{"action":"created","issue":{"url":"https://api.github.com/repos/SysBioChalmers/GECKO/issues/60","repository_url":"https://api.github.com/repos/SysBioChalmers/GECKO","labels_url":"https://api.github.com/repos/SysBioChalmers/GECKO/issues/60/labels{/name}","comments_url":"https://api.github.com/repos/SysBioChalmers/GECKO/issues/60/comments","events_url":"https://api.github.com/repos/SysBioChalmers/GECKO/issues/60/events","html_url":"https://github.com/SysBioChalmers/GECKO/pull/60","id":387825855,"node_id":"MDExOlB1bGxSZXF1ZXN0MjM2MjI4ODYz","number":60,"title":"refactor: getConstrainedModel uses constrainPool directly","user":{"login":"edkerk","id":7326655,"node_id":"MDQ6VXNlcjczMjY2NTU=","avatar_url":"https://avatars3.githubusercontent.com/u/7326655?v=4","gravatar_id":"","url":"https://api.github.com/users/edkerk","html_url":"https://github.com/edkerk","followers_url":"https://api.github.com/users/edkerk/followers","following_url":"https://api.github.com/users/edkerk/following{/other_user}","gists_url":"https://api.github.com/users/edkerk/gists{/gist_id}","starred_url":"https://api.github.com/users/edkerk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/edkerk/subscriptions","organizations_url":"https://api.github.com/users/edkerk/orgs","repos_url":"https://api.github.com/users/edkerk/repos","events_url":"https://api.github.com/users/edkerk/events{/privacy}","received_events_url":"https://api.github.com/users/edkerk/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-12-05T16:01:04Z","updated_at":"2018-12-05T16:09:26Z","closed_at":"2018-12-05T16:09:26Z","author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/SysBioChalmers/GECKO/pulls/60","html_url":"https://github.com/SysBioChalmers/GECKO/pull/60","diff_url":"https://github.com/SysBioChalmers/GECKO/pull/60.diff","patch_url":"https://github.com/SysBioChalmers/GECKO/pull/60.patch"},"body":"- refactor:\r\n  - instead of parsing through `constrainEnzymes`, which is confusing as no enzymes are individually constrained, directly call `constrainPool`\r\n  - `constrainPool` has alternative option where all enzymes are assumed non-measured \r\n\r\nTo me it has been confusing that `constrainEnzymes` is called when only the pool is constrained. Perhaps there are good reasons for this, in that case please discard this PR."},"comment":{"url":"https://api.github.com/repos/SysBioChalmers/GECKO/issues/comments/444541625","html_url":"https://github.com/SysBioChalmers/GECKO/pull/60#issuecomment-444541625","issue_url":"https://api.github.com/repos/SysBioChalmers/GECKO/issues/60","id":444541625,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NDU0MTYyNQ==","user":{"login":"BenjaSanchez","id":9384349,"node_id":"MDQ6VXNlcjkzODQzNDk=","avatar_url":"https://avatars1.githubusercontent.com/u/9384349?v=4","gravatar_id":"","url":"https://api.github.com/users/BenjaSanchez","html_url":"https://github.com/BenjaSanchez","followers_url":"https://api.github.com/users/BenjaSanchez/followers","following_url":"https://api.github.com/users/BenjaSanchez/following{/other_user}","gists_url":"https://api.github.com/users/BenjaSanchez/gists{/gist_id}","starred_url":"https://api.github.com/users/BenjaSanchez/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BenjaSanchez/subscriptions","organizations_url":"https://api.github.com/users/BenjaSanchez/orgs","repos_url":"https://api.github.com/users/BenjaSanchez/repos","events_url":"https://api.github.com/users/BenjaSanchez/events{/privacy}","received_events_url":"https://api.github.com/users/BenjaSanchez/received_events","type":"User","site_admin":false},"created_at":"2018-12-05T16:09:26Z","updated_at":"2018-12-05T16:09:26Z","author_association":"MEMBER","body":"@edkerk `constrainEnzymes.m` is also used when constraining the model with proteomic data, it has inputs `pIDs` & `data` for this. That being said:\r\n1. We should improve the documentation of both `constrainEnzymes.m` and `constrainPool.m` to explain this (connected to https://github.com/SysBioChalmers/GECKO/issues/51).\r\n2. We should also add an example in the tool showing an integration with proteomics data, for instance in `/geckomat/utilities`, or possibly in a `/tutorials` folder."}}
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