{"__v":6,"_id":"5771813d3dd24019004c9130","category":{"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","_id":"5771811e27a5c20e00030dcd","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-06-27T19:40:14.237Z","from_sync":false,"order":28,"slug":"public-projects","title":"PUBLIC PROJECTS"},"parentDoc":null,"project":"55faf11ba62ba1170021a9a7","user":"5613e4f8fdd08f2b00437620","version":{"__v":37,"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","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"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-06-27T19:40:45.975Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":1,"body":"The Cancer Cell Line Encyclopedia (CCLE) public project contains large <a href=\"http://docs.sevenbridges.com/v1.0/page/ccle-open-access-data\" target=\"blank\">Open Access files</a> from the <a href=\"http://www.broadinstitute.org/ccle/home\" target=\"blank\">CCLE</a> which you can use on the CGC.\n[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"On this page:\",\n  \"body\": \"* [Overview](#section-overview)\\n* [What's contained in the project?](#section-what-s-contained-in-the-project-)\\n* [Access the CCLE public project](#section-access-the-ccle-public-project)\\n* [Use the CCLE public project](#section-use-the-ccle-public-project)\\n* [Use the entire project](#section-use-the-entire-project)\\n * [Copy the entire project](#section-copy-the-entire-project)\\n * [Run a task in a copied CCLE project](#section-run-a-task-a-copied-CCLE-project)\\n* [Use a subset of the data](#section-use-a-subset-of-the-data)\"\n}\n[/block]\n##Overview\n\nThe CCLE is made possible through a collaboration between the <a href=\"http://www.broadinstitute.org/\" target=\"blank\">Broad Institute</a>, the <a href=\"https://www.nibr.com/\" target=\"blank\">Novartis Institutes for Biomedical Research</a>, and the <a href=\"https://www.gnf.nibr.com/\" target=\"blank\">Genomics Institute of the Novartis Research Foundation</a> to perform detailed genetic and pharmacologic characterization of a large number of human cancer models.\n\nThe CCLE public project contains Open Access sequencing data (in the form of reads aligned to the hg19 broad variant reference genome) for nearly 1000 cancer cell line samples, as available from <a href=\"https://cghub.ucsc.edu/\" target=\"blank\">cgHub</a> on May 11, 2016.\n[block:callout]\n{\n  \"type\": \"info\",\n  \"title\": \"Open Access\",\n  \"body\": \"You don't need special access or authorization status to use the data in this project. In fact, any data you copy from this public project into your own projects will not count towards your storage. This data is ideal for interrogating the genomic landscape of cancer cell lines, testing new analysis methods, or getting to know the CGC.\"\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##What's contained in the project?\nThe CCLE public project contains the following distribution of samples and files by experimental strategy.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/ehKg9yl5ScSbSe4Rpn0V_Screen%20Shot%202016-06-14%20at%2012.18.03%20PM.jpeg\",\n        \"Screen Shot 2016-06-14 at 12.18.03 PM.jpeg\",\n        \"1270\",\n        \"356\",\n        \"#c3c3c3\",\n        \"\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"Additional array data and processed data are available from the <a href=\\\"http://www.broadinstitute.org/ccle/home\\\" target=\\\"blank\\\">CCLE data portal</a>.\"\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Access the CCLE public project\n\nTo access the CCLE public project:\n1. Click on **Public projects** from the top navigation bar.\n2. Select **Cancer Cell Line Encyclopedia (CCLE)**, as shown below.\n \nYou'll be taken to the main dashboard of the CCLE public project.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/pw77bK9IRyGYXbhgtJKP_Screen%20Shot%202016-06-27%20at%205.15.14%20PM.png\",\n        \"Screen Shot 2016-06-27 at 5.15.14 PM.png\",\n        \"516\",\n        \"162\",\n        \"#185393\",\n        \"\"\n      ],\n      \"border\": true,\n      \"sizing\": \"80\"\n    }\n  ]\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Use the CCLE public project\n\nAll CGC users automatically have copy permissions for this project. This means that while you while you cannot upload data or tools to the project or execute any of the workflows contained within it, you can copy the available data, tools, and workflows to your own projects on the Platform and execute analyses in your own projects.\n\nYou have the options to:\n\n  * [Use the entire project](#section-use-the-entire-project) - Copy the entire project to replicate analyses or conduct further analysis on CCLE data.\n  * [Select and use a subset of the data in your own project](#section-use-a-subset-of-the-data) - Copy the selected data to use within your own analyses.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Use the entire project\n\nTo help you get started, the CGC bioinformatics team has run some tasks on the CCLE data using [public apps](apps-on-the-cgc) and [reference files](file-repositories-on-the-cgc).\n\nWhile you cannot directly execute the workflows in the CCLE public project, you can make a copy of the entire project to [perform further analyses](#section-run-a-task-in-a-copied-ccle-project).\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Copy the entire project\n\nTo copy the entire project:\n\n1. Access the CCLE public project by selecting **Cancer Cell Line Encyclopedia (CCLE)** from **Public projects** in the top navigation bar.\n2. 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/hITPyV3SOm8FN2uSZdDP_Screen%20Shot%202016-06-27%20at%202.50.58%20PM.jpg\",\n        \"Screen Shot 2016-06-27 at 2.50.58 PM.jpg\",\n        \"2372\",\n        \"1152\",\n        \"#4a7dab\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n3. In the pop-up window, you can name your copy of the project and select a [billing group](account-settings-and-billing).\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/44FwsehrS5OWCsiCscTH_Screen%20Shot%202016-06-27%20at%203.10.13%20PM.jpeg\",\n        \"Screen Shot 2016-06-27 at 3.10.13 PM.jpeg\",\n        \"978\",\n        \"792\",\n        \"#3fb157\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n4. Once you've customized the details, click **Copy** to copy the entire project.\n\nYou'll be redirected to the dashboard of your cloned project when it is ready, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/TtsIy19tQoaNsJZtReMO_Screen%20Shot%202016-06-27%20at%203.11.49%20PM.jpeg\",\n        \"Screen Shot 2016-06-27 at 3.11.49 PM.jpeg\",\n        \"2376\",\n        \"1372\",\n        \"#40b25a\",\n        \"\"\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\">top</a></div>\n\n###Run a task in a copied CCLE project\n\nFor instance, you can replicate one of the tasks in the project. The **RNA-seq Differential Expression** task in the copied project is a great starting point to run other differential expression analyses. All you have to do is change the input files.\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"Once you've copied the project, you can run tasks in it.\"\n}\n[/block]\n1. Navigate to the **Tasks** tab on your copied CCLE project's dashboard.\n2. Select one of the previously run tasks.\n3. Click **Edit and rerun **in the upper right hand corner, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/jdStHB7qRYOgu9NWZpll_Screen%20Shot%202016-06-27%20at%203.15.00%20PM.jpg\",\n        \"Screen Shot 2016-06-27 at 3.15.00 PM.jpg\",\n        \"2378\",\n        \"1384\",\n        \"#477eae\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n4. You'll be redirected to the **DRAFT** task page, where you can select different inputs. Simply click **Pick file(s)**, as you can see in the image below, to select different files.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/zHKsQsJlRBe3VvuSbCKD_Screen%20Shot%202016-06-27%20at%203.16.58%20PM.jpg\",\n        \"Screen Shot 2016-06-27 at 3.16.58 PM.jpg\",\n        \"2220\",\n        \"1302\",\n        \"#427cb0\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n5. When you've selected your inputs, click **Run** in the upper righthand corner, as shown above.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Use a subset of the data\n\nInstead of cloning the entire project, you can choose to select and copy a subset of the data.\nTo copy a subset of the data:\n\n1. Access the CCLE public project by selecting **Cancer Cell Line Encyclopedia (CCLE)** from **Public projects** in the top navigation bar. You'll be taken to the project dashboard of the CCLE public project, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/bULWot7gSNyl4kVqs1l5_Screen%20Shot%202016-06-27%20at%203.11.49%20PM%20(1).jpeg\",\n        \"Screen Shot 2016-06-27 at 3.11.49 PM (1).jpeg\",\n        \"2376\",\n        \"1372\",\n        \"#40b25a\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n2. Click on the **Files** tab in the upper righthand corner. This will take you to the **Files** page for the CCLE project, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/W7q6ZF7rSc6yjKcXbQzM_Screen%20Shot%202016-06-27%20at%203.19.10%20PM.jpeg\",\n        \"Screen Shot 2016-06-27 at 3.19.10 PM.jpeg\",\n        \"2340\",\n        \"1222\",\n        \"#40b459\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n3. Filter or search for the desired files. You can filter by:\n  * **Keywords** - You can use the search bar at the top of the page to find files by entering the file name or notes associated with a file.\n  * **Metadata fields** - Next to the search bar, you will see drop-down menus for the metadata fields **File extension**, **Sample ID**, and **Task**. Selecting a particular metadata value from one of these menus displays only files that match the value. You can add additional drop-down menus to filter by other metadata fields by clicking the **+** icon.\n\n4. You can choose specific files by selecting the corresponding checkbox in front of the file name.\n5. Select as many files as you desire and click **Copy to**.\n6. Select your desired project from the drop-down menu.\n\nNow, you can start using the CCLE files you've added to your personal project in your own analysis.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>","excerpt":"<a name=\"top\"></a>","slug":"ccle","type":"basic","title":"Cancer Cell Line Encyclopedia (CCLE)"}

Cancer Cell Line Encyclopedia (CCLE)

<a name="top"></a>

The Cancer Cell Line Encyclopedia (CCLE) public project contains large <a href="http://docs.sevenbridges.com/v1.0/page/ccle-open-access-data" target="blank">Open Access files</a> from the <a href="http://www.broadinstitute.org/ccle/home" target="blank">CCLE</a> which you can use on the CGC. [block:callout] { "type": "warning", "title": "On this page:", "body": "* [Overview](#section-overview)\n* [What's contained in the project?](#section-what-s-contained-in-the-project-)\n* [Access the CCLE public project](#section-access-the-ccle-public-project)\n* [Use the CCLE public project](#section-use-the-ccle-public-project)\n* [Use the entire project](#section-use-the-entire-project)\n * [Copy the entire project](#section-copy-the-entire-project)\n * [Run a task in a copied CCLE project](#section-run-a-task-a-copied-CCLE-project)\n* [Use a subset of the data](#section-use-a-subset-of-the-data)" } [/block] ##Overview The CCLE is made possible through a collaboration between the <a href="http://www.broadinstitute.org/" target="blank">Broad Institute</a>, the <a href="https://www.nibr.com/" target="blank">Novartis Institutes for Biomedical Research</a>, and the <a href="https://www.gnf.nibr.com/" target="blank">Genomics Institute of the Novartis Research Foundation</a> to perform detailed genetic and pharmacologic characterization of a large number of human cancer models. The CCLE public project contains Open Access sequencing data (in the form of reads aligned to the hg19 broad variant reference genome) for nearly 1000 cancer cell line samples, as available from <a href="https://cghub.ucsc.edu/" target="blank">cgHub</a> on May 11, 2016. [block:callout] { "type": "info", "title": "Open Access", "body": "You don't need special access or authorization status to use the data in this project. In fact, any data you copy from this public project into your own projects will not count towards your storage. This data is ideal for interrogating the genomic landscape of cancer cell lines, testing new analysis methods, or getting to know the CGC." } [/block] <div align="right"><a href="#top">top</a></div> ##What's contained in the project? The CCLE public project contains the following distribution of samples and files by experimental strategy. [block:image] { "images": [ { "image": [ "https://files.readme.io/ehKg9yl5ScSbSe4Rpn0V_Screen%20Shot%202016-06-14%20at%2012.18.03%20PM.jpeg", "Screen Shot 2016-06-14 at 12.18.03 PM.jpeg", "1270", "356", "#c3c3c3", "" ], "border": true } ] } [/block] [block:callout] { "type": "info", "body": "Additional array data and processed data are available from the <a href=\"http://www.broadinstitute.org/ccle/home\" target=\"blank\">CCLE data portal</a>." } [/block] <div align="right"><a href="#top">top</a></div> ##Access the CCLE public project To access the CCLE public project: 1. Click on **Public projects** from the top navigation bar. 2. Select **Cancer Cell Line Encyclopedia (CCLE)**, as shown below. You'll be taken to the main dashboard of the CCLE public project. [block:image] { "images": [ { "image": [ "https://files.readme.io/pw77bK9IRyGYXbhgtJKP_Screen%20Shot%202016-06-27%20at%205.15.14%20PM.png", "Screen Shot 2016-06-27 at 5.15.14 PM.png", "516", "162", "#185393", "" ], "border": true, "sizing": "80" } ] } [/block] <div align="right"><a href="#top">top</a></div> ##Use the CCLE public project All CGC users automatically have copy permissions for this project. This means that while you while you cannot upload data or tools to the project or execute any of the workflows contained within it, you can copy the available data, tools, and workflows to your own projects on the Platform and execute analyses in your own projects. You have the options to: * [Use the entire project](#section-use-the-entire-project) - Copy the entire project to replicate analyses or conduct further analysis on CCLE data. * [Select and use a subset of the data in your own project](#section-use-a-subset-of-the-data) - Copy the selected data to use within your own analyses. <div align="right"><a href="#top">top</a></div> ##Use the entire project To help you get started, the CGC bioinformatics team has run some tasks on the CCLE data using [public apps](apps-on-the-cgc) and [reference files](file-repositories-on-the-cgc). While you cannot directly execute the workflows in the CCLE public project, you can make a copy of the entire project to [perform further analyses](#section-run-a-task-in-a-copied-ccle-project). <div align="right"><a href="#top">top</a></div> ###Copy the entire project To copy the entire project: 1. Access the CCLE public project by selecting **Cancer Cell Line Encyclopedia (CCLE)** from **Public projects** in the top navigation bar. 2. Click** Copy this project**, next to the project's title, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/hITPyV3SOm8FN2uSZdDP_Screen%20Shot%202016-06-27%20at%202.50.58%20PM.jpg", "Screen Shot 2016-06-27 at 2.50.58 PM.jpg", "2372", "1152", "#4a7dab", "" ] } ] } [/block] 3. In the pop-up window, you can name your copy of the project and select a [billing group](account-settings-and-billing). [block:image] { "images": [ { "image": [ "https://files.readme.io/44FwsehrS5OWCsiCscTH_Screen%20Shot%202016-06-27%20at%203.10.13%20PM.jpeg", "Screen Shot 2016-06-27 at 3.10.13 PM.jpeg", "978", "792", "#3fb157", "" ] } ] } [/block] 4. Once you've customized the details, click **Copy** to copy the entire project. You'll be redirected to the dashboard of your cloned project when it is ready, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/TtsIy19tQoaNsJZtReMO_Screen%20Shot%202016-06-27%20at%203.11.49%20PM.jpeg", "Screen Shot 2016-06-27 at 3.11.49 PM.jpeg", "2376", "1372", "#40b25a", "" ] } ] } [/block] You can now use the data and workflows contained within this project to conduct your own analyses. <div align="right"><a href="#top">top</a></div> ###Run a task in a copied CCLE project For instance, you can replicate one of the tasks in the project. The **RNA-seq Differential Expression** task in the copied project is a great starting point to run other differential expression analyses. All you have to do is change the input files. [block:callout] { "type": "info", "body": "Once you've copied the project, you can run tasks in it." } [/block] 1. Navigate to the **Tasks** tab on your copied CCLE project's dashboard. 2. Select one of the previously run tasks. 3. Click **Edit and rerun **in the upper right hand corner, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/jdStHB7qRYOgu9NWZpll_Screen%20Shot%202016-06-27%20at%203.15.00%20PM.jpg", "Screen Shot 2016-06-27 at 3.15.00 PM.jpg", "2378", "1384", "#477eae", "" ] } ] } [/block] 4. You'll be redirected to the **DRAFT** task page, where you can select different inputs. Simply click **Pick file(s)**, as you can see in the image below, to select different files. [block:image] { "images": [ { "image": [ "https://files.readme.io/zHKsQsJlRBe3VvuSbCKD_Screen%20Shot%202016-06-27%20at%203.16.58%20PM.jpg", "Screen Shot 2016-06-27 at 3.16.58 PM.jpg", "2220", "1302", "#427cb0", "" ] } ] } [/block] 5. When you've selected your inputs, click **Run** in the upper righthand corner, as shown above. <div align="right"><a href="#top">top</a></div> ##Use a subset of the data Instead of cloning the entire project, you can choose to select and copy a subset of the data. To copy a subset of the data: 1. Access the CCLE public project by selecting **Cancer Cell Line Encyclopedia (CCLE)** from **Public projects** in the top navigation bar. You'll be taken to the project dashboard of the CCLE public project, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/bULWot7gSNyl4kVqs1l5_Screen%20Shot%202016-06-27%20at%203.11.49%20PM%20(1).jpeg", "Screen Shot 2016-06-27 at 3.11.49 PM (1).jpeg", "2376", "1372", "#40b25a", "" ] } ] } [/block] 2. Click on the **Files** tab in the upper righthand corner. This will take you to the **Files** page for the CCLE project, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/W7q6ZF7rSc6yjKcXbQzM_Screen%20Shot%202016-06-27%20at%203.19.10%20PM.jpeg", "Screen Shot 2016-06-27 at 3.19.10 PM.jpeg", "2340", "1222", "#40b459", "" ] } ] } [/block] 3. Filter or search for the desired files. You can filter by: * **Keywords** - You can use the search bar at the top of the page to find files by entering the file name or notes associated with a file. * **Metadata fields** - Next to the search bar, you will see drop-down menus for the metadata fields **File extension**, **Sample ID**, and **Task**. Selecting a particular metadata value from one of these menus displays only files that match the value. You can add additional drop-down menus to filter by other metadata fields by clicking the **+** icon. 4. You can choose specific files by selecting the corresponding checkbox in front of the file name. 5. Select as many files as you desire and click **Copy to**. 6. Select your desired project from the drop-down menu. Now, you can start using the CCLE files you've added to your personal project in your own analysis. <div align="right"><a href="#top">top</a></div>