{"action":"created","issue":{"url":"https://api.github.com/repos/LoLab-VU/pysb/issues/34","repository_url":"https://api.github.com/repos/LoLab-VU/pysb","labels_url":"https://api.github.com/repos/LoLab-VU/pysb/issues/34/labels{/name}","comments_url":"https://api.github.com/repos/LoLab-VU/pysb/issues/34/comments","events_url":"https://api.github.com/repos/LoLab-VU/pysb/issues/34/events","html_url":"https://github.com/LoLab-VU/pysb/issues/34","id":157097566,"number":34,"title":"we need a pre equilibration function.","user":{"login":"ortega2247","id":4613881,"avatar_url":"https://avatars.githubusercontent.com/u/4613881?v=3","gravatar_id":"","url":"https://api.github.com/users/ortega2247","html_url":"https://github.com/ortega2247","followers_url":"https://api.github.com/users/ortega2247/followers","following_url":"https://api.github.com/users/ortega2247/following{/other_user}","gists_url":"https://api.github.com/users/ortega2247/gists{/gist_id}","starred_url":"https://api.github.com/users/ortega2247/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ortega2247/subscriptions","organizations_url":"https://api.github.com/users/ortega2247/orgs","repos_url":"https://api.github.com/users/ortega2247/repos","events_url":"https://api.github.com/users/ortega2247/events{/privacy}","received_events_url":"https://api.github.com/users/ortega2247/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-05-26T23:01:53Z","updated_at":"2016-06-17T22:15:54Z","closed_at":null,"body":"pre equilibration refers to the period of time where reactants and intermediate species interact until they reach equilibration, which means that the net reaction rate = 0. This function would be important because usually cells can be assumed that are in equilibrium and then a drug or ligand is applied and takes the cell from the equilibrium and generates different dynamics and responses.\r\n\r\nFor example if we have an enzyme that binds a substrate with initial conditions E0 and S0, and with want to perturbate that interaction with a drug D with initial condition D0. If we simulate the system where we put E, S, and D at the same time they are going to be out of equilibrium from the beginning and the dynamics could be completely different than when we allow a pre-equilibration phase between E and S and then we applied the drug that takes the system out of equilibrium."},"comment":{"url":"https://api.github.com/repos/LoLab-VU/pysb/issues/comments/226894329","html_url":"https://github.com/LoLab-VU/pysb/issues/34#issuecomment-226894329","issue_url":"https://api.github.com/repos/LoLab-VU/pysb/issues/34","id":226894329,"user":{"login":"ortega2247","id":4613881,"avatar_url":"https://avatars.githubusercontent.com/u/4613881?v=3","gravatar_id":"","url":"https://api.github.com/users/ortega2247","html_url":"https://github.com/ortega2247","followers_url":"https://api.github.com/users/ortega2247/followers","following_url":"https://api.github.com/users/ortega2247/following{/other_user}","gists_url":"https://api.github.com/users/ortega2247/gists{/gist_id}","starred_url":"https://api.github.com/users/ortega2247/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ortega2247/subscriptions","organizations_url":"https://api.github.com/users/ortega2247/orgs","repos_url":"https://api.github.com/users/ortega2247/repos","events_url":"https://api.github.com/users/ortega2247/events{/privacy}","received_events_url":"https://api.github.com/users/ortega2247/received_events","type":"User","site_admin":false},"created_at":"2016-06-17T22:15:54Z","updated_at":"2016-06-17T22:15:54Z","body":"I created a very rustic pre_equilibration function:  pre_equilibration(model, time_search, tolerance=1e-6, ligand=None, ligand_value=None, parameters=None). It solves that system during the time_search and returns the time to equilibration and the concentration of species at the time of equilibration so it can be passed to the as a parameter for solving the system again. I don't know how bad of idea this is... thoughts?"}}
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