{"action":"created","issue":{"url":"https://api.github.com/repos/cBioPortal/GSoC/issues/17","repository_url":"https://api.github.com/repos/cBioPortal/GSoC","labels_url":"https://api.github.com/repos/cBioPortal/GSoC/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/cBioPortal/GSoC/issues/17/comments","events_url":"https://api.github.com/repos/cBioPortal/GSoC/issues/17/events","html_url":"https://github.com/cBioPortal/GSoC/issues/17","id":132876825,"number":17,"title":"Build a pipeline to map mutations to protein 3D structures","user":{"login":"jjgao","id":840895,"avatar_url":"https://avatars.githubusercontent.com/u/840895?v=3","gravatar_id":"","url":"https://api.github.com/users/jjgao","html_url":"https://github.com/jjgao","followers_url":"https://api.github.com/users/jjgao/followers","following_url":"https://api.github.com/users/jjgao/following{/other_user}","gists_url":"https://api.github.com/users/jjgao/gists{/gist_id}","starred_url":"https://api.github.com/users/jjgao/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jjgao/subscriptions","organizations_url":"https://api.github.com/users/jjgao/orgs","repos_url":"https://api.github.com/users/jjgao/repos","events_url":"https://api.github.com/users/jjgao/events{/privacy}","received_events_url":"https://api.github.com/users/jjgao/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cBioPortal/GSoC/labels/cBioPortal","name":"cBioPortal","color":"207de5"},{"url":"https://api.github.com/repos/cBioPortal/GSoC/labels/Genome-Nexus","name":"Genome-Nexus","color":"207de5"},{"url":"https://api.github.com/repos/cBioPortal/GSoC/labels/Java","name":"Java","color":"5319e7"},{"url":"https://api.github.com/repos/cBioPortal/GSoC/labels/JSON","name":"JSON","color":"5319e7"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2016-02-11T03:13:42Z","updated_at":"2016-03-07T03:25:54Z","closed_at":null,"body":"**Background**: Protein 3D structures are very useful when studying the effect of mutations in cancer. For example, oftentimes mutations tend to occur in the same 3D space. In the cBioPortal, we map and visualize cancer mutations to protein structures. \r\n\r\n![image](https://cloud.githubusercontent.com/assets/840895/12979410/d9c633c0-d0a4-11e5-8903-eee3fccac1bc.png)\r\n\r\n**Goal**: \r\n\r\n- Build sequence alignments of all human proteins (including all their isoforms) against PDB structures.\r\n- Build an automated pipeline to update protein structure data in cBioPortal.\r\n\r\n**Approach**: \r\n\r\n- Using BLAST (or other sequence alignment tools) to search human proteins against PDB strctures.\r\n- Save alignments in to Genome Nexus database.\r\n- Develop a JSON based API to expose the alignment data.\r\n- Build a pipeline to periodically check PDB for new structures. \r\n\r\n**Need skills**: Bioinformatics, Java, JSON\r\n\r\n**Possible mentors**: [JJ Gao](https://github.com/jjgao), [Onur Sumer](https://github.com/onursumer), [Benjamin Gross](https://github.com/n1zea144), [Angelica Ochoa](https://github.com/angelicaochoa)"},"comment":{"url":"https://api.github.com/repos/cBioPortal/GSoC/issues/comments/193074052","html_url":"https://github.com/cBioPortal/GSoC/issues/17#issuecomment-193074052","issue_url":"https://api.github.com/repos/cBioPortal/GSoC/issues/17","id":193074052,"user":{"login":"jjgao","id":840895,"avatar_url":"https://avatars.githubusercontent.com/u/840895?v=3","gravatar_id":"","url":"https://api.github.com/users/jjgao","html_url":"https://github.com/jjgao","followers_url":"https://api.github.com/users/jjgao/followers","following_url":"https://api.github.com/users/jjgao/following{/other_user}","gists_url":"https://api.github.com/users/jjgao/gists{/gist_id}","starred_url":"https://api.github.com/users/jjgao/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jjgao/subscriptions","organizations_url":"https://api.github.com/users/jjgao/orgs","repos_url":"https://api.github.com/users/jjgao/repos","events_url":"https://api.github.com/users/jjgao/events{/privacy}","received_events_url":"https://api.github.com/users/jjgao/received_events","type":"User","site_admin":false},"created_at":"2016-03-07T03:25:54Z","updated_at":"2016-03-07T03:25:54Z","body":"@p-sun please send leave an email to the discussion group (without including your proposal link). I'll get back to you from there."}}