or is it a kinetic model of metabolism?
I guess kinetic model?
is the iAF1260 model
a GSMM
oh wait
give me a moment
Ok, here's the paper about the model https://www.ncbi.nlm.nih.gov/pubmed/17593909
you'll see it is a GSMM and you need to look for COBRA https://opencobra.github.io/
What confused me was the .m file (Octave, MATLAB) that you can download from https://www.ebi.ac.uk/biomodels/MODEL3023641273#Files
if you look the .m file, you'll see a kinetic model
well, because a GSMM is S*v = 0
take a look into this paper https://www.nature.com/articles/srep39647
(I said "simulating" because GSMM are optimization problems)
I have the optimization part sorted out by scipy.optimize.minimize
Ok I'm stupid. Just found there's cobrapy.
@glucksfall thanks a ton fot telling me there's a difference between kinetic model and GSMM model!
I assumed you were starting with GSMMs. That because I said details you already know
Still, if you need help with pycobra, I can look at old scripts I have. I work now with PySB and kappa to model and simulate metabolism.
PySB v1.9.1 is now out, which contains a bug fix for the
BngSimulator. See the release notes for details.
I'm a mac user and when I type in the command "conda install -c alubbock pysb" again it tells me "#all requested packages already installed"
when I type in "pip install pysb" each line says "requirement already satisfied"
I've installed python 3.7
type which python3 (python3.7) in a terminal to know where is installed python
*where is python
also, pip, pip2 and pip3 are related to different python versions
Hi, I have a question about monomer specifications. Does pySB automatically handle under-specifying a monomer by performing the operation on all possible versions of the monomer? for example, if I have defined a monomer X and it can be bound or unbound, and have two states: 'active' or 'inactive'. If I refer to that monomer, but I dont care whether the monomer is active or inactive, can I just not specifiy that i.e. just specific bound or not bound, and leave the specification for the activity empty? Will pySB handle this or do I have to explicity define all possible states whenever I refer to a monomer? With a larger number of states this would be time-consuming. I also have a question about applying rules to complexes. For example, lets say I have 10 monomers and I generate rules that form all possbible complexes between them. Is it possible to then refer to these complexes somehow at a later time in my code? It seems like there is a .monomer object but not a .complex object?
You need to refer to specific states when using Init. If not, the simulator assign the initial quantity to default states. The same applies for observables. Your monomers can have 4 states, so observables range from
X() accounting for all monomers (bound and unbound, active and inactives) to specific ones stating the state of each site. However, in Rules, you define only the states needed for the reaction (for instance, to dimerize, X must be inactive, active, or you don't care about it)
This is an example from a model I dev: first, I "aliased" the dimer
cplx_rpoa_rpoa = Prot_rpoA(PBD_01 = 1, PBD_02 = None) % Prot_rpoA(PBD_01 = None, PBD_02 = 1)
Hi @opurcell, rule-based modeling frameworks like PySB are designed to handle exactly the kinds of scenarios you mention. In rules or observables, if you don't specify states or bonds for a particular site, the pattern matches any state or bond (bound or unbound). In your example, if you just specify
X() in a rule or observable, it will match both states, regardless of whether it is bound or not. You can also generate model components (rules, observables, initial conditions etc.) programmatically using a for loop or similar.
