{"action":"created","issue":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/3370","repository_url":"https://api.github.com/repos/OpenMS/OpenMS","labels_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/3370/labels{/name}","comments_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/3370/comments","events_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/3370/events","html_url":"https://github.com/OpenMS/OpenMS/pull/3370","id":312114889,"number":3370,"title":"[FEATURE] Additional scores for OpenSWATH","user":{"login":"grosenberger","id":4172900,"avatar_url":"https://avatars0.githubusercontent.com/u/4172900?v=4","gravatar_id":"","url":"https://api.github.com/users/grosenberger","html_url":"https://github.com/grosenberger","followers_url":"https://api.github.com/users/grosenberger/followers","following_url":"https://api.github.com/users/grosenberger/following{/other_user}","gists_url":"https://api.github.com/users/grosenberger/gists{/gist_id}","starred_url":"https://api.github.com/users/grosenberger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/grosenberger/subscriptions","organizations_url":"https://api.github.com/users/grosenberger/orgs","repos_url":"https://api.github.com/users/grosenberger/repos","events_url":"https://api.github.com/users/grosenberger/events{/privacy}","received_events_url":"https://api.github.com/users/grosenberger/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":13,"created_at":"2018-04-06T20:55:10Z","updated_at":"2018-04-26T21:44:34Z","closed_at":null,"author_association":"MEMBER","pull_request":{"url":"https://api.github.com/repos/OpenMS/OpenMS/pulls/3370","html_url":"https://github.com/OpenMS/OpenMS/pull/3370","diff_url":"https://github.com/OpenMS/OpenMS/pull/3370.diff","patch_url":"https://github.com/OpenMS/OpenMS/pull/3370.patch"},"body":"This PR proposes a set of new scores for OpenSWATH/IPF. The implementation is based on [MIToolkit](https://github.com/Craigacp/MIToolbox), a small C++/Matlab toolkit released under the 3-clause BSD license that provides commonly used metrics from information theory.\r\n\r\nTo make these functions available in OpenSWATH, I suggest two alternative options:\r\n- Adding MIToolbox to ``OpenMS/contrib``. I have implemented such a solution [here](https://github.com/grosenberger/contrib/tree/feature/mitoolbox).\r\n- Adding MIToolbox directly to ``OpenSwathAlgo`` (this PR).\r\n\r\nThe benefit of the ``contrib`` approach is of course better modularity. On the other hand, this increases the maintenance efforts for all platforms agains. Further, MIToolbox is super small, so the overhead of directlu integrating this within ``OpenSwathAlgo`` would be minimal.\r\n\r\nWhich option is preferred by the core developers?"},"comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/comments/384798615","html_url":"https://github.com/OpenMS/OpenMS/pull/3370#issuecomment-384798615","issue_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/3370","id":384798615,"user":{"login":"grosenberger","id":4172900,"avatar_url":"https://avatars0.githubusercontent.com/u/4172900?v=4","gravatar_id":"","url":"https://api.github.com/users/grosenberger","html_url":"https://github.com/grosenberger","followers_url":"https://api.github.com/users/grosenberger/followers","following_url":"https://api.github.com/users/grosenberger/following{/other_user}","gists_url":"https://api.github.com/users/grosenberger/gists{/gist_id}","starred_url":"https://api.github.com/users/grosenberger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/grosenberger/subscriptions","organizations_url":"https://api.github.com/users/grosenberger/orgs","repos_url":"https://api.github.com/users/grosenberger/repos","events_url":"https://api.github.com/users/grosenberger/events{/privacy}","received_events_url":"https://api.github.com/users/grosenberger/received_events","type":"User","site_admin":false},"created_at":"2018-04-26T21:44:34Z","updated_at":"2018-04-26T21:44:34Z","author_association":"MEMBER","body":"Thanks for spotting the pyOpenMS issue. I have unrelated issues building pyOpenMS with OpenMS/develop on macOS 10.12, but I could not resolve the issue there yet.\r\n\r\nIn my tests, the MI scores also improve the sensitivity for standard OpenSWATH MS2 peak group scoring. But of course this comes at some computational costs and thus it might make sense to disable them by default. I will change this accordingly."}}
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