reaction('|A| => |G|'))
        self.database.set_reaction('rxn_4', parse_reaction('|B| => |H|'))
        self.database.set_reaction('rxn_5', parse_reaction('|B| => |C| + |F|'))
        self.database.set_reaction('rxn_6', parse_reaction('|C| => |D|'))
        self.database.set_reaction('rxn_7', parse_reaction('|E| <=> |D|'))
        self.database.set_reaction('rxn_9', parse_reaction('|I| => |J|'))
        self.database.set_reaction('rxn_10', parse_reaction('|J| => |K|'))
        self.database.set_reaction('rxn_A', parse_reaction('=> |A|'))
        self.database.set_reaction('rxn_G', parse_reaction('|G| =>'))
        self.database.set_reaction('rxn_E', parse_reaction('|E| =>'))
        self.database.set_reaction(
            'rxn_bio', parse_reaction('|D| + (2.5) |F| =>'))
        self.model = MetabolicModel.load_model(
            self.database, self.database.reactions)

        try:
            self.solver = generic.Solver()
        except generic.RequirementsError:
            self.skipTest('Unable to find an LP solver for tests')