BOFdat

BOFdat copied to clipboard

Expand applicability of Step1 to a broader range of identifiers

2

I downloaded a xml- model constructed by others, the file is using SEED ID for metabolite and when I ran DNA/RNA/protein_coefficients, it gives: AttributeError: DictList has no attribute or entry...

greenetarget

Solver issue in Step3

2

When trying BOFdat step3 an exception is raised. Tried both with COBRApy 0.15.3 and 0.16.0. step3.generate_initial_population(population_name, path_to_model, base_biomass_path, exp_essentiality_path, number_of_populations=5) **Assessing individual metabolite solvability function raised gurobi is not a...

Christiansj83

Hello, I am new to this in-silico work. I want to know how to us dummy data for BOF without experimental data. Specially the maintenance file.

Shakra-A

jclachance

jclachance

error when trying to update biomass

3

--------------------------------------------------------------------------- TypeError Traceback (most recent call last) in () ----> 1 update.update_biomass(d,model_so) ~/.local/lib/python3.6/site-packages/BOFdat-0.1.7-py3.6.egg/BOFdat/util/update.py in update_biomass(dict_of_coefficients, model) 115 :return: none 116 """ --> 117 biomass = _get_biomass_objective_function(model) 118 find_in_biomass(biomass, dict_of_coefficients) 119...

Christiansj83

Error when trying to update BOF step 1 (1.8)

3

AttributeError Traceback (most recent call last) in () ----> 1 bofdat_step1 = update.make_new_BOF(model_so,False,True,dna_coefficients,rna_coefficients,protein_coefficients,) ~/.local/lib/python3.6/site-packages/BOFdat-0.1.7-py3.6.egg/BOFdat/util/update.py in make_new_BOF(model, update_model, update_NGAM, *args, **kwargs) 159 ppi_coeff, h2o_coeff, atp_coeff = [], [], [] 160 remove_keys...

Christiansj83

Bumps [scipy](https://github.com/scipy/scipy) from 0.19.1 to 1.10.0. Release notes Sourced from scipy's releases. SciPy 1.10.0 Release Notes SciPy 1.10.0 is the culmination of 6 months of hard work. It contains many...

dependabot[bot]

Bumps [scipy](https://github.com/scipy/scipy) from 0.19.1 to 1.10.0. Release notes Sourced from scipy's releases. SciPy 1.10.0 Release Notes SciPy 1.10.0 is the culmination of 6 months of hard work. It contains many...

dependabot[bot]