{"_id":"56045766e5102a0d0070f96e","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"},"user":"554290cd6592e60d00027d17","__v":47,"parentDoc":null,"category":{"_id":"5604570090ee490d00440551","__v":12,"version":"55faf11ba62ba1170021a9aa","pages":["56045766e5102a0d0070f96e","560457748d58900d0051eb38","560457968d58900d0051eb3a","560457a6188994170059ce87","560457b38d58900d0051eb3c","564270918c503f17002d6a1c","5642723db0dc090d00f884f1","56427319b0dc090d00f884f5","5667254066debc1700503f33","56d06ccd167e1e1b00807973","56d48956de40c70b00823e6a","56d82004c83c5f0b00d28721"],"project":"55faf11ba62ba1170021a9a7","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-09-24T20:03:12.010Z","from_sync":false,"order":3,"slug":"manage-an-analysis-environment","title":"MANAGE AN ANALYSIS ENVIRONMENT"},"project":"55faf11ba62ba1170021a9a7","updates":[],"next":{"pages":[],"description":""},"createdAt":"2015-09-24T20:04:54.670Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":0,"body":"Projects are the core building blocks of the CGC. Each project corresponds to a distinct scientific investigation and serves as a container for its data, analysis workflows, and results. Multiple workflow executions can be carried out within a project.\n\nAccess to a project is restricted to the [collaborators](http://docs.cancergenomicscloud.org/docs/collaboration-on-the-cgc) in the investigation. Each project has at least one administrator, who controls the [project members' permissions](http://docs.cancergenomicscloud.org/docs/set-permissions) to execute analyses.\n\nFor example, you may be involved in two projects: the first is a breast cancer study using RNA-Seq and second is a whole genome sequencing study of prostate cancer. Each of these projects can involve different teams of researchers. See our documentation for more about [collaborating on the CGC](http://docs.cancergenomicscloud.org/docs/collaboration-on-the-cgc).\n\nThe CGC hosts both [TCGA Open and Controlled Data](https://wiki.nci.nih.gov/display/TCGA/Open+Access+and+Controlled+Access+Data), which require different levels of access permissions. To protect TCGA Controlled Data, there are 2 types of projects on the CGC: <a href=\"http://docs.cancergenomicscloud.org/docs/glossary#section--open-data-project-\">**Open**</a> and <a href=\"http://docs.cancergenomicscloud.org/docs/glossary#section--controlled-data-project-\">**Controlled Data Projects**</a>. Note that you can always [upload your private data ](http://docs.cancergenomicscloud.org/docs/upload-to-the-cgc)into either of these project types.\n[block:callout]\n{\n  \"type\": \"success\",\n  \"body\": \"See here for a <a href=\\\"https://tcga-data.nci.nih.gov/tcga/tcgaDataType.jsp\\\" target=\\\"_blank\\\">full list of TCGA data types</a>.\",\n  \"title\": \"TCGA data types\"\n}\n[/block]\n##Open Data Projects\nOpen Data Projects are designed to host both **TCGA Open Data** and **your private data**. TCGA Open Data contains data which is not unique to an individual, such as de-identified clinical data, gene expression data, copy number alterations in regions of the genome, epigenetic data, and summaries of data compiled across individuals. \n[block:callout]\n{\n  \"type\": \"danger\",\n  \"body\": \"TCGA Controlled Data cannot be copied inside an Open Data Project.\",\n  \"title\": \"Warning\"\n}\n[/block]\nTCGA Open Data is available to all the users on the CGC. To access TCGA Open Data on the CGC, simply log in using your eRA Commons credentials or create an CGC account. \n[block:callout]\n{\n  \"type\": \"success\",\n  \"body\": \"All users are automatically granted access to Open Data upon sign-up as long as they agree to the data use restrictions and requirements outlined in <a href=\\\"http://cancergenome.nih.gov/publications/publicationguidelines\\\" target=\\\"blank\\\">TCGA publication guidelines</a>.\",\n  \"title\": \"Accessing TCGA Open Data\"\n}\n[/block]\n##Controlled Data Projects\nControlled Data Projects host both **TCGA Open and Controlled Data** as well as **your private data**. TCGA Controlled Data contains data which may allow individuals to be identified, such as primary sequence data (BAM and FASTQ files), SNP6 array level 1 and 2 data, exon array level 1 and 2 data, and VCFs. The CGC restricts access to Controlled Data following TCGA's model. This security ensures that TCGA Data is as widely available as possible while protecting the privacy of study participants. Only users with <a href=\"https://dbgap.ncbi.nlm.nih.gov/\" target=\"blank\">Database of Genotypes and Phenotypes (dbGaP)</a> permissions can access TCGA Controlled Data on the CGC. \n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"Access to Controlled Data must be obtained through dbGaP. After obtaining permission, Controlled Data users need to register for the CGC with their eRA Commons credentials and agree to <a href=\\\"http://cancergenome.nih.gov/pdfs/Data_Use_Certv082014\\\" target=\\\"blank\\\">TCGA Data Use Certifications</a> and the <a href=\\\"http://cancergenome.nih.gov/publications/publicationguidelines\\\" target=\\\"blank\\\">TCGA publication guidelines</a>. See our documentation [for more details on accessing the CGC](http://docs.cancergenomicscloud.org/docs/sign-up-for-the-cgc).\",\n  \"title\": \"Accessing TCGA Controlled Data\"\n}\n[/block]\nControlled Data Projects are labeled **TCGA** with a red tag and a lock symbol so you can recognize them easily.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/i3URNLUQDSjAN425nDaZ_Conrolled%20Data%20project%20lock%20.jpg\",\n        \"Conrolled Data project lock .jpg\",\n        \"702\",\n        \"96\",\n        \"#785959\",\n        \"\"\n      ],\n      \"caption\": \"Controlled Data Projects\"\n    }\n  ]\n}\n[/block]\nIf a collaborator lose TCGA Controlled Data access at any point, all Controlled Data Project resources will become read-only: they can see project resources and file metadata but cannot access and copy files or execute analyses. Read more about [collaboration on the CGC](http://docs.cancergenomicscloud.org/docs/collaboration-on-the-cgc).","excerpt":"","slug":"projects-on-the-cgc","type":"basic","title":"Projects on the CGC"}

Projects on the CGC


Projects are the core building blocks of the CGC. Each project corresponds to a distinct scientific investigation and serves as a container for its data, analysis workflows, and results. Multiple workflow executions can be carried out within a project. Access to a project is restricted to the [collaborators](http://docs.cancergenomicscloud.org/docs/collaboration-on-the-cgc) in the investigation. Each project has at least one administrator, who controls the [project members' permissions](http://docs.cancergenomicscloud.org/docs/set-permissions) to execute analyses. For example, you may be involved in two projects: the first is a breast cancer study using RNA-Seq and second is a whole genome sequencing study of prostate cancer. Each of these projects can involve different teams of researchers. See our documentation for more about [collaborating on the CGC](http://docs.cancergenomicscloud.org/docs/collaboration-on-the-cgc). The CGC hosts both [TCGA Open and Controlled Data](https://wiki.nci.nih.gov/display/TCGA/Open+Access+and+Controlled+Access+Data), which require different levels of access permissions. To protect TCGA Controlled Data, there are 2 types of projects on the CGC: <a href="http://docs.cancergenomicscloud.org/docs/glossary#section--open-data-project-">**Open**</a> and <a href="http://docs.cancergenomicscloud.org/docs/glossary#section--controlled-data-project-">**Controlled Data Projects**</a>. Note that you can always [upload your private data ](http://docs.cancergenomicscloud.org/docs/upload-to-the-cgc)into either of these project types. [block:callout] { "type": "success", "body": "See here for a <a href=\"https://tcga-data.nci.nih.gov/tcga/tcgaDataType.jsp\" target=\"_blank\">full list of TCGA data types</a>.", "title": "TCGA data types" } [/block] ##Open Data Projects Open Data Projects are designed to host both **TCGA Open Data** and **your private data**. TCGA Open Data contains data which is not unique to an individual, such as de-identified clinical data, gene expression data, copy number alterations in regions of the genome, epigenetic data, and summaries of data compiled across individuals. [block:callout] { "type": "danger", "body": "TCGA Controlled Data cannot be copied inside an Open Data Project.", "title": "Warning" } [/block] TCGA Open Data is available to all the users on the CGC. To access TCGA Open Data on the CGC, simply log in using your eRA Commons credentials or create an CGC account. [block:callout] { "type": "success", "body": "All users are automatically granted access to Open Data upon sign-up as long as they agree to the data use restrictions and requirements outlined in <a href=\"http://cancergenome.nih.gov/publications/publicationguidelines\" target=\"blank\">TCGA publication guidelines</a>.", "title": "Accessing TCGA Open Data" } [/block] ##Controlled Data Projects Controlled Data Projects host both **TCGA Open and Controlled Data** as well as **your private data**. TCGA Controlled Data contains data which may allow individuals to be identified, such as primary sequence data (BAM and FASTQ files), SNP6 array level 1 and 2 data, exon array level 1 and 2 data, and VCFs. The CGC restricts access to Controlled Data following TCGA's model. This security ensures that TCGA Data is as widely available as possible while protecting the privacy of study participants. Only users with <a href="https://dbgap.ncbi.nlm.nih.gov/" target="blank">Database of Genotypes and Phenotypes (dbGaP)</a> permissions can access TCGA Controlled Data on the CGC. [block:callout] { "type": "info", "body": "Access to Controlled Data must be obtained through dbGaP. After obtaining permission, Controlled Data users need to register for the CGC with their eRA Commons credentials and agree to <a href=\"http://cancergenome.nih.gov/pdfs/Data_Use_Certv082014\" target=\"blank\">TCGA Data Use Certifications</a> and the <a href=\"http://cancergenome.nih.gov/publications/publicationguidelines\" target=\"blank\">TCGA publication guidelines</a>. See our documentation [for more details on accessing the CGC](http://docs.cancergenomicscloud.org/docs/sign-up-for-the-cgc).", "title": "Accessing TCGA Controlled Data" } [/block] Controlled Data Projects are labeled **TCGA** with a red tag and a lock symbol so you can recognize them easily. [block:image] { "images": [ { "image": [ "https://files.readme.io/i3URNLUQDSjAN425nDaZ_Conrolled%20Data%20project%20lock%20.jpg", "Conrolled Data project lock .jpg", "702", "96", "#785959", "" ], "caption": "Controlled Data Projects" } ] } [/block] If a collaborator lose TCGA Controlled Data access at any point, all Controlled Data Project resources will become read-only: they can see project resources and file metadata but cannot access and copy files or execute analyses. Read more about [collaboration on the CGC](http://docs.cancergenomicscloud.org/docs/collaboration-on-the-cgc).