{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/2746","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2746/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2746/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2746/events","html_url":"https://github.com/broadinstitute/gatk/issues/2746","id":230806958,"number":2746,"title":"Implement prototype JNI layer for 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a prototype JNI layer for STAN (http://mc-stan.org/) using its C++ API (doesn't need to be exhaustive at this point, just a minimal proof of concept), write some client code against it, and assess both the complexity of writing/maintaining the JNI layer and the ease/difficulty of writing the client code in Java."},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/318674946","html_url":"https://github.com/broadinstitute/gatk/issues/2746#issuecomment-318674946","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2746","id":318674946,"user":{"login":"samuelklee","id":11076296,"avatar_url":"https://avatars0.githubusercontent.com/u/11076296?v=4","gravatar_id":"","url":"https://api.github.com/users/samuelklee","html_url":"https://github.com/samuelklee","followers_url":"https://api.github.com/users/samuelklee/followers","following_url":"https://api.github.com/users/samuelklee/following{/other_user}","gists_url":"https://api.github.com/users/samuelklee/gists{/gist_id}","starred_url":"https://api.github.com/users/samuelklee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/samuelklee/subscriptions","organizations_url":"https://api.github.com/users/samuelklee/orgs","repos_url":"https://api.github.com/users/samuelklee/repos","events_url":"https://api.github.com/users/samuelklee/events{/privacy}","received_events_url":"https://api.github.com/users/samuelklee/received_events","type":"User","site_admin":false},"created_at":"2017-07-28T14:58:02Z","updated_at":"2017-07-28T14:58:02Z","body":"Another library that just popped up on my radar---and this one is actually in Java!\r\n\r\nhttp://www.amidsttoolbox.com/\r\nhttps://arxiv.org/abs/1704.01427\r\nhttps://arxiv.org/abs/1604.07990\r\n\r\nThe approach is quite different from the other libraries we have been considering; here, the focus seems to be on streaming/parallel data and inference via message passing.  I think our models can be expressed in their framework (although, at a glance, the modeling language is not as nice as Stan---it looks like you have to build DAGs explicitly), but I have to admit that I am not familiar with message passing and how performance compares to MCMC, ADVI, etc.  @mbabadi @davidbenjamin any thoughts?\r\n\r\nI still think it's worth playing around with this library.  We could investigate how quick it would be to implement a streaming/minibatch version of VQSR, for example, which might be useful for @eitanbanks @ldgauthier."}}
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