{"action":"closed","issue":{"url":"https://api.github.com/repos/euba/BacArena/issues/107","repository_url":"https://api.github.com/repos/euba/BacArena","labels_url":"https://api.github.com/repos/euba/BacArena/issues/107/labels{/name}","comments_url":"https://api.github.com/repos/euba/BacArena/issues/107/comments","events_url":"https://api.github.com/repos/euba/BacArena/issues/107/events","html_url":"https://github.com/euba/BacArena/issues/107","id":309768709,"node_id":"MDU6SXNzdWUzMDk3Njg3MDk=","number":107,"title":"No uptake for reaction","user":{"login":"fairquestion","id":35567113,"node_id":"MDQ6VXNlcjM1NTY3MTEz","avatar_url":"https://avatars0.githubusercontent.com/u/35567113?v=4","gravatar_id":"","url":"https://api.github.com/users/fairquestion","html_url":"https://github.com/fairquestion","followers_url":"https://api.github.com/users/fairquestion/followers","following_url":"https://api.github.com/users/fairquestion/following{/other_user}","gists_url":"https://api.github.com/users/fairquestion/gists{/gist_id}","starred_url":"https://api.github.com/users/fairquestion/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fairquestion/subscriptions","organizations_url":"https://api.github.com/users/fairquestion/orgs","repos_url":"https://api.github.com/users/fairquestion/repos","events_url":"https://api.github.com/users/fairquestion/events{/privacy}","received_events_url":"https://api.github.com/users/fairquestion/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-03-29T14:06:33Z","updated_at":"2018-09-19T13:59:50Z","closed_at":"2018-09-19T13:59:50Z","author_association":"NONE","body":"Dear all,\r\n\r\nWhen working with the sybil's Ecoli core model I have tried to modify this model by introducing a test reaction:\r\n\r\n\"EX_no2(e)\"\t\"no2 exchange\"\t\"[e] : no2 <==> \"\t\"Reversible\"\t\"C_e\"\t-10\t1000\t0\t\"\"\t\"Exchange\"\r\n\"no2t\"\t\"no2 transporter via diffusion\"\t\"no2[e] --> no2[c]\"\t\"Irreversible\"\t\"C_c, C_e\"\t0\t1000\t0\t\"s0001\"\t\"Transport, Extracellular\"\r\n\"13tv\"\t\"testreaction\"\t\"[c] : no2 --> no3\"\t\"Irreversible\"\t\"C_c\"\t0\t1000\t0\t\"\"\t\"energy\"\r\n\"no3t\"\t\"no3 transporter via diffusion\"\t\"no3[c] --> no3[e]\"\t\"Irreversible\"\t\"C_c, C_e\"\t0\t1000\t0\t\"s0001\"\t\"Transport, Extracellular\"\r\n\"EX_no3(e)\"\t\"no3 exchange\"\t\"[e] : no3 <==> \"\t\"Reversible\"\t\"C_e\"\t0\t1000\t0\t\"\"\t\"Exchange\"\r\n\r\nAs you can see it just takes no2, converts it into no3 and releases it again. However no uptake is detected (there is growth cell and everything like in the normal core model). Do you have any idea? \r\nno2 and no3 have been added to metabolites file and no errors where detected when running BacArena.\r\n\r\nThanks.\r\n\r\n"}}
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