{"action":"created","issue":{"url":"https://api.github.com/repos/SBRG/bigg_models/issues/197","repository_url":"https://api.github.com/repos/SBRG/bigg_models","labels_url":"https://api.github.com/repos/SBRG/bigg_models/issues/197/labels{/name}","comments_url":"https://api.github.com/repos/SBRG/bigg_models/issues/197/comments","events_url":"https://api.github.com/repos/SBRG/bigg_models/issues/197/events","html_url":"https://github.com/SBRG/bigg_models/issues/197","id":151951966,"number":197,"title":"rxnGeneMat in matlab version of models missing","user":{"login":"labhset1","id":6921527,"avatar_url":"https://avatars.githubusercontent.com/u/6921527?v=3","gravatar_id":"","url":"https://api.github.com/users/labhset1","html_url":"https://github.com/labhset1","followers_url":"https://api.github.com/users/labhset1/followers","following_url":"https://api.github.com/users/labhset1/following{/other_user}","gists_url":"https://api.github.com/users/labhset1/gists{/gist_id}","starred_url":"https://api.github.com/users/labhset1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/labhset1/subscriptions","organizations_url":"https://api.github.com/users/labhset1/orgs","repos_url":"https://api.github.com/users/labhset1/repos","events_url":"https://api.github.com/users/labhset1/events{/privacy}","received_events_url":"https://api.github.com/users/labhset1/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2016-04-29T19:36:54Z","updated_at":"2016-04-29T21:56:31Z","closed_at":null,"body":"Hello,\r\nI tried downloading matlab version of iJO1366 and iMM904 form bigg website and both had rxnGeneMat field missing. Is there a reason why they have been removes? They were really useful. \r\nCheers,\r\nPiyush Labhsetwar"},"comment":{"url":"https://api.github.com/repos/SBRG/bigg_models/issues/comments/215892361","html_url":"https://github.com/SBRG/bigg_models/issues/197#issuecomment-215892361","issue_url":"https://api.github.com/repos/SBRG/bigg_models/issues/197","id":215892361,"user":{"login":"nel3","id":3577516,"avatar_url":"https://avatars.githubusercontent.com/u/3577516?v=3","gravatar_id":"","url":"https://api.github.com/users/nel3","html_url":"https://github.com/nel3","followers_url":"https://api.github.com/users/nel3/followers","following_url":"https://api.github.com/users/nel3/following{/other_user}","gists_url":"https://api.github.com/users/nel3/gists{/gist_id}","starred_url":"https://api.github.com/users/nel3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nel3/subscriptions","organizations_url":"https://api.github.com/users/nel3/orgs","repos_url":"https://api.github.com/users/nel3/repos","events_url":"https://api.github.com/users/nel3/events{/privacy}","received_events_url":"https://api.github.com/users/nel3/received_events","type":"User","site_admin":false},"created_at":"2016-04-29T21:56:31Z","updated_at":"2016-04-29T21:56:31Z","body":"That makes more sense. Those were made in cobrapy, so we will rebuild them\nwith the matrix.\n\nThanks for pointing that out\n\n*Nathan E. Lewis*\n\nAssistant Professor\nDepartment of Pediatrics\nUniversity of California, San Diego\nTel: (858) 997 - 5844\nhttp://lewislab.ucsd.edu/\n\nOn Fri, Apr 29, 2016 at 2:54 PM, Piyush Labhsetwar <notifications@github.com\n> wrote:\n\n> I downloaded the matlab files from bigg database and they also didn't have\n> the rxnGeneMat field in the moel struct. I didn't try to read sbml file\n> into matlab.\n>\n> Piyush Labhsetwar\n> Doctoral Student\n> Center for Biophysics and Computational Biology\n> University of Illinois at Urbana Champaign (UIUC)\n> Illinois, USA\n> labhset1@illinois.edu\n>\n> 2016-04-29 16:47 GMT-05:00 Nathan Lewis <notifications@github.com>:\n>\n> > Then I don't think it is an issue with the models. The matrix isnt in the\n> > sbml... rather is is built by the sbml parsers in cobrapy and yhe matlab\n> > toolbox. This has been fixed in cobrapy:\n> >\n> >\n> >\n> https://github.com/opencobra/cobrapy/commit/aa36f92d08796f834a413b78576936891cfff027\n> >\n> > If you are using the matlab toolbox, you will want to post the question\n> on\n> > tgeir page.\n> >\n> > Sent from my Android phone.\n> > On Apr 29, 2016 5:19 PM, \"Piyush Labhsetwar\" <notifications@github.com>\n> >\n> > wrote:\n> >\n> > > Yes it didn't appear as a field in the model struct in matlab variable.\n> > >\n> > > Piyush Labhsetwar\n> > > Doctoral Student\n> > > Center for Biophysics and Computational Biology\n> > > University of Illinois at Urbana Champaign (UIUC)\n> > > Illinois, USA\n> > > labhset1@illinois.edu\n> > >\n> > > 2016-04-29 15:15 GMT-05:00 Nathan Lewis <notifications@github.com>:\n> > >\n> > > > Hi Piyush,\n> > > >\n> > > > In what way was the rxnGeneMat field missing? Did it not appear in\n> your\n> > > > model when you imported it into the COBRA Toolbox?\n> > > >\n> > > > *Nathan E. Lewis*\n> > > >\n> > > > Assistant Professor\n> > > > Department of Pediatrics\n> > > > University of California, San Diego\n> > > > Tel: (858) 997 - 5844\n> > > > http://lewislab.ucsd.edu/\n> > > >\n> > > > On Fri, Apr 29, 2016 at 12:36 PM, Piyush Labhsetwar <\n> > > > notifications@github.com> wrote:\n> > > >\n> > > > > Hello,\n> > > > > I tried downloading matlab version of iJO1366 and iMM904 form bigg\n> > > > website\n> > > > > and both had rxnGeneMat field missing. Is there a reason why they\n> > have\n> > > > been\n> > > > > removes? They were really useful.\n> > > > > Cheers,\n> > > > > Piyush Labhsetwar\n> > > > >\n> > > > > —\n> > > > > You are receiving this because you are subscribed to this thread.\n> > > > > Reply to this email directly or view it on GitHub\n> > > > > <https://github.com/SBRG/bigg_models/issues/197>\n> > > > >\n> > > >\n> > > > —\n> > > > You are receiving this because you authored the thread.\n> > > > Reply to this email directly or view it on GitHub\n> > > > <\n> > >\n> >\n> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_SBRG_bigg-5Fmodels_issues_197-23issuecomment-2D215868624&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=P1mh8jYb6mw2O8fH5DP9qw0KFNp6QCLw4UKFrptO6Y4&m=XUFwns7xGcZ8TJEBa0vtZfS6zzs7bFQOFg3ayA3N22w&s=lnEDhkgRnRrBKMpeDvLTzlXZhZdnbeVvq9B_I8j_FDk&e=\n> > > >\n> > > >\n> > >\n> > > —\n> > > You are receiving this because you commented.\n> > > Reply to this email directly or view it on GitHub\n> > > <https://github.com/SBRG/bigg_models/issues/197#issuecomment-215884651\n> >\n> > >\n> >\n> > —\n> > You are receiving this because you authored the thread.\n> > Reply to this email directly or view it on GitHub\n> > <\n> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_SBRG_bigg-5Fmodels_issues_197-23issuecomment-2D215890188&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=P1mh8jYb6mw2O8fH5DP9qw0KFNp6QCLw4UKFrptO6Y4&m=eWu0Sw_yp4MU157pdaGcS0hVdbAlzqmBwDMHfhClETs&s=budA7STjjDv_dtCKibpIcC4qQRd7AODHEOWdWSGz-_g&e=\n> >\n> >\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly or view it on GitHub\n> <https://github.com/SBRG/bigg_models/issues/197#issuecomment-215891927>\n>\n"}}