{"_id":"57dac93813ca3b0e0015b057","project":"55faf11ba62ba1170021a9a7","__v":0,"user":"5613e4f8fdd08f2b00437620","category":{"_id":"5771811e27a5c20e00030dcd","version":"55faf11ba62ba1170021a9aa","__v":0,"project":"55faf11ba62ba1170021a9a7","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-06-27T19:40:14.237Z","from_sync":false,"order":28,"slug":"public-projects","title":"PUBLIC PROJECTS"},"version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":37,"createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","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"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"parentDoc":null,"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-09-15T16:15:52.175Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":2,"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. Click **Copy this project**, next to the project's title, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/dc3e60d-Screen_Shot_2016-09-12_at_4.29.01_PM.jpg\",\n        \"Screen Shot 2016-09-12 at 4.29.01 PM.jpg\",\n        2586,\n        1418,\n        \"#464c43\"\n      ]\n    }\n  ]\n}\n[/block]\n4. In the pop-up window, you can name your copy of the project and select a [billing group](doc:account-settings-and-billing#section-billing). You are granted $100 of Pilot Funds when you sign up for the CGC. To use these, select **Pilot Funds** as your billing group, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/7a14b2a-Screen_Shot_2016-09-12_at_4.35.51_PM.jpeg\",\n        \"Screen Shot 2016-09-12 at 4.35.51 PM.jpeg\",\n        1192,\n        812,\n        \"#eceff0\"\n      ]\n    }\n  ]\n}\n[/block]\n5. 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>","excerpt":"","slug":"dream-challenge","type":"basic","title":"ICGC-TCGA DREAM Somatic Mutation Calling Challenge"}

ICGC-TCGA DREAM Somatic Mutation Calling Challenge


[block:callout] { "type": "warning", "title": "On this page:", "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)" } [/block] ##Overview The 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. To 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/). To 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. <div align right><a href="#top"></a></div> ##Access ICGC-TCGA DREAM Somatic Mutation Calling Challenge resources on the CGC To access the project: 1. Select **Public projects** from the top navigation bar on the CGC, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/81c927d-Screen_Shot_2016-09-12_at_2.13.06_PM.jpeg", "Screen Shot 2016-09-12 at 2.13.06 PM.jpeg", 596, 282, "#1e5494" ] } ] } [/block] 2. Choose **ICGC-TCGA DREAM Somatic Mutation Calling Challenge - RNA** from the dropdown menu. You can either browse through the project and its resources or make a copy of the project to perform further analyses. <div align right><a href="#top"></a></div> ##Copy the ICGC-TCGA DREAM Somatic Mutation Calling public project To copy the entire project: 1. Select **Public projects **from the top navigation bar. 2. Choose **ICGC-TCGA DREAM Somatic Mutation Calling Challenge - RNA** from the dropdown menu. 3. Click **Copy this project**, next to the project's title, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/dc3e60d-Screen_Shot_2016-09-12_at_4.29.01_PM.jpg", "Screen Shot 2016-09-12 at 4.29.01 PM.jpg", 2586, 1418, "#464c43" ] } ] } [/block] 4. In the pop-up window, you can name your copy of the project and select a [billing group](doc:account-settings-and-billing#section-billing). You are granted $100 of Pilot Funds when you sign up for the CGC. To use these, select **Pilot Funds** as your billing group, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/7a14b2a-Screen_Shot_2016-09-12_at_4.35.51_PM.jpeg", "Screen Shot 2016-09-12 at 4.35.51 PM.jpeg", 1192, 812, "#eceff0" ] } ] } [/block] 5. Once you've customized the details, click **Copy** to copy the entire project. You'll be redirected to the dashboard of your cloned project, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/b22ed14-Screen_Shot_2016-09-12_at_4.39.56_PM.jpeg", "Screen Shot 2016-09-12 at 4.39.56 PM.jpeg", 2576, 1428, "#435059" ] } ] } [/block] You can now use the data and workflows contained within this project to conduct your own analyses. <div align right><a href="#top"></a></div> ##Learn more Find 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. <div align right><a href="#top"></a></div> ###Webinar: Visual interface This webinar covers how to deploy tools and workflows with the CGC SDK and evaluate their performance with DREAM Challenge data through the visual interface. [block:embed] { "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>", "url": "https://www.youtube.com/watch?v=JdCsL_MSOrE", "title": "CGC DREAM Webinar 1 - Visual Interface", "favicon": "https://s.ytimg.com/yts/img/favicon-vflz7uhzw.ico", "image": "https://i.ytimg.com/vi/JdCsL_MSOrE/hqdefault.jpg" } [/block] ###Webinar: Python and API This 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. [block:embed] { "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>", "url": "https://www.youtube.com/watch?v=tDzzRq4YN9M", "title": "CGC DREAM Webinar 2 - Python and API", "favicon": "https://s.ytimg.com/yts/img/favicon-vflz7uhzw.ico", "image": "https://i.ytimg.com/vi/tDzzRq4YN9M/hqdefault.jpg" } [/block] <div align right><a href="#top"></a></div> ###Resources Additional 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. <div align right><a href="#top"></a></div>