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
I worked with GSMMs. I can help you if you need it. Probably is a good discussion if PySB should allow supports for GSMM, but COBRA (for python, matlab, and others) does a good job "simulating" and analysing GSMMs
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.
Thankyou everyone for your quick replies, its very helpful. I think between you you have answered everything and I can make some progress. I realize that these things can be determined through trial and error but sometimes it's good to know what should/shouldnt work rather than hoping error handling makes it clear. I realized I have one more question - is it possible to represent multimerization in a single rule declaration? i.e. A % A % A for a heterotrimer or e.g. A % B % C % D for a homotetramer . I know that technically anything above dimerization is not physically possible in a single instance of time, but its much simpler to do that than representing all possible orderings of reactions to the multimer, so its a simplication I am happy to make.
Short answer is yes, you could do that (for instace:
'R1' A(),X(),X() <-> X(),X(),X() @ 'a1','a2'; is kappa code, but I think you understand the idea). Gillespie argued that trimolecular (and higher order) reactions have very low probability (because molecules should collide at the same time and with correct orientation and velocity or energy). Just be aware of the rule rate. The propensivity is the multiplication of the rule rate (a1 in the example) and the quantities of A and X (sort of), so you could have a rule with very high probability of ocurrence. The example rule is part of the Schloegl's model, and there are papers showing the propensivity for each reaction.
Great, thanks very much. Really just asking what I couldnt seem to find in the documentation but what I know I will need for the future. @glucksfall thanks I will be careful of the rate rules. @lh64 in an earlier message you said I could access complexes through model.species. I have built my model, and at the end would like to run through all the species and set the initial conditions. However model.species is empty in my model? model.monomers, monomers.parameters and model.rules all returns what I would expect, so my model is correctly populated. Do I have to do something to generate the species from the monomers and rules?
PySB v1.10 is now out, including support for BioNetGen local functions and an improved Kappa simulation engine. Release notes: http://pysb.org/news/pysb-v1-10-0-released
PySB v1.11 adds JSON model import/export, improves import of SBML and BNGL models. Release notes: http://pysb.org/news/pysb-v1-11-0-released
@opurcell Did your issue get resolved? You need to generate the network before you can access model species, reactions, and ODEs:
from pysb.bng import generate_equations
generate_equations(model)