{"metadata":{"image":[],"title":"","description":""},"api":{"url":"","auth":"required","params":[],"results":{"codes":[]},"settings":""},"next":{"description":"","pages":[]},"title":"ICGC-TCGA DREAM Somatic Mutation Calling Challenge","type":"basic","slug":"dream-challenge","excerpt":"","body":"[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"On this page:\",\n  \"body\": \"* [Overview](#section-overview)\\n* [Access ICGC-TCGA DREAM Somatic Mutation Calling Challenge resources on the CGC](#section-access-icgc-tcga-dream-somatic-mutation-calling-challenge-resources-on-the-cgc)\\n* [Copy the ICGC-TCGA DREAM Somatic Mutation Calling public project](#section-copy-the-icgc-tcga-dream-somatic-mutation-calling-public-project)\\n* [Learn more](#section-learn-more)\\n * [Webinar: Visual interface](#section-webinar-visual-interface)\\n * [Webinar: Python and API](section-webinar-python-and-api)\\n *  [Resources](#section-resources)\"\n}\n[/block]\n##Overview\n\nThe Seven Bridges CGC is proud to launch the <a href=\"https://www.synapse.org/#!Synapse:syn2813589\" target=\"blank\">ICGC-TCGA DREAM Somatic Mutation Calling – RNA Challenge (SMC-RNA)</a>. The mission of this latest DREAM Challenge is to generate **more accurate**, **reproducible methods** for **quantifying known isoforms** and **detecting gene fusions** from RNA-Sequencing data.\n\nTo help you get started, the CGC has collated challenge resources, including data, example applications, and sample analyses, within a [public project on the CGC](https://cgc.sbgenomics.com/u/gauravCGC/icgc-tcga-dream-somatic-mutation-calling-challenge-rna/).\n\nTo preserve the integrity of the public projects' resources, you only have read permissions for these projects. You can make a copy of the entire project to conduct further analyses.\n\n<div align right><a href=\"#top\"></a></div>\n\n##Access ICGC-TCGA DREAM Somatic Mutation Calling Challenge resources on the CGC\n\nTo access the project:\n1. Select **Public projects** from the top navigation bar on the CGC, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/81c927d-Screen_Shot_2016-09-12_at_2.13.06_PM.jpeg\",\n        \"Screen Shot 2016-09-12 at 2.13.06 PM.jpeg\",\n        596,\n        282,\n        \"#1e5494\"\n      ]\n    }\n  ]\n}\n[/block]\n2. Choose **ICGC-TCGA DREAM Somatic Mutation Calling Challenge - RNA** from the dropdown menu.\n\nYou can either browse through the project and its resources or make a copy of the project to perform further analyses.\n\n<div align right><a href=\"#top\"></a></div>\n\n##Copy the ICGC-TCGA DREAM Somatic Mutation Calling public project\n\nTo copy the entire project:\n1. Select **Public projects **from the top navigation bar.\n2. Choose **ICGC-TCGA DREAM Somatic Mutation Calling Challenge - RNA** from the dropdown menu.\n3. Place your mouse cursor over the project title. Project information box is displayed.\n4. In the bottom-right part of the project information box, click **Copy project**.\n5. In the pop-up window, you can name your copy of the project, select a billing group and modify [execution settings](doc:modify-project-settings#section-modify-execution-settings) if needed.\n6. Once you've customized the details, click **Copy** to copy the entire project.\nYou'll be redirected to the dashboard of your cloned project, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/b22ed14-Screen_Shot_2016-09-12_at_4.39.56_PM.jpeg\",\n        \"Screen Shot 2016-09-12 at 4.39.56 PM.jpeg\",\n        2576,\n        1428,\n        \"#435059\"\n      ]\n    }\n  ]\n}\n[/block]\nYou can now use the data and workflows contained within this project to conduct your own analyses.\n\n<div align right><a href=\"#top\"></a></div>\n\n##Learn more\n\nFind out more about the [DREAM Challenge on the Cancer Genomics Cloud](http://www.cancergenomicscloud.org/dreamchallenge). Or, view the webinars and [resources](#section-resources) below.\n\n<div align right><a href=\"#top\"></a></div>\n\n###Webinar: Visual interface\n\nThis webinar covers how to deploy tools and workflows with the CGC SDK and evaluate their performance with DREAM Challenge data through the visual interface.\n[block:embed]\n{\n  \"html\": \"<iframe class=\\\"embedly-embed\\\" src=\\\"//cdn.embedly.com/widgets/media.html?src=https%3A%2F%2Fwww.youtube.com%2Fembed%2FJdCsL_MSOrE%3Ffeature%3Doembed&url=http%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DJdCsL_MSOrE&image=https%3A%2F%2Fi.ytimg.com%2Fvi%2FJdCsL_MSOrE%2Fhqdefault.jpg&key=02466f963b9b4bb8845a05b53d3235d7&type=text%2Fhtml&schema=youtube\\\" width=\\\"640\\\" height=\\\"480\\\" scrolling=\\\"no\\\" frameborder=\\\"0\\\" allowfullscreen></iframe>\",\n  \"url\": \"https://www.youtube.com/watch?v=JdCsL_MSOrE\",\n  \"title\": \"CGC DREAM Webinar 1 - Visual Interface\",\n  \"favicon\": \"https://s.ytimg.com/yts/img/favicon-vflz7uhzw.ico\",\n  \"image\": \"https://i.ytimg.com/vi/JdCsL_MSOrE/hqdefault.jpg\"\n}\n[/block]\n###Webinar: Python and API\n\nThis webinar focuses on using the [API](page:the-cgc-api) to programmatically access resources and test algorithms, then automate the evaluation of tools on all training data in Python.\n[block:embed]\n{\n  \"html\": \"<iframe class=\\\"embedly-embed\\\" src=\\\"//cdn.embedly.com/widgets/media.html?src=https%3A%2F%2Fwww.youtube.com%2Fembed%2FtDzzRq4YN9M%3Ffeature%3Doembed&url=http%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DtDzzRq4YN9M&image=https%3A%2F%2Fi.ytimg.com%2Fvi%2FtDzzRq4YN9M%2Fhqdefault.jpg&key=02466f963b9b4bb8845a05b53d3235d7&type=text%2Fhtml&schema=youtube\\\" width=\\\"640\\\" height=\\\"480\\\" scrolling=\\\"no\\\" frameborder=\\\"0\\\" allowfullscreen></iframe>\",\n  \"url\": \"https://www.youtube.com/watch?v=tDzzRq4YN9M\",\n  \"title\": \"CGC DREAM Webinar 2 - Python and API\",\n  \"favicon\": \"https://s.ytimg.com/yts/img/favicon-vflz7uhzw.ico\",\n  \"image\": \"https://i.ytimg.com/vi/tDzzRq4YN9M/hqdefault.jpg\"\n}\n[/block]\n<div align right><a href=\"#top\"></a></div>\n\n###Resources\n\nAdditional webinar resources are located at on the <a href=\"https://github.com/sbg/dreamwebinars\">Seven Bridges Github repository</a>. Here, you can find notebooks to help you get started as well as a library of helper function.\n\n<div align right><a href=\"#top\"></a></div>","updates":[],"order":3,"isReference":false,"hidden":false,"sync_unique":"","link_url":"","link_external":false,"_id":"57dac93813ca3b0e0015b057","createdAt":"2016-09-15T16:15:52.175Z","githubsync":"","project":"55faf11ba62ba1170021a9a7","__v":1,"user":"5613e4f8fdd08f2b00437620","category":{"sync":{"isSync":false,"url":""},"pages":[],"title":"PUBLIC PROJECTS","slug":"public-projects","order":7,"from_sync":false,"reference":false,"_id":"5771811e27a5c20e00030dcd","version":"55faf11ba62ba1170021a9aa","__v":0,"project":"55faf11ba62ba1170021a9a7","createdAt":"2016-06-27T19:40:14.237Z"},"version":{"version":"1.0","version_clean":"1.0.0","codename":"","is_stable":true,"is_beta":true,"is_hidden":false,"is_deprecated":false,"categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77","59a555bccdbd85001bfb1442","5a2a81f688574d001e9934f5","5b080c8d7833b20003ddbb6f","5c222bed4bc358002f21459a","5c22412594a2a5005cc9e919","5c41ae1c33592700190a291e","5c8a525e2ba7b2003f9b153c","5cbf14d58c79c700ef2b502e","5db6f03a6e187c006f667fa4"],"_id":"55faf11ba62ba1170021a9aa","releaseDate":"2015-09-17T16:58:03.490Z","createdAt":"2015-09-17T16:58:03.490Z","project":"55faf11ba62ba1170021a9a7","__v":46},"parentDoc":null}