{"action":"created","issue":{"url":"https://api.github.com/repos/bio4j/gsoc14/issues/8","labels_url":"https://api.github.com/repos/bio4j/gsoc14/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/bio4j/gsoc14/issues/8/comments","events_url":"https://api.github.com/repos/bio4j/gsoc14/issues/8/events","html_url":"https://github.com/bio4j/gsoc14/issues/8","id":27308833,"number":8,"title":"Integrate sequence data into bio4j","user":{"login":"eparejatobes","id":204693,"avatar_url":"https://avatars.githubusercontent.com/u/204693?v=3","gravatar_id":"","url":"https://api.github.com/users/eparejatobes","html_url":"https://github.com/eparejatobes","followers_url":"https://api.github.com/users/eparejatobes/followers","following_url":"https://api.github.com/users/eparejatobes/following{/other_user}","gists_url":"https://api.github.com/users/eparejatobes/gists{/gist_id}","starred_url":"https://api.github.com/users/eparejatobes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eparejatobes/subscriptions","organizations_url":"https://api.github.com/users/eparejatobes/orgs","repos_url":"https://api.github.com/users/eparejatobes/repos","events_url":"https://api.github.com/users/eparejatobes/events{/privacy}","received_events_url":"https://api.github.com/users/eparejatobes/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/bio4j/gsoc14/labels/aws","name":"aws","color":"207de5"},{"url":"https://api.github.com/repos/bio4j/gsoc14/labels/biology","name":"biology","color":"207de5"},{"url":"https://api.github.com/repos/bio4j/gsoc14/labels/idea","name":"idea","color":"006b75"},{"url":"https://api.github.com/repos/bio4j/gsoc14/labels/medium","name":"medium","color":"fbca04"},{"url":"https://api.github.com/repos/bio4j/gsoc14/labels/scala","name":"scala","color":"207de5"}],"state":"open","locked":false,"assignee":{"login":"evdokim","id":1071153,"avatar_url":"https://avatars.githubusercontent.com/u/1071153?v=3","gravatar_id":"","url":"https://api.github.com/users/evdokim","html_url":"https://github.com/evdokim","followers_url":"https://api.github.com/users/evdokim/followers","following_url":"https://api.github.com/users/evdokim/following{/other_user}","gists_url":"https://api.github.com/users/evdokim/gists{/gist_id}","starred_url":"https://api.github.com/users/evdokim/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/evdokim/subscriptions","organizations_url":"https://api.github.com/users/evdokim/orgs","repos_url":"https://api.github.com/users/evdokim/repos","events_url":"https://api.github.com/users/evdokim/events{/privacy}","received_events_url":"https://api.github.com/users/evdokim/received_events","type":"User","site_admin":false},"milestone":null,"comments":12,"created_at":"2014-02-10T22:53:50Z","updated_at":"2015-02-10T20:41:25Z","closed_at":null,"body":"https://github.com/bio4j/gsoc14/wiki/integrate-sequence-data-into-bio4j"},"comment":{"url":"https://api.github.com/repos/bio4j/gsoc14/issues/comments/73779387","html_url":"https://github.com/bio4j/gsoc14/issues/8#issuecomment-73779387","issue_url":"https://api.github.com/repos/bio4j/gsoc14/issues/8","id":73779387,"user":{"login":"ajmazurie","id":240550,"avatar_url":"https://avatars.githubusercontent.com/u/240550?v=3","gravatar_id":"","url":"https://api.github.com/users/ajmazurie","html_url":"https://github.com/ajmazurie","followers_url":"https://api.github.com/users/ajmazurie/followers","following_url":"https://api.github.com/users/ajmazurie/following{/other_user}","gists_url":"https://api.github.com/users/ajmazurie/gists{/gist_id}","starred_url":"https://api.github.com/users/ajmazurie/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ajmazurie/subscriptions","organizations_url":"https://api.github.com/users/ajmazurie/orgs","repos_url":"https://api.github.com/users/ajmazurie/repos","events_url":"https://api.github.com/users/ajmazurie/events{/privacy}","received_events_url":"https://api.github.com/users/ajmazurie/received_events","type":"User","site_admin":false},"created_at":"2015-02-10T20:41:25Z","updated_at":"2015-02-10T20:41:25Z","body":"Hi folks,\r\nI am quite interested in this discussion, and was wondering if you came up with an idea about the best architecture for a BLAST-like query on a Bio4j (or Neo4j) hosted set of sequences. I am interested in exploring graphs of reads and contigs collected across samples, and querying those objects based on their sequences is high in our features request list.\r\n\r\nBased on your discussion and my own exploration, I can see at least two solutions:\r\n(a) deploying a sequence alignment as a map/reduce job connected to a Neo4j database\r\n(b) storing sequences outside of the Neo4j store, and running a regular BLAST on the former\r\n\r\nSolution (b) would work for sure, but (a) seems more elegant, if the current state of the technologies involved is advanced enough. What are your thought?\r\n\r\nBest,\r\nAurelien"}}