From 50ebc192b07b387533c298f9e7a0a2cefe528ff5 Mon Sep 17 00:00:00 2001
From: Peter Schubert <Peter.Schubert@hhu.de>
Date: Tue, 19 Jul 2022 16:39:41 +0200
Subject: [PATCH] Initial base functionality
---
modelpruner/core/model_pruner.py | 199 ++++--
modelpruner/core/protected_parts.py | 6 +-
modelpruner/models/fba_model.py | 130 +++-
modelpruner/problems/lp_problem.py | 80 ++-
sample_data/SBML_models/Deniz_model_fba.xml | 698 ++++++++++++++++++++
sample_data/data/Deniz_model_fba_nrp2.xlsx | Bin 0 -> 14046 bytes
sample_prune_model.py | 50 ++
7 files changed, 1030 insertions(+), 133 deletions(-)
create mode 100644 sample_data/SBML_models/Deniz_model_fba.xml
create mode 100644 sample_data/data/Deniz_model_fba_nrp2.xlsx
create mode 100644 sample_prune_model.py
diff --git a/modelpruner/core/model_pruner.py b/modelpruner/core/model_pruner.py
index f2cd574..742cf3e 100644
--- a/modelpruner/core/model_pruner.py
+++ b/modelpruner/core/model_pruner.py
@@ -1,9 +1,11 @@
+import sys
import os
import re
import time
import numpy as np
+import pickle
import sbmlxdf
from modelpruner.models.fba_model import FbaModel
@@ -12,97 +14,172 @@ from modelpruner.core.protected_parts import ProtectedParts
class ModelPruner:
- def __init__(self, sbml_fname, protected_parts, reduced_fname=None):
+ def __init__(self, sbml_fname, protected_parts, reduced_fname=None, resume=False):
if reduced_fname is None:
- self.reduced_fname = re.sub('.xml', '_red.xml', sbml_fname)
-
- if os.path.exists(sbml_fname):
- self.sbml_model = sbmlxdf.Model(sbml_fname)
- print(f'Protected data loaded: {sbml_fname} '
- f'(last modified: {time.ctime(os.path.getmtime(sbml_fname))})')
+ self.reduced_fname = re.sub(r'.xml$', '_red.xml', sbml_fname)
+ self._snapshot_sbml = re.sub(r'.xml$', '_snapshot.xml', sbml_fname)
+ self._snapshot_pkl = re.sub(r'.xml$', '_snapshot.pkl', sbml_fname)
+
+ if resume is True:
+ if os.path.exists(self._snapshot_sbml):
+ self.sbml_model = sbmlxdf.Model(self._snapshot_sbml)
+ print(f'Resume from snapshot from {self._snapshot_sbml} '
+ f'(last modified: {time.ctime(os.path.getmtime(self._snapshot_sbml))})')
+ else:
+ print(f'{self._snapshot_sbml} not found!')
+ raise FileNotFoundError
else:
- print(f'{sbml_fname} not found!')
- raise FileNotFoundError
+ if os.path.exists(sbml_fname):
+ self.sbml_model = sbmlxdf.Model(sbml_fname)
+ print(f'Full SBML model loaded from {sbml_fname} '
+ f'(last modified: {time.ctime(os.path.getmtime(sbml_fname))})')
+ else:
+ print(f'{sbml_fname} not found!')
+ raise FileNotFoundError
self.tolerance = 1e-8 # later accessible by set_params() ?
self.fba_model = FbaModel(self.sbml_model)
self.nrp = ProtectedParts(protected_parts)
+ self.protected_sids = self.nrp.initial_protected_sids
+
+ if resume is True and os.path.exists(self._snapshot_pkl):
+ with open(self._snapshot_pkl, 'rb') as f:
+ self.protected_rids = pickle.load(f)
+ print(f'snapshot restored at {len(self.fba_model.rids):4d} remaining reactions '
+ f'from: {self._snapshot_pkl}')
+ else:
+ self.protected_rids = self.get_total_protected_rids(self.nrp.initial_protected_rids)
+
+ self.fba_model.update_flux_bounds(self.nrp.overwrite_bounds)
self.base_obj_dir = self.fba_model.obj_dir
self.base_flux_bounds = self.fba_model.flux_bounds.copy()
self.base_coefs = self.fba_model.obj_coefs.copy()
- self.protected_sids = set(self.nrp.initial_protected_sids)
- self.protected_rids = self.get_total_protected_rids(set(self.nrp.initial_protected_rids))
- self.essential_rids = self.protected_rids
- self.free_rids = set(self.fba_model.rids).difference(self.essential_rids)
+
self.set_function_optimum()
self.check_protected_parts()
- # overwrite bounds on fba
- self.fba_model.update_flux_bounds(self.nrp.overwrite_bounds)
-
def check_protected_parts(self):
extra_p_rids = self.protected_rids.difference(set(self.fba_model.rids))
extra_p_sids = self.protected_sids.difference(set(self.fba_model.sids))
pf_rids = set()
for pf in self.nrp.protected_functions.values():
- pf_rids = pf_rids.union({rid for rid in pf.objective})
- pf_rids = pf_rids.union({rid for rid in pf.overwrite_bounds})
+ pf_rids |= {rid for rid in pf.objective}
+ pf_rids |= {rid for rid in pf.overwrite_bounds}
if pf.fba_success is False:
print(f'protected function {pf.obj_id} has unsuccessful FBA '
f' with optimal value {pf.optimal}')
extra_pf_rids = pf_rids.difference(set(self.fba_model.rids))
+ pf_unprotected_rids = pf_rids.difference(set(self.protected_rids))
if len(extra_p_rids) > 0:
print('protected reactions that do not exist in model:', extra_p_rids)
if len(extra_p_sids) > 0:
print('protected metabolites that do not exist in model:', extra_p_sids)
if len(extra_pf_rids) > 0:
- print('reactions in protected function that do not exist in model:', extra_pf_rids)
+ print('reactions in protected functions that do not exist in model:', extra_pf_rids)
+ if len(pf_unprotected_rids) > 0:
+ print('reactions in protected functions that are not protected:', pf_unprotected_rids)
- zero_flux_rids = self.get_blocked_reactions()
- blocked_p_rids = self.protected_rids.intersection(zero_flux_rids)
- blocked_pf_rids = pf_rids.intersection(zero_flux_rids)
+ blocked_rids = self.reaction_types_fva(self.fba_model.rids)['blocked_rids']
+ blocked_p_rids = self.nrp.initial_protected_sids.intersection(blocked_rids)
+ blocked_pf_rids = pf_rids.intersection(blocked_rids)
if len(blocked_p_rids) > 0:
print('protected reactions that are blocked (no flux):', blocked_p_rids)
if len(blocked_pf_rids) > 0:
- print('reactions in protected function that are blocked (no flux):', blocked_pf_rids)
-
- def get_blocked_reactions(self):
- # identify blocked reactions
- # check that none of the blocked reactions are protected
- # actually remove blocked reactions, even they are included in
-
- fba_solution = self.fba_model.fba_optimize()
- zero_flux_mask = np.abs(fba_solution['x']) < self.tolerance
- zero_flux_rids = self.fba_model.rids[zero_flux_mask]
-
- fva_solution = self.fba_model.fva_optimize(zero_flux_rids, fract_of_optimum=0.0)
- flux_ranges = np.vstack((fva_solution['min'], fva_solution['max'])).T
- zero_flux_mask = np.all(abs(flux_ranges) < self.tolerance, axis=1)
- zero_flux_rids = set(fva_solution['rids'][zero_flux_mask])
- return zero_flux_rids
-
- def prune(self):
+ print('reactions in protected functions that are blocked (no flux):', blocked_pf_rids)
+ def prune(self, snapshot_freq=None):
+ print(f'initial S-matrix: {self.fba_model.s_mat.shape}; '
+ f' protected reactions: {len(self.protected_rids)}:', self.protected_rids)
self.remove_parallel_reactions()
+ print('protected functions feasibility:', self.check_pf_feasibility())
- def reaction_types_fva(self):
-
- free_rids = list(set(self.fba_model.rids).difference(self.protected_rids))
+ if type(snapshot_freq) is int:
+ next_snapshot = max(0, len(self.fba_model.rids) - snapshot_freq)
+ else:
+ next_snapshot = None
+
+ while len(self.protected_rids) < self.fba_model.s_mat.shape[1]:
+ free_rids = list(set(self.fba_model.rids).difference(self.protected_rids))
+ reaction_types = self.reaction_types_fva(free_rids)
+ if len(reaction_types['blocked_rids']) > 0:
+ self.fba_model.remove_reactions(reaction_types['blocked_rids'], self.protected_rids)
+ print(f"{len(reaction_types['blocked_rids'])} blocked reaction(s) removed:",
+ reaction_types['blocked_rids'])
+ if len(reaction_types['essential_rids']) > 0:
+ self.protected_rids |= reaction_types['essential_rids']
+ print(f"{len(reaction_types['essential_rids'])} reaction(s) added to protected reactions:",
+ reaction_types['essential_rids'])
+
+ print(f"{len(reaction_types['candidate_rids_sorted'])} candidates:",
+ reaction_types['candidate_rids_sorted'][:4], '...')
+ # try to remove one reaction while still satisfying all protected functions
+ feasible = False
+ essential_rids = set()
+ for rid in reaction_types['candidate_rids_sorted']:
+ orig_flux_bounds = self.fba_model.get_flux_bounds(rid)
+ self.fba_model.update_flux_bounds({rid: [0.0, 0.0]})
+ feasible = self.check_pf_feasibility()
+ self.fba_model.update_flux_bounds({rid: orig_flux_bounds})
+ if feasible:
+ self.fba_model.remove_reactions({rid}, self.protected_rids)
+ print(f'{rid} removed from the model')
+ break
+ else:
+ essential_rids.add(rid)
+ if len(essential_rids) > 0:
+ self.protected_rids |= essential_rids
+ print(f"{len(essential_rids)} reaction(s) added to protected reactions:", essential_rids)
+
+ if feasible is False:
+ print('no more reactions to remove')
+
+ # store intermediate results (snapshots)
+ print(f'snapshot check next: {next_snapshot}, rids: {len(self.fba_model.rids)}')
+ if (next_snapshot is not None) and (len(self.fba_model.rids) < next_snapshot):
+ self.export_pruned_model(self._snapshot_sbml)
+ with open(self._snapshot_pkl, 'wb') as f:
+ pickle.dump(self.protected_rids, f)
+ next_snapshot = max(0, len(self.fba_model.rids) - snapshot_freq)
+ print('snapshot data saved.')
+
+ print(f'S-matrix: {self.fba_model.s_mat.shape}; '
+ f'protected reactions: {len(self.protected_rids)}')
+
+ # check if blocked reactions exist in the finally pruned model
+ blocked_rids = self.reaction_types_fva(self.fba_model.rids)['blocked_rids']
+ if len(blocked_rids) > 0:
+ print(f'{len(blocked_rids)} blocked reaction(s) in pruned model', blocked_rids)
+
+ # remove any snapshot files
+ for fname in [self._snapshot_sbml, self._snapshot_pkl]:
+ if os.path.exists(fname):
+ os.remove(fname)
+
+ def reaction_types_fva(self, free_rids):
flux_min_pfs = np.zeros((len(self.nrp.protected_functions), len(free_rids)))
flux_max_pfs = np.zeros((len(self.nrp.protected_functions), len(free_rids)))
+ n_pf = len(self.nrp.protected_functions)
for idx, pf in enumerate(self.nrp.protected_functions.values()):
self.set_temp_func_conditions(pf)
res = self.fba_model.fva_optimize(free_rids, fract_of_optimum=0.0)
self.restore_base_conditions()
+ if res['success'] is False:
+ print('FVA unsuccessful')
+ return {'blocked_rids': [], 'essential_rids': [], 'candidate_rids_sorted': []}
+
flux_min_pfs[idx] = res['min']
flux_max_pfs[idx] = res['max']
+ sys.stdout.write('\rFVA[{}{}] {:3.0f}%'.format(
+ '=' * int(idx+1), ' ' * int(n_pf - idx-1), (idx+1)/n_pf*100))
+ sys.stdout.flush()
+ print()
flux_min_pfs[np.abs(flux_min_pfs) < self.tolerance] = 0.0
flux_max_pfs[np.abs(flux_max_pfs) < self.tolerance] = 0.0
@@ -144,18 +221,17 @@ class ModelPruner:
drop_group_rids = set(group_rids) - {reversible}
else:
drop_group_rids = set(group_rids[1:])
- drop_rids = drop_rids.union(drop_group_rids)
+ drop_rids |= drop_group_rids
self.fba_model.remove_reactions(drop_rids, self.protected_sids)
- print(f'{len(drop_rids)} parallel reactions dropped:', drop_rids)
+ print(f'{len(drop_rids)} parallel reaction(s) dropped:', drop_rids)
def set_function_optimum(self):
"""using FBA to set optimal value for protected functions"""
- for obj_id in self.nrp.protected_functions:
- pf = self.nrp.protected_functions[obj_id]
+ for obj_id, pf in self.nrp.protected_functions.items():
self.set_temp_func_conditions(pf)
-
res = self.fba_model.fba_optimize(short_result=True)
+ self.restore_base_conditions()
pf.optimal = res['fun']
pf.fba_success = res['success']
@@ -165,8 +241,6 @@ class ModelPruner:
else:
pf.set_target_lb(pf.target_frac * pf.optimal)
- self.restore_base_conditions()
-
def get_total_protected_rids(self, protected_rids):
# identify reactions that need protection due to protected metabolites
# over and above the protected rids provided in protected parts
@@ -179,11 +253,12 @@ class ModelPruner:
# identify rids in protected functions and ensure they are protected
pf_rids = set()
for pf in self.nrp.protected_functions.values():
- pf_rids = pf_rids.union({rid for rid in pf.objective})
- pf_rids = pf_rids.union({rid for rid in pf.overwrite_bounds})
+ pf_rids |= {rid for rid in pf.objective}
+ pf_rids |= {rid for rid in pf.overwrite_bounds}
- total_protect_rids = protected_rids.union(protected_sid_rids).union(pf_rids)
- return total_protect_rids
+ protected_rids |= protected_sid_rids
+ protected_rids |= pf_rids
+ return protected_rids
def check_pf_feasibility(self):
"""check that current model still satisfies the protected functions
@@ -217,8 +292,8 @@ class ModelPruner:
def restore_base_conditions(self):
self.fba_model.obj_dir = self.base_obj_dir
- self.fba_model.flux_bounds = self.base_flux_bounds
- self.fba_model.obj_coefs = self.base_coefs
+ self.fba_model.flux_bounds = self.base_flux_bounds.copy()
+ self.fba_model.obj_coefs = self.base_coefs.copy()
def get_reduction_status(self):
""" Return status in model reduction process
@@ -231,12 +306,18 @@ class ModelPruner:
status = self.fba_model.get_model_status()
status['n_protected_rids'] = len(self.protected_rids)
status['n_protected_sids'] = len(self.protected_sids)
- status['essential_rids'] = len(self.essential_rids)
return status
def print_status(self):
status = self.get_reduction_status()
print("reactions removed/remaining/protected: "
- f"{status['n_full_rids' ] -status['n_red_rids']:4d}/{status['n_red_rids']:4d}/"
- f"{status['essential_rids']:4d}; dof: {status['dof']:3d}")
+ f"{status['n_full_rids' ] - status['n_rids']:4d}/{status['n_rids']:4d}/"
+ f"/{len(self.protected_rids):4d}; dof: {status['dof']:3d}")
+
+ def export_pruned_model(self, pruned_sbml):
+ success = self.fba_model.export_pruned_model(pruned_sbml)
+ if success is True:
+ print('pruned model exported to', pruned_sbml)
+ else:
+ print('pruned model could not be exported')
diff --git a/modelpruner/core/protected_parts.py b/modelpruner/core/protected_parts.py
index 71de8b2..b35343a 100644
--- a/modelpruner/core/protected_parts.py
+++ b/modelpruner/core/protected_parts.py
@@ -14,7 +14,7 @@ class ProtectedParts:
if type(protected_parts) == str:
if os.path.exists(protected_parts):
nrp = self.load_raw_protected_data(protected_parts)
- print(f'Protected data loaded: {protected_parts} '
+ print(f'Protected data loaded from {protected_parts} '
f'(last modified: {time.ctime(os.path.getmtime(protected_parts))})')
else:
print(f'{protected_parts} not found!')
@@ -23,8 +23,8 @@ class ProtectedParts:
assert type(protected_parts) == dict, 'expected filename or a dict'
nrp = protected_parts
- self.initial_protected_rids = nrp.get('reactions', [])
- self.initial_protected_sids = nrp.get('metabolites', [])
+ self.initial_protected_rids = set(nrp.get('reactions', []))
+ self.initial_protected_sids = set(nrp.get('metabolites', []))
if 'bounds' in nrp:
num_cols = ['fbcLb', 'fbcUb']
nrp['bounds'][num_cols] = nrp['bounds'][num_cols].applymap(
diff --git a/modelpruner/models/fba_model.py b/modelpruner/models/fba_model.py
index 8e8ae17..3496c3a 100644
--- a/modelpruner/models/fba_model.py
+++ b/modelpruner/models/fba_model.py
@@ -1,5 +1,6 @@
+import re
import math
import numpy as np
import sbmlxdf
@@ -11,10 +12,10 @@ class FbaModel:
def __init__(self, sbml_model):
- model_dict = sbml_model.to_df()
- df_reactions = model_dict['reactions']
- df_species = model_dict['species']
- df_fbc_objectives = model_dict['fbcObjectives']
+ self.model_dict = sbml_model.to_df()
+ df_reactions = self.model_dict['reactions']
+ df_species = self.model_dict['species']
+ df_fbc_objectives = self.model_dict['fbcObjectives']
self.full_model_shape = {'n_full_rids': len(df_reactions),
'n_full_sids': len(df_species)}
@@ -105,6 +106,7 @@ class FbaModel:
if lp is None:
return {'success': False, 'message': 'not an FBA model'}
res = lp.solve(short_result)
+ del lp
if short_result is False:
res['x'] = self.combine_fwd_bwd(res['x'])
res['reduced_costs'] = self.combine_fwd_bwd(res['reduced_costs'])
@@ -125,40 +127,42 @@ class FbaModel:
return {'success': False, 'message': 'not an FBA model'}
res = lp.solve(short_result=True)
+ if res['success'] is False:
+ del lp
+ return {'success': False, 'message': res['generic_status']}
+
if rids is None:
rids = self.rids
-
flux_min = np.zeros(len(rids))
flux_max = np.zeros(len(rids))
- if res['success']:
- # fix FBA objective as constraint
- fwd_bwd_obj_coefs = np.hstack((self.obj_coefs, -self.obj_coefs[self.reversible]))
- if self.obj_dir == 'maximize':
- row_bds = np.array([res['fun'] * fract_of_optimum, np.nan])
+ # fix FBA objective as constraint
+ fwd_bwd_obj_coefs = np.hstack((self.obj_coefs, -self.obj_coefs[self.reversible]))
+ if self.obj_dir == 'maximize':
+ row_bds = np.array([res['fun'] * fract_of_optimum, np.nan])
+ else:
+ if fract_of_optimum > 0.0:
+ row_bds = np.array([np.nan, res['fun'] / fract_of_optimum])
else:
- if fract_of_optimum > 0.0:
- row_bds = np.array([np.nan, res['fun'] / fract_of_optimum])
- else:
- row_bds = np.array([np.nan, 1000.0])
- lp.add_constraint(fwd_bwd_obj_coefs, row_bds)
-
- n_cols = len(self.rids)
- for idx, rid in enumerate(rids):
- # select reaction maximize/minimize flux
- new_obj_coefs = np.zeros(n_cols)
- new_obj_coefs[self.rid2idx[rid]] = 1
- new_fwd_bwd_obj_coefs = np.hstack((new_obj_coefs, -new_obj_coefs[self.reversible]))
- lp.set_obj_coefs(new_fwd_bwd_obj_coefs)
-
- lp.set_obj_dir('minimize')
- res = lp.solve(short_result=True)
- flux_min[idx] = res['fun'] if res['success'] else np.nan
-
- lp.set_obj_dir('maximize')
- res = lp.solve(short_result=True)
- flux_max[idx] = res['fun'] if res['success'] else np.nan
-
- return {'rids': np.array(rids), 'min': flux_min, 'max': flux_max}
+ row_bds = np.array([np.nan, 1000.0])
+ lp.add_constraint(fwd_bwd_obj_coefs, row_bds)
+
+ n_cols = len(self.rids)
+ for idx, rid in enumerate(rids):
+ # select reaction maximize/minimize flux
+ new_obj_coefs = np.zeros(n_cols)
+ new_obj_coefs[self.rid2idx[rid]] = 1
+ new_fwd_bwd_obj_coefs = np.hstack((new_obj_coefs, -new_obj_coefs[self.reversible]))
+ lp.set_obj_coefs(new_fwd_bwd_obj_coefs)
+
+ lp.set_obj_dir('minimize')
+ res = lp.solve(short_result=True)
+ flux_min[idx] = res['fun'] if res['success'] else np.nan
+
+ lp.set_obj_dir('maximize')
+ res = lp.solve(short_result=True)
+ flux_max[idx] = res['fun'] if res['success'] else np.nan
+ del lp
+ return {'success': True, 'rids': np.array(rids), 'min': flux_min, 'max': flux_max}
def update_flux_bounds(self, flux_bounds):
"""selectivly set lower/upper flux bounds for given reactions.
@@ -169,6 +173,7 @@ class FbaModel:
:type flux_bounds: dict (key: reaction id, value: list with two float values for lower/upper bound)
"""
for rid, (lb, ub) in flux_bounds.items():
+ assert rid in self.rids
if math.isfinite(lb):
self.flux_bounds[0, self.rid2idx[rid]] = lb
if lb < 0:
@@ -176,6 +181,10 @@ class FbaModel:
if math.isfinite(ub):
self.flux_bounds[1, self.rid2idx[rid]] = ub
+ def get_flux_bounds(self, rid):
+ assert rid in self.rids
+ return [self.flux_bounds[0, self.rid2idx[rid]], self.flux_bounds[1, self.rid2idx[rid]]]
+
def remove_reactions(self, drop_rids, protected_sids):
# remove_reactions
# also remove corresponding metabolite columns
@@ -242,8 +251,8 @@ class FbaModel:
:rtype: dict
"""
status = {'dof': self.s_mat.shape[1] - np.linalg.matrix_rank(self.s_mat),
- 'n_red_rids': len(self.rids),
- 'n_red_sids': len(self.sids)}
+ 'n_rids': len(self.rids),
+ 'n_sids': len(self.sids)}
status.update(self.full_model_shape)
return status
@@ -257,3 +266,54 @@ class FbaModel:
self.__obj_dir = 'minimize'
else:
self.__obj_dir = 'maximize'
+
+ def export_pruned_model(self, pruned_sbml):
+
+ pruned_mdict = self.model_dict.copy()
+ pruned_mdict['reactions'] = self.model_dict['reactions'].loc[self.rids]
+ pruned_mdict['species'] = self.model_dict['species'].loc[self.sids]
+
+ # update model attributes (ids, names and modification date)
+ pruned_mdict['modelAttrs']['id'] += '_pruned'
+ pruned_mdict['modelAttrs']['name'] += '_pruned'
+ pruned_mdict['modelAttrs']['metaid'] += '_pruned'
+ pruned_mdict['modelAttrs']['modifiedHistory'] += '; localtime'
+
+ # clean groups table
+ keep_idxs = []
+ if 'groups' in pruned_mdict:
+ df_groups_pruned = pruned_mdict['groups'].copy()
+ for idx, row in df_groups_pruned.iterrows():
+ members_pruned = []
+ for member in sbmlxdf.misc.record_generator(row['members']):
+ params = sbmlxdf.misc.extract_params(member)
+ if 'idRef' in params:
+ if params['idRef'] in self.rids:
+ members_pruned.append(member)
+ else:
+ members_pruned.append(member)
+ df_groups_pruned.at[idx, 'members'] = '; '.join(members_pruned)
+ if len(members_pruned) > 0:
+ keep_idxs.append(idx)
+ pruned_mdict['groups'] = df_groups_pruned.loc[keep_idxs]
+
+ # clean gene products
+ gp_ids = set()
+ if 'fbcGeneProdAssoc' in pruned_mdict['reactions']:
+ for gpr in pruned_mdict['reactions']['fbcGeneProdAssoc']:
+ if type(gpr) is str:
+ if 'assoc=' in gpr:
+ gpr = re.sub('assoc=', '', gpr)
+ gpr = re.sub(r'[()]', ' ', gpr)
+ gpr = re.sub(r'and', ' ', gpr)
+ gpr = re.sub(r'or', ' ', gpr)
+ gp_ids = gp_ids.union(set(re.findall(r'\w+', gpr)))
+ if 'fbcGeneProducts' in pruned_mdict:
+ pruned_mdict['fbcGeneProducts'] = pruned_mdict['fbcGeneProducts'].loc[list(gp_ids)]
+
+ pruned_model = sbmlxdf.Model()
+ pruned_model.from_df(pruned_mdict)
+ err = pruned_model.validate_sbml()
+ if len(err) > 0:
+ print('SBML validation result: %s', ', '.join([k + ': ' + str(v) for k, v in err.items()]))
+ return pruned_model.export_sbml(pruned_sbml)
diff --git a/modelpruner/problems/lp_problem.py b/modelpruner/problems/lp_problem.py
index b52d803..3bc4932 100644
--- a/modelpruner/problems/lp_problem.py
+++ b/modelpruner/problems/lp_problem.py
@@ -14,43 +14,43 @@ import swiglpk as glpk
# status reported
simplex_status = {
0: 'LP problem instance successfully solved',
- 1: 'Unable to start search, initial basis specified in the '
+ glpk.GLP_EBADB: 'Unable to start search, initial basis specified in the '
'problem object is invalid. Number basic variables is not same as the number rows.',
- 2: 'Unable to start search, basis matrix corresponding to initial basis is singular.',
- 3: 'Unable to start search, basis matrix corresponding to initial basis is ill-conditioned.',
- 4: 'Unable to start search, some double-bounded variables have incorrect bounds.',
- 5: 'Search prematurely terminated: solver failure.',
- 6: 'Search prematurely terminated: objective function being '
+ glpk.GLP_ESING: 'Unable to start search, basis matrix corresponding to initial basis is singular.',
+ glpk.GLP_ECOND: 'Unable to start search, basis matrix corresponding to initial basis is ill-conditioned.',
+ glpk.GLP_EBOUND: 'Unable to start search, some double-bounded variables have incorrect bounds.',
+ glpk.GLP_EFAIL: 'Search prematurely terminated: solver failure.',
+ glpk.GLP_EOBJLL: 'Search prematurely terminated: objective function being '
'maximized reached its lower limit and continues decreasing.',
- 7: 'Search prematurely terminated: objective function being '
+ glpk.GLP_EOBJUL: 'Search prematurely terminated: objective function being '
'minimized reached its upper limit and continues increasing.',
- 8: 'Search prematurely terminated: simplex iteration limit exceeded.',
- 9: 'Search prematurely terminated: time limit exceeded.',
- 10: 'LP problem instance has no primal feasible solution.',
- 11: 'LP problem instance has no dual feasible solution.'}
-
-generic_status = {1: 'solution is undefined',
- 2: 'solution is feasible',
- 3: 'solution is infeasible',
- 4: 'problem has no feasible solution',
- 5: 'solution is optimal',
- 6: 'problem has unbounded solution'}
-
-dual_status = {1: 'dual solution is undefined',
- 2: 'dual solution is feasible',
- 3: 'dual solution is infeasible',
- 4: 'no dual feasible solution exists'}
-
-prim_status = {1: 'primal solution is undefined',
- 2: 'primal solution is feasible',
- 3: 'primal solution is infeasible',
- 4: 'no primal feasible solution exists'}
-
-var_status = {1: 'basic variable',
- 2: 'non-basic variable on its lower bound',
- 3: 'non-basic variable on its upper bound',
- 4: 'non-basic free (unbounded) variable',
- 5: 'non-basic fixed variable'}
+ glpk.GLP_EITLIM: 'Search prematurely terminated: simplex iteration limit exceeded.',
+ glpk.GLP_ETMLIM: 'Search prematurely terminated: time limit exceeded.',
+ glpk.GLP_ENOPFS: 'LP problem instance has no primal feasible solution.',
+ glpk.GLP_ENODFS: 'LP problem instance has no dual feasible solution.'}
+
+generic_status = {glpk.GLP_UNDEF: 'solution is undefined',
+ glpk.GLP_FEAS: 'solution is feasible',
+ glpk.GLP_INFEAS: 'solution is infeasible',
+ glpk.GLP_NOFEAS: 'problem has no feasible solution',
+ glpk.GLP_OPT: 'solution is optimal',
+ glpk.GLP_UNBND: 'problem has unbounded solution'}
+
+dual_status = {glpk.GLP_UNDEF: 'dual solution is undefined',
+ glpk.GLP_FEAS: 'dual solution is feasible',
+ glpk.GLP_INFEAS: 'dual solution is infeasible',
+ glpk.GLP_NOFEAS: 'no dual feasible solution exists'}
+
+prim_status = {glpk.GLP_UNDEF: 'primal solution is undefined',
+ glpk.GLP_FEAS: 'primal solution is feasible',
+ glpk.GLP_INFEAS: 'primal solution is infeasible',
+ glpk.GLP_NOFEAS: 'no primal feasible solution exists'}
+
+var_status = {glpk.GLP_BS: 'basic variable',
+ glpk.GLP_NL: 'non-basic variable on its lower bound',
+ glpk.GLP_NU: 'non-basic variable on its upper bound',
+ glpk.GLP_NF: 'non-basic free (unbounded) variable',
+ glpk.GLP_NS: 'non-basic fixed variable'}
scaling_options = {'GM': glpk.GLP_SF_GM,
'EQ': glpk.GLP_SF_EQ,
@@ -69,6 +69,8 @@ class LpProblem:
self.lp = glpk.glp_create_prob()
self.ncols = 0
self.nrows = 0
+ self.msg_lev = glpk.GLP_MSG_ERR
+ self.tm_lim = 10 * 1000
self.res = {}
@staticmethod
@@ -245,12 +247,18 @@ class LpProblem:
:return: result information from the optimization stored in a dictionary
:rtype: dict
"""
+ # configure options
+ smcp = glpk.glp_smcp()
+ glpk.glp_init_smcp(smcp)
+ smcp.msg_lev = self.msg_lev
+ smcp.tm_lim = self.tm_lim
+
if scaling is not None:
opt = scaling_options.get(scaling, glpk.GLP_SF_AUTO)
glpk.glp_scale_prob(self.lp, opt)
# sjj = [glpk.glp_get_sjj(self.lp, 1+i) for i in range(glpk.glp_get_num_cols(self.lp))]
# rii = [glpk.glp_get_rii(self.lp, 1+i) for i in range(glpk.glp_get_num_rows(self.lp))]
- simplex_result = glpk.glp_simplex(self.lp, None)
+ simplex_result = glpk.glp_simplex(self.lp, smcp)
return self.results(simplex_result, short_result)
def get_row_value(self, row):
@@ -279,6 +287,7 @@ class LpProblem:
self.res = {
'fun': glpk.glp_get_obj_val(self.lp),
'success': glpk.glp_get_status(self.lp) == glpk.GLP_OPT,
+ 'generic_status': generic_status[glpk.glp_get_status(self.lp)],
}
if short_result is False:
self.res['x'] = np.array([glpk.glp_get_col_prim(self.lp, 1 + i) for i in range(self.ncols)])
@@ -286,7 +295,6 @@ class LpProblem:
self.res['shadow_prices'] = np.array([glpk.glp_get_row_dual(self.lp, 1 + i) for i in range(self.nrows)])
self.res['simplex_result'] = simplex_result
self.res['simplex_message'] = simplex_status[simplex_result],
- self.res['generic_status'] = generic_status[glpk.glp_get_status(self.lp)]
self.res['primal_status'] = prim_status[glpk.glp_get_prim_stat(self.lp)]
self.res['dual_status'] = dual_status[glpk.glp_get_dual_stat(self.lp)]
return self.res
diff --git a/sample_data/SBML_models/Deniz_model_fba.xml b/sample_data/SBML_models/Deniz_model_fba.xml
new file mode 100644
index 0000000..e3b9f55
--- /dev/null
+++ b/sample_data/SBML_models/Deniz_model_fba.xml
@@ -0,0 +1,698 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by sbmlxdf version 0.2.7 on 2022-07-18 14:55 with libSBML version 5.19.0. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" level="3" version="2" fbc:required="false" groups:required="false">
+ <model metaid="Deniz_model_fba" id="Deniz_model_fba" name="Deniz_model_fba" substanceUnits="substance" timeUnits="time" extentUnits="substance" fbc:strict="true">
+ <notes>
+ <body xmlns="http://www.w3.org/1999/xhtml">
+ <h2>FBA model based on Deinz's model 11_12, presented Nov. 2020. </h2>
+ <p> including biomass reaction, external metabolites, ATPM maintenance reaction, oxidative and fermenative phenotypes</p>
+ <p>Based on Deniz Sezer </p>
+ </body>
+ </notes>
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#Deniz_model_fba">
+ <dcterms:creator>
+ <rdf:Bag>
+ <rdf:li rdf:parseType="Resource">
+ <vCard4:hasName rdf:parseType="Resource">
+ <vCard4:family-name>Schubert</vCard4:family-name>
+ <vCard4:given-name>Peter</vCard4:given-name>
+ </vCard4:hasName>
+ <vCard4:hasEmail>Peter.Schubert@hhu.de</vCard4:hasEmail>
+ <vCard4:organization-name>HHU-CCB</vCard4:organization-name>
+ </rdf:li>
+ </rdf:Bag>
+ </dcterms:creator>
+ <dcterms:created rdf:parseType="Resource">
+ <dcterms:W3CDTF>2022-07-18T14:55:18+02:00</dcterms:W3CDTF>
+ </dcterms:created>
+ <dcterms:modified rdf:parseType="Resource">
+ <dcterms:W3CDTF>2022-07-18T14:55:18+02:00</dcterms:W3CDTF>
+ </dcterms:modified>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfUnitDefinitions>
+ <unitDefinition id="mmol_per_gDW_per_hr" name="Millimoles per gram (dry weight) per hour">
+ <listOfUnits>
+ <unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
+ <unit kind="gram" exponent="-1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="3600"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="substance" name="Millimoles per gram (dry weight)">
+ <listOfUnits>
+ <unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
+ <unit kind="gram" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="time" name="Hour">
+ <listOfUnits>
+ <unit kind="second" exponent="1" scale="0" multiplier="3600"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" name="cytosol" spatialDimensions="3" size="1e-06" units="litre" constant="true"/>
+ <compartment id="e" name="extracellular space" spatialDimensions="3" size="1" units="litre" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="M_aa_c" name="M_aa_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_aapre_c" name="M_aapre_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_accoa_c" name="M_accoa_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_adp_c" name="M_adp_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_atp_c" name="M_atp_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_co2_c" name="M_co2_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_for_c" name="M_for_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_glc__D_c" name="M_glc__D_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_lac_c" name="M_lac_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_nh4_c" name="M_nh4_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_o2_c" name="M_o2_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_aa_e" name="M_aa_e" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_co2_e" name="M_co2_e" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_for_e" name="M_for_e" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_glc__D_e" name="M_glc__D_e" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <notes>
+ <body xmlns="http://www.w3.org/1999/xhtml"> main carbon source </body>
+ </notes>
+ </species>
+ <species id="M_lac_e" name="M_lac_e" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_nh4_e" name="M_nh4_e" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_o2_e" name="M_o2_e" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="M_rib_c" name="M_rib_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="Biomass" name="Biomass" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <notes>
+ <body xmlns="http://www.w3.org/1999/xhtml"> this is a note </body>
+ </notes>
+ </species>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id="default_lb" name="default_lb" value="-1000" units="mmol_per_gDW_per_hr" constant="true"/>
+ <parameter id="default_ub" name="default_ub" value="1000" units="mmol_per_gDW_per_hr" constant="true"/>
+ <parameter id="zero_bound" name="zero_bound" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
+ <parameter id="R_EX_glc__D_e_lb" name="R_EX_glc__D_e_lb" value="-10" units="mmol_per_gDW_per_hr" constant="true"/>
+ <parameter id="R_ATPM_lb" name="R_ATPM_lb" value="3.15" units="mmol_per_gDW_per_hr" constant="true"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id="R_EX_aa" name="R_EX_aa" reversible="true" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_aa_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ <reaction id="R_EX_co2" name="R_EX_co2" reversible="true" fbc:lowerFluxBound="default_lb" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_co2_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ <reaction id="R_EX_for" name="R_EX_for" reversible="true" fbc:lowerFluxBound="default_lb" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_for_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ <reaction id="R_EX_glc__D" name="R_EX_glc__D" reversible="true" fbc:lowerFluxBound="R_EX_glc__D_e_lb" fbc:upperFluxBound="default_ub">
+ <notes>
+ <body xmlns="http://www.w3.org/1999/xhtml"> carbon source transporter </body>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_glc__D_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ <reaction id="R_EX_lac" name="R_EX_lac" reversible="true" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_lac_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ <reaction id="R_EX_nh4" name="R_EX_nh4" reversible="true" fbc:lowerFluxBound="default_lb" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_nh4_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ <reaction id="R_EX_o2" name="R_EX_o2" reversible="true" fbc:lowerFluxBound="default_lb" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_o2_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ <reaction id="R_DM_Biomass" name="R_DM_Biomass" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="Biomass" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ <reaction id="R_aa_imp" name="R_aa_imp" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_aa_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_aa_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_co2_tex" name="R_co2_tex" reversible="true" fbc:lowerFluxBound="default_lb" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_co2_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_for_tex" name="R_for_tex" reversible="true" fbc:lowerFluxBound="default_lb" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_for_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_for_texi" name="R_for_texi" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_for_e" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_glc__D_tex" name="R_glc__D_tex" reversible="true" fbc:lowerFluxBound="default_lb" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_glc__D_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_lac_tex" name="R_lac_tex" reversible="true" fbc:lowerFluxBound="default_lb" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_lac_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_lac_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3670"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b3671"/>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0077"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b0078"/>
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_nh4_imp" name="R_nh4_imp" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_nh4_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_o2_tex" name="R_o2_tex" reversible="true" fbc:lowerFluxBound="default_lb" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_o2_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_mr2" name="R_mr2" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_accoa_c" stoichiometry="3" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0929"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_ppp1" name="R_ppp1" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_rib_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_ppp2" name="R_ppp2" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_rib_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_accoa_c" stoichiometry="3" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4034"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_mrOx" name="R_mrOx" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_adp_c" stoichiometry="4" constant="true"/>
+ <speciesReference species="M_o2_c" stoichiometry="2" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_atp_c" stoichiometry="4" constant="true"/>
+ <speciesReference species="M_co2_c" stoichiometry="2" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4033"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_mrFerm" name="R_mrFerm" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_adp_c" stoichiometry="2" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_atp_c" stoichiometry="2" constant="true"/>
+ <speciesReference species="M_for_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4032"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_mr5" name="R_mr5" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_aapre_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4035"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_mr7" name="R_mr7" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_aapre_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_aa_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4036"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_mr9" name="R_mr9" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_lac_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4213"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_mr11" name="R_mr11" reversible="true" fbc:lowerFluxBound="default_lb" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_aa_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_accoa_c" stoichiometry="3" constant="true"/>
+ <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_ATPM" name="R_ATPM" reversible="false" fbc:lowerFluxBound="R_ATPM_lb" fbc:upperFluxBound="default_ub">
+ <listOfReactants>
+ <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction id="R_Biomass_core" name="R_Biomass_core" reversible="false" fbc:lowerFluxBound="zero_bound" fbc:upperFluxBound="default_ub">
+ <notes>
+ <body xmlns="http://www.w3.org/1999/xhtml"> biomass reaction </body>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_aa_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_atp_c" stoichiometry="3" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_adp_c" stoichiometry="3" constant="true"/>
+ <speciesReference species="Biomass" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfObjectives fbc:activeObjective="obj">
+ <fbc:objective fbc:id="obj" fbc:type="maximize">
+ <fbc:listOfFluxObjectives>
+ <fbc:fluxObjective fbc:reaction="R_Biomass_core" fbc:coefficient="1"/>
+ </fbc:listOfFluxObjectives>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ <fbc:listOfGeneProducts>
+ <fbc:geneProduct metaid="G_b1377" fbc:id="G_b1377" fbc:label="b1377">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#G_b1377">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/uniprot/P77747"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0004608"/>
+ <rdf:li rdf:resource="http://identifiers.org/ecogene/EG13375"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/946313"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16129338"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct metaid="G_b2215" fbc:id="G_b2215" fbc:label="b2215">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#G_b2215">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/uniprot/P06996"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0007321"/>
+ <rdf:li rdf:resource="http://identifiers.org/ecogene/EG10670"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/946716"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16130152"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct metaid="G_b0929" fbc:id="G_b0929" fbc:label="b0929">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#G_b0929">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/uniprot/P02931"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0003153"/>
+ <rdf:li rdf:resource="http://identifiers.org/ecogene/EG10671"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/945554"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16128896"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct metaid="G_b0241" fbc:id="G_b0241" fbc:label="b0241">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#G_b0241">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/uniprot/P02932"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0000823"/>
+ <rdf:li rdf:resource="http://identifiers.org/ecogene/EG10729"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/944926"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16128227"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct metaid="G_b4034" fbc:id="G_b4034" fbc:label="b4034">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#G_b4034">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/uniprot/P0AEX9"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0013200"/>
+ <rdf:li rdf:resource="http://identifiers.org/ecogene/EG10554"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/948538"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16131860"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct metaid="G_b4033" fbc:id="G_b4033" fbc:label="b4033">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#G_b4033">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/uniprot/P02916"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0013195"/>
+ <rdf:li rdf:resource="http://identifiers.org/ecogene/EG10555"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/948532"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16131859"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct metaid="G_b4032" fbc:id="G_b4032" fbc:label="b4032">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#G_b4032">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/uniprot/P68183"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0013193"/>
+ <rdf:li rdf:resource="http://identifiers.org/ecogene/EG10556"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/948530"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16131858"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct metaid="G_b4035" fbc:id="G_b4035" fbc:label="b4035">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#G_b4035">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/uniprot/P68187"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0013216"/>
+ <rdf:li rdf:resource="http://identifiers.org/ecogene/EG10558"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/948537"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16131861"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct metaid="G_b4036" fbc:id="G_b4036" fbc:label="b4036">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#G_b4036">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/uniprot/P02943"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0013218"/>
+ <rdf:li rdf:resource="http://identifiers.org/ecogene/EG10528"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/948548"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16131862"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct metaid="G_b4213" fbc:id="G_b4213" fbc:label="b4213">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#G_b4213">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/uniprot/P08331"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0013782"/>
+ <rdf:li rdf:resource="http://identifiers.org/ecogene/EG10160"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/948729"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16132035"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct metaid="G_b2835" fbc:id="G_b2835" fbc:label="b2835">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#G_b2835">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/uniprot/P39196"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0009300"/>
+ <rdf:li rdf:resource="http://identifiers.org/ecogene/EG12455"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/947317"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16130739"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct metaid="G_b2836" fbc:id="G_b2836" fbc:label="b2836">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#G_b2836">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/uniprot/P31119"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/asap/ABE-0009302"/>
+ <rdf:li rdf:resource="http://identifiers.org/ecogene/EG11679"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/947315"/>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigi/gi:16130740"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct metaid="G_b3670" fbc:id="G_b3670" fbc:label="b3670"/>
+ <fbc:geneProduct metaid="G_b3671" fbc:id="G_b3671" fbc:label="b3671"/>
+ <fbc:geneProduct metaid="G_b0077" fbc:id="G_b0077" fbc:label="b0077"/>
+ <fbc:geneProduct metaid="G_b0078" fbc:id="G_b0078" fbc:label="b0078"/>
+ </fbc:listOfGeneProducts>
+ <groups:listOfGroups>
+ <groups:group groups:id="g1" groups:name="Carbon metabolism" groups:kind="partonomy">
+ <groups:listOfMembers>
+ <groups:member groups:idRef="R_mr2"/>
+ <groups:member groups:idRef="R_mr5"/>
+ <groups:member groups:idRef="R_mr7"/>
+ <groups:member groups:idRef="R_mr9"/>
+ <groups:member groups:idRef="R_mr11"/>
+ </groups:listOfMembers>
+ </groups:group>
+ <groups:group groups:id="g2" groups:name="Fermentation" groups:kind="partonomy">
+ <groups:listOfMembers>
+ <groups:member groups:idRef="R_mrFerm"/>
+ </groups:listOfMembers>
+ </groups:group>
+ <groups:group groups:id="g3" groups:name="Maintenance" groups:kind="partonomy">
+ <groups:listOfMembers>
+ <groups:member groups:idRef="R_ATPM"/>
+ </groups:listOfMembers>
+ </groups:group>
+ <groups:group groups:id="g4" groups:name="Oxidative Phosphorylation" groups:kind="partonomy">
+ <groups:listOfMembers>
+ <groups:member groups:idRef="R_mrOx"/>
+ </groups:listOfMembers>
+ </groups:group>
+ <groups:group groups:id="g5" groups:name="Glucolysis" groups:kind="partonomy">
+ <groups:listOfMembers>
+ <groups:member groups:idRef="R_mr2"/>
+ </groups:listOfMembers>
+ </groups:group>
+ <groups:group groups:id="g6" groups:name="Pentose Phosphate Pathway" groups:kind="partonomy">
+ <groups:listOfMembers>
+ <groups:member groups:idRef="R_ppp1"/>
+ <groups:member groups:idRef="R_ppp2"/>
+ </groups:listOfMembers>
+ </groups:group>
+ <groups:group groups:id="g7" groups:name="Transporter" groups:kind="partonomy">
+ <groups:listOfMembers>
+ <groups:member groups:idRef="R_co2_tex"/>
+ <groups:member groups:idRef="R_glc__D_tex"/>
+ <groups:member groups:idRef="R_lac_tex"/>
+ <groups:member groups:idRef="R_o2_tex"/>
+ </groups:listOfMembers>
+ </groups:group>
+ <groups:group groups:id="g8" groups:name="Transport, Exporter" groups:kind="partonomy">
+ <groups:listOfMembers>
+ <groups:member groups:idRef="R_for_texi"/>
+ </groups:listOfMembers>
+ </groups:group>
+ <groups:group groups:id="g9" groups:name="Transport, Importer" groups:kind="partonomy">
+ <groups:listOfMembers>
+ <groups:member groups:idRef="R_aa_imp"/>
+ <groups:member groups:idRef="R_nh4_imp"/>
+ </groups:listOfMembers>
+ </groups:group>
+ </groups:listOfGroups>
+ </model>
+</sbml>
diff --git a/sample_data/data/Deniz_model_fba_nrp2.xlsx b/sample_data/data/Deniz_model_fba_nrp2.xlsx
new file mode 100644
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diff --git a/sample_prune_model.py b/sample_prune_model.py
new file mode 100644
index 0000000..134b319
--- /dev/null
+++ b/sample_prune_model.py
@@ -0,0 +1,50 @@
+# sample_reduce_model.py
+# sample script for network reduction of a SBML fbc model
+
+import sys
+import os
+# import logging
+
+import modelpruner
+
+
+def prune_model():
+
+ # activate logging
+ # logfile = './log/nr.log'
+ # logformat = '%(asctime)s %(levelname)s:%(name)s %(message)s'
+ # logdir = os.path.dirname(logfile)
+ # if not os.path.exists(logdir):
+ # os.mkdir(logdir)
+ # logging.basicConfig(filename=logfile, filemode='w',
+ # level=logging.INFO, format=logformat)
+ # logging.info('Started')
+
+ # print some environment information
+ print('Python version: {:d}.{:d}.{:d}'.format(sys.version_info.major,
+ sys.version_info.minor,
+ sys.version_info.micro))
+ print('modelpruner version: {:s}'.format(modelpruner.__version__))
+ print('working directory :', os.getcwd())
+
+ # file names
+ full_sbml = 'sample_data/SBML_models/Deniz_model_fba.xml'
+ pruned_sbml = 'sample_data/SBML_models/Deniz_model_fba_reduced.xml'
+ protected_fname = 'sample_data/data/Deniz_model_fba_nrp2.xlsx'
+
+ # load the original model
+ mp = modelpruner.ModelPruner(full_sbml, protected_fname)
+
+ print('---- network reduction -----')
+ mp.prune()
+
+ # export pruned model in sbml format
+ mp.export_pruned_model(pruned_sbml)
+ print('pruned model converted to SBML:', pruned_sbml)
+ print('finally protected reactions:', mp.protected_rids)
+ print(mp.print_status())
+ # logging.info('Finished')
+
+
+if __name__ == '__main__':
+ prune_model()
--
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