{"_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":7,"slug":"public-projects","title":"PUBLIC PROJECTS"},"version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":40,"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","59a555bccdbd85001bfb1442","5a2a81f688574d001e9934f5","5b080c8d7833b20003ddbb6f"],"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":3,"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"}

GET STARTED

TUTORIALS

ACCESS THE CGC

MANAGE AN ANALYSIS ENVIRONMENT

COLLABORATE SECURELY

DATASETS HUB

PUBLIC PROJECTS

BRING YOUR PRIVATE DATA

SET METADATA ASSOCIATED WITH A PRIVATE FILE

SEARCH FILES

ADD FILES TO A PROJECT

ORGANIZE FILES

ARCHIVE FILES

FIND APPS

BRING YOUR TOOLS

DESCRIBE YOUR TOOL

TOOL WRAPPING TIPS AND TRICKS

EDIT AN APP

ARCHIVE APPS

RUN AN ANALYSIS

TASK EXECUTION

REVIEW A TASK

VIEW ANALYSIS RESULTS

INTERACTIVE ANALYSIS

DOWNLOAD RESULTS

DEVELOPER TOOLS

CONNECT CLOUD STORAGE

API Hub

API Reference

FOLDERS API (Advance Access)

BULK API ACTIONS

WATCH AND LEARN

DATA CRUNCHER

SBFS (Beta)

SBFS Command Reference

GLOSSARY

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>