{"action":"created","issue":{"url":"https://api.github.com/repos/trvrb/sismid/issues/9","labels_url":"https://api.github.com/repos/trvrb/sismid/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/trvrb/sismid/issues/9/comments","events_url":"https://api.github.com/repos/trvrb/sismid/issues/9/events","html_url":"https://github.com/trvrb/sismid/issues/9","id":96691325,"number":9,"title":"Reorganization for 2016","user":{"login":"trvrb","id":1176109,"avatar_url":"https://avatars.githubusercontent.com/u/1176109?v=3","gravatar_id":"","url":"https://api.github.com/users/trvrb","html_url":"https://github.com/trvrb","followers_url":"https://api.github.com/users/trvrb/followers","following_url":"https://api.github.com/users/trvrb/following{/other_user}","gists_url":"https://api.github.com/users/trvrb/gists{/gist_id}","starred_url":"https://api.github.com/users/trvrb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/trvrb/subscriptions","organizations_url":"https://api.github.com/users/trvrb/orgs","repos_url":"https://api.github.com/users/trvrb/repos","events_url":"https://api.github.com/users/trvrb/events{/privacy}","received_events_url":"https://api.github.com/users/trvrb/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-07-22T23:37:38Z","updated_at":"2015-07-23T03:25:40Z","closed_at":null,"body":"I wanted to write some notes on this now while the course is still fresh. I'd propose the following:\r\n\r\nI would take over the first lecture that would incorporate the more biological material from \"competition\" and from \"flu\". This would aim to give an overview of different sorts of pathogens, and their strategies to escape immunity. Would touch on flu, HIV, malaria, HPV, rhinoviruses, etc... \r\n\r\nYou'd follow with a biological oriented immunity lecture that would be basically the B cell lecture from day 3, but would cover T cells and adaptive immunity as well.\r\n\r\nI feel like my weakest link was actually the BEAST exercise. A large proportion of people had done exactly this exercise the week before. And I didn't like the step-by-step nature it entails. Better to tell people it exists and they can do it on their own time. This would free up some time.\r\n\r\nI'd propose replacing \"serology\" with a more general \"antigenic evolution\" section. I could cover serology and you could cover things like the Hensley age distribution story you talked about [here](http://bedford.io/projects/sismid/bcells/slides.html#/30).\r\n\r\nI'm propose to end with a \"synthesis\" discussion / exercise where students are given timeseries, trees, antigenic maps for say EV 71 and they're supposed to come to some conclusions about what's going on. Or maybe have people break up into groups and each group studies a particular pathogen and then reports to the class. We'd supply figures for each pathogen. So everything would be interpretation rather than data gathering.\r\n\r\nNotice also that this makes it so you don't have a completely full day 1 and I don't have a completely full day 2.\r\n\r\n### Day 1\r\n* Session A: Biological lecture on pathogens *(Trevor)*\r\n* Session B: Biological lecture on immunity *(Sarah)*\r\n* Session C: Epi Models *(Sarah)*\r\n* Session D: Fitting *(Sarah)*\r\n\r\n### Day 2\r\n* Session A: SSR *(Sarah)*\r\n* Session B: Coalescent *(Trevor)*\r\n* Session C: Phylogenetics *(Trevor)*\r\n* Session D: Selection *(Trevor)*\r\n\r\n### Day 3\r\n* Session A: Antigenic evolution *(Both)*\r\n* Session B: Synthesis *(Both)*\r\n"},"comment":{"url":"https://api.github.com/repos/trvrb/sismid/issues/comments/123951214","html_url":"https://github.com/trvrb/sismid/issues/9#issuecomment-123951214","issue_url":"https://api.github.com/repos/trvrb/sismid/issues/9","id":123951214,"user":{"login":"sarahCobey","id":1193794,"avatar_url":"https://avatars.githubusercontent.com/u/1193794?v=3","gravatar_id":"","url":"https://api.github.com/users/sarahCobey","html_url":"https://github.com/sarahCobey","followers_url":"https://api.github.com/users/sarahCobey/followers","following_url":"https://api.github.com/users/sarahCobey/following{/other_user}","gists_url":"https://api.github.com/users/sarahCobey/gists{/gist_id}","starred_url":"https://api.github.com/users/sarahCobey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sarahCobey/subscriptions","organizations_url":"https://api.github.com/users/sarahCobey/orgs","repos_url":"https://api.github.com/users/sarahCobey/repos","events_url":"https://api.github.com/users/sarahCobey/events{/privacy}","received_events_url":"https://api.github.com/users/sarahCobey/received_events","type":"User","site_admin":false},"created_at":"2015-07-23T03:25:40Z","updated_at":"2015-07-23T03:25:40Z","body":"Excellent ideas!\r\n\r\nThe only change I might make to your proposal is to extend the epi fitting over two sessions, perhaps focusing on population time series in Session D of Day 1 and on longitudinal data in Session A of Day 2. It may not be worth spending time fitting population data if MIF remains the obvious choice, however. (I am performing head-to-head competitions of methods this summer, so I should have a better sense if this is the case in a few months.) Covering inference well seems more important than SSR.\r\n\r\nI also plan to include more small quizzes and exercises throughout my sessions.\r\n\r\nIt might be worth framing each session in the first two days in the most problem-oriented way possible, e.g., \"This pathogen has a lot of types/high genetic diversity/fast turnover. How do we know if immune-mediated selection is a cause?\" We then discuss population genetic measures, inference from mechanistic models, etc., in the context of major hypotheses. We could even assign pathogens to groups randomly on the first day (without providing the data then) so people listen with a specific context in mind. It might even make sense to provide data incrementally, e.g., some pertinent immunology after the immunology session, time series after the time series session, etc., if it wouldn't fragment the day too much."}}