{"_id":"55fafa5aa62ba1170021a9c1","parentDoc":null,"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"},"__v":28,"project":"55faf11ba62ba1170021a9a7","user":"554290cd6592e60d00027d17","category":{"_id":"55faf11ca62ba1170021a9ab","pages":["55faf11da62ba1170021a9ad","55fafa5aa62ba1170021a9c1","55fafa6ca62ba1170021a9c3","5632a29b49e16d0d0012243e","5637c1d67ca5de0d00286ad9","5665b988e93ae70d00b969c7"],"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","__v":6,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-09-17T16:58:04.483Z","from_sync":false,"order":2,"slug":"access-the-cgc","title":"ACCESS THE CGC"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2015-09-17T17:37:30.453Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":2,"body":"The CGC is designed to provide resources for biologists, bioinformaticians, and developers in the cancer research community. To help you with your research, we have built both a visual interface and the API. To access these resources, sign up for the CGC. \n\nThe CGC has a user-friendly graphical interface to facilitate your interaction with the platform. The visual interface enables you to [visualize TCGA data](the-case-explorer), [filter it with our smart query mechanism](the-case-explorer), and [execute analyses](set-up-a-task). You can [build custom analysis workflows](the-pipeline-editor), [change tool parameters](the-pipeline-editor#section-expose-tool-parameters-for-configuration), and keep track of [workflow versions](app-versions) using the workflow editor. You can [view all task details](review-task-page), including input files, workflow specifications, and output files on the task page. You can also visualize the results of your analysis using the integrated genome browser.\n\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Main Dashboard\n\nThe main dashboard is the first page you see when you log into the CGC. It provides information about your projects, your tasks, apps, and data. The dashboard has four main panels: [**Getting started**](#section-learn-the-cgc-features), [**Projects**](#section-manage-your-projects), [**Public Data and Apps**](#section-explore-data-and-apps), and [**Tasks**](#section-track-your-tasks).\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/QU7NH5cOQXG7mPZQ6QVk_Screen%20Shot%202015-11-21%20at%2010.10.00%20PM.png\",\n        \"Screen Shot 2015-11-21 at 10.10.00 PM.png\",\n        \"1412\",\n        \"628\",\n        \"#5681c2\",\n        \"\"\n      ],\n      \"caption\": \"The Main Dashboard\"\n    }\n  ]\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Learn the CGC features \n\nThe top right **Getting Started **panel contains links to the CGC documentation on the [**Knowledge Center**](http://docs.cancergenomicscloud.org/). These links are listed as a checklist to help you orient yourself and start using the CGC. When you no longer need this panel, you can permanently hide it by clicking **Hide this forever** on the bottom right of the panel.\n[block:callout]\n{\n  \"type\": \"warning\",\n  \"body\": \"Some parts of the Knowledge Center are still under construction. We will do our best to make the documentation available to you as soon as possible.\",\n  \"title\": \"Coming soon!\"\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Manage your projects\n\nYou can view recent projects and create new projects with the top left **Projects** panel. To access a recent project, click the project name. To create a new project, click **+ Create a project **on the bottom left of the panel. For more information on creating a project, see [here](create-a-project).\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"you can also navigate to **Projects** on the navigation bar on the main dashboard.\",\n  \"title\": \"To view all your projects...\"\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Explore data and apps\n\nThe **Public Data and Apps** panel located on the bottom left includes links to the TCGA data exploration tools and public apps on the CGC.\n\nTo explore [TCGA dataset](tcga-data) based on disease type and gene mutations using the [Case Explorer](http://docs.cancergenomicscloud.org/docs/the-case-explorer), click **Explore Cases**. You can also build queries to filter TCGA data by clicking [**Browse Public Data**](http://docs.cancergenomicscloud.org/docs/the-data-browser).\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"you can also navigate to **Data** on the top navigation bar.\",\n  \"title\": \"To access the Case Explorer and the Data Browser...\"\n}\n[/block]\nTo access open source bioinformatics [tools](apps-on-the-cgc) on the CGC, click **Browse Apps**. To access [pre-built workflows](http://docs.cancergenomicscloud.org/docs/the-pipeline-editor), click **Browse Workflows**.\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"you can also navigate to **Apps** on the top navigation bar.\",\n  \"title\": \"To access public tools and workflows...\"\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Track your tasks\n\nYou can view the progress of recently executed analyses in the bottom right **Tasks** panel. You can also reach tasks in individual projects. To learn more about tasks, read about [running an analysis](set-up-a-task).\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Contextual help\nClick on the help icon on the top navigation bar from any page for contextual links to the Knowledge Center.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>","excerpt":"","slug":"access-via-the-visual-interface","type":"basic","title":"Access via the visual interface"}

Access via the visual interface


The CGC is designed to provide resources for biologists, bioinformaticians, and developers in the cancer research community. To help you with your research, we have built both a visual interface and the API. To access these resources, sign up for the CGC. The CGC has a user-friendly graphical interface to facilitate your interaction with the platform. The visual interface enables you to [visualize TCGA data](the-case-explorer), [filter it with our smart query mechanism](the-case-explorer), and [execute analyses](set-up-a-task). You can [build custom analysis workflows](the-pipeline-editor), [change tool parameters](the-pipeline-editor#section-expose-tool-parameters-for-configuration), and keep track of [workflow versions](app-versions) using the workflow editor. You can [view all task details](review-task-page), including input files, workflow specifications, and output files on the task page. You can also visualize the results of your analysis using the integrated genome browser. <div align="right"><a href="#top">top</a></div> ##Main Dashboard The main dashboard is the first page you see when you log into the CGC. It provides information about your projects, your tasks, apps, and data. The dashboard has four main panels: [**Getting started**](#section-learn-the-cgc-features), [**Projects**](#section-manage-your-projects), [**Public Data and Apps**](#section-explore-data-and-apps), and [**Tasks**](#section-track-your-tasks). [block:image] { "images": [ { "image": [ "https://files.readme.io/QU7NH5cOQXG7mPZQ6QVk_Screen%20Shot%202015-11-21%20at%2010.10.00%20PM.png", "Screen Shot 2015-11-21 at 10.10.00 PM.png", "1412", "628", "#5681c2", "" ], "caption": "The Main Dashboard" } ] } [/block] <div align="right"><a href="#top">top</a></div> ###Learn the CGC features The top right **Getting Started **panel contains links to the CGC documentation on the [**Knowledge Center**](http://docs.cancergenomicscloud.org/). These links are listed as a checklist to help you orient yourself and start using the CGC. When you no longer need this panel, you can permanently hide it by clicking **Hide this forever** on the bottom right of the panel. [block:callout] { "type": "warning", "body": "Some parts of the Knowledge Center are still under construction. We will do our best to make the documentation available to you as soon as possible.", "title": "Coming soon!" } [/block] <div align="right"><a href="#top">top</a></div> ###Manage your projects You can view recent projects and create new projects with the top left **Projects** panel. To access a recent project, click the project name. To create a new project, click **+ Create a project **on the bottom left of the panel. For more information on creating a project, see [here](create-a-project). [block:callout] { "type": "info", "body": "you can also navigate to **Projects** on the navigation bar on the main dashboard.", "title": "To view all your projects..." } [/block] <div align="right"><a href="#top">top</a></div> ###Explore data and apps The **Public Data and Apps** panel located on the bottom left includes links to the TCGA data exploration tools and public apps on the CGC. To explore [TCGA dataset](tcga-data) based on disease type and gene mutations using the [Case Explorer](http://docs.cancergenomicscloud.org/docs/the-case-explorer), click **Explore Cases**. You can also build queries to filter TCGA data by clicking [**Browse Public Data**](http://docs.cancergenomicscloud.org/docs/the-data-browser). [block:callout] { "type": "info", "body": "you can also navigate to **Data** on the top navigation bar.", "title": "To access the Case Explorer and the Data Browser..." } [/block] To access open source bioinformatics [tools](apps-on-the-cgc) on the CGC, click **Browse Apps**. To access [pre-built workflows](http://docs.cancergenomicscloud.org/docs/the-pipeline-editor), click **Browse Workflows**. [block:callout] { "type": "info", "body": "you can also navigate to **Apps** on the top navigation bar.", "title": "To access public tools and workflows..." } [/block] <div align="right"><a href="#top">top</a></div> ###Track your tasks You can view the progress of recently executed analyses in the bottom right **Tasks** panel. You can also reach tasks in individual projects. To learn more about tasks, read about [running an analysis](set-up-a-task). <div align="right"><a href="#top">top</a></div> ##Contextual help Click on the help icon on the top navigation bar from any page for contextual links to the Knowledge Center. <div align="right"><a href="#top">top</a></div>