<jupyter_start><jupyter_text>cobrame<jupyter_code>import cobra
import numpy as np
import matplotlib.pyplot
import cobrame
import pickle
import bacillusme.util.helper_functions as hf
with open('./iJL1678b.pickle', 'rb') as f:
    model = pickle.load(f)
dir(model)
len(model.reactions),len(model.metabolites),len(model.genes)
hf.solve_me_model(model, max_mu = 0.5, min_mu = .05, using_soplex=False,
                   precision = 1e-6,verbosity=2,mu_fix=False)
model.solution
import bacillusme.util.helper_functions as hf<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.11293260473588343, 'fraction_numerical': 0.020036429872495445, 'mean_word_length': 5.7073170731707314, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '1', 'dir': 'jupyter-structured-clean-dedup', 'id': '468928', 'license': 'MIT', 'n_tokens_mistral': 220, 'n_tokens_neox': 207, 'n_words': 38, 'path': '.ipynb_checkpoints/3_cobrame-checkpoint.ipynb', 'repo_name': 'omoyne/modeling-basics', 'size': '549'}