diff --git a/docs/genomics-platform/faq/index.md b/docs/genomics-platform/faq/index.md index 2db4ecc6..33c3bbf2 100644 --- a/docs/genomics-platform/faq/index.md +++ b/docs/genomics-platform/faq/index.md @@ -41,7 +41,7 @@ at St. Jude) or an external user. If you are a St. Jude Employee, please refer to the dedicated [intranet page](https://home.stjude.org/computational-biology/Pages/bioinformatics-self-service-cloud.aspx) for instructions. If you are not a St. Jude Employee, please refer to our -[Create an Account](./accounts-and-billing.md#billing-setup) guide. +[Create an Account](../accounts-and-billing/#billing-setup) guide. ## Does St. Jude Cloud allow for-profit companies to access genomics data? @@ -51,7 +51,7 @@ We do not allow for-profit companies to access any of our restricted access geno ## Why do I need to sign the Data Access Agreement (DAA)? The [data access -agreement](./requesting-data/glossary.md#data-access-agreement) +agreement](../requesting-data/glossary/#data-access-agreement) serves many purposes. Ultimately, the terms included in the data access agreement are in place to protect our patients. We take patient security very seriously, and we require that requesters are committed to protecting that @@ -80,19 +80,19 @@ You can download the latest version of the DAA You can submit your Data Access Agreement in the drag and drop box on the [last step of the data request -process](./requesting-data/data-request.md#requesting-data). +process](../requesting-data/making-a-data-request/#requesting-data). ## What if I did not fill out the Data Download Permission section of the original DAA, but now I want to download data? This would be a change in terms from the original agreement, you would need to fill out a new DAA (including the [Data Download Permission -section](./requesting-data/how-to-fill-out-DAA.md#the-data-access-agreement) +section](../requesting-data/how-to-fill-out-daa/#the-data-access-agreement) for any data sets you want to download. ## What clinical information is available about samples in St. Jude Cloud? You can view the basic clinical and phenotypic information we currently provide -[here](./requesting-data/about-our-data.md#metadata). +[here](../requesting-data/about-our-data/#metadata). ## Can I gain access to further clinical information than what is currently available? @@ -117,11 +117,11 @@ storage cost without any benefit. Several tools exist that you can leverage to revert BAM to FASTQ files — we recommend using Picard SamToFastq to revert BAM files. You can efficiently revert BAMs to FASTQs in the cloud by wrapping the conversion tool of your choice into a [Cloud -App](./analyzing-data/creating-a-cloud-app.md) +App](../analyzing-data/creating-a-cloud-app) ## How can I work with genomics data in the cloud? -You can view [this guide](./analyzing-data/creating-a-cloud-app.md) to learn how +You can view [this guide](../analyzing-data/creating-a-cloud-app) to learn how create a cloud application. ## Why am I getting a connectivity error when connecting to DNAnexus API via SSH? diff --git a/docs/genomics-platform/managing-data/how-to-fill-out-extension/index.md b/docs/genomics-platform/managing-data/how-to-fill-out-extension/index.md index 98ad9805..31e470fe 100644 --- a/docs/genomics-platform/managing-data/how-to-fill-out-extension/index.md +++ b/docs/genomics-platform/managing-data/how-to-fill-out-extension/index.md @@ -5,7 +5,7 @@ title: Filling Out The Extension Addendum #Filling Out The Extension Addendum -The St. Jude Cloud [Data Access Agreement (DAA)](../requesting-data/glossary.md#data-access-agreement) is only valid for one year after the date it was approved. When your DAA is about to expire, you will get an automated email from notifications@stjude.cloud with the name of the DAA that is expiring and a link to the St. Jude Cloud Extension Addendum. +The St. Jude Cloud [Data Access Agreement (DAA)](../../requesting-data/glossary/#data-access-agreement) is only valid for one year after the date it was approved. When your DAA is about to expire, you will get an automated email from notifications@stjude.cloud with the name of the DAA that is expiring and a link to the St. Jude Cloud Extension Addendum. In order to extend your DAA, you must fill out an Extension Addendum. The Extension Addendum will extend the previous agreement for an additional year. Please note that if you do not fill out an Extension Addendum, you will be expected to delete all copies of the data subject to the expiring agreement. @@ -22,7 +22,7 @@ Follow the steps below to ensure that you have accurately filled out all section 2. **Page 2** - * Check exactly the datasets that you were granted access to by the terms of the original DAA. *The datasets checked on the original DAA and any extensions must match.* If you would like to apply for access to additional datasets, please [make a new data request](../requesting-data/data-request.md) for the additional dataset(s). + * Check exactly the datasets that you were granted access to by the terms of the original DAA. *The datasets checked on the original DAA and any extensions must match.* If you would like to apply for access to additional datasets, please [make a new data request](../../requesting-data/making-a-data-request) for the additional dataset(s). * The Principal Investigator (PI) or faculty level supervisor on the project must sign and date the extension. *The PI who signed the original DAA must match the PI signing any extensions.* @@ -46,5 +46,5 @@ Once you have finished filling out the Extension Addendum, you may upload the co ## Similar Topics -[About our Decision Process & Terminology](../requesting-data/glossary.md) -[Filling Out a Data Access Agreement](../requesting-data/how-to-fill-out-DAA.md) \ No newline at end of file +[About our Decision Process & Terminology](../../requesting-data/glossary) +[Filling Out a Data Access Agreement](../../requesting-data/how-to-fill-out-daa) \ No newline at end of file diff --git a/docs/genomics-platform/managing-data/working-with-our-data/index.md b/docs/genomics-platform/managing-data/working-with-our-data/index.md index 3664f729..acbedf57 100644 --- a/docs/genomics-platform/managing-data/working-with-our-data/index.md +++ b/docs/genomics-platform/managing-data/working-with-our-data/index.md @@ -3,12 +3,12 @@ title: Working With Our Data --- -In this overview, we will explain how to manage your data request(s) from St. Jude Cloud's genomics platform [My Dashboard page](https://platform.stjude.cloud/dashboard) and how to access and manage your data (once it has been vended to you) from within a DNAnexus project. The [DNAnexus](https://www.dnanexus.com/) genomic ecosystem is the backbone for the computation and storage in St. Jude Cloud. This means that each data request in St. Jude Cloud corresponds to a project in DNAnexus. If you'd like, you can read an introduction to the DNAnexus ecosystem [here](https://documentation.dnanexus.com/). If you haven't already, follow [this guide](../requesting-data/data-request.md) to request access to St. Jude data in this secure cloud ecosystem. +In this overview, we will explain how to manage your data request(s) from St. Jude Cloud's genomics platform [My Dashboard page](https://platform.stjude.cloud/dashboard) and how to access and manage your data (once it has been vended to you) from within a DNAnexus project. The [DNAnexus](https://www.dnanexus.com/) genomic ecosystem is the backbone for the computation and storage in St. Jude Cloud. This means that each data request in St. Jude Cloud corresponds to a project in DNAnexus. If you'd like, you can read an introduction to the DNAnexus ecosystem [here](https://documentation.dnanexus.com/). If you haven't already, follow [this guide](../../requesting-data/making-a-data-request) to request access to St. Jude data in this secure cloud ecosystem. ## Managing Your Data Requests -Below is a snapshot of the [My Dashboard](https://platform.stjude.cloud/dashboard) on our Genomcis Platform. From this page you can check the status of your data request, complete an [EDAA](../requesting-data/how-to-fill-out-DAA.md#the-electronic-data-access-agreement-process) draft, upload a revised [DAA](../requesting-data/how-to-fill-out-DAA.md) or an [Extension Addendum](how-to-fill-out-Extension.md), or link to your DNAnexus project folder for a specific data request. +Below is a snapshot of the [My Dashboard](https://platform.stjude.cloud/dashboard) on our Genomcis Platform. From this page you can check the status of your data request, complete an [EDAA](../../requesting-data/how-to-fill-out-daa/#the-electronic-data-access-agreement-process) draft, upload a revised [DAA](../../requesting-data/how-to-fill-out-daa) or an [Extension Addendum](../how-to-fill-out-extension), or link to your DNAnexus project folder for a specific data request. ![](./docs-manage-data-page-labelled-tagged.png) @@ -38,18 +38,18 @@ project_space/ └── SAMPLE_INFO.txt ``` -The `SAMPLE_INFO.txt` file provides all the [metadata](../requesting-data/about-our-data.md#metadata) associated with the request, and the restricted folder contains all the data for which you were approved separated by file type. +The `SAMPLE_INFO.txt` file provides all the [metadata](../../requesting-data/about-our-data/#metadata) associated with the request, and the restricted folder contains all the data for which you were approved separated by file type. ## Using Your Data There are two primary ways you can interact with data vended to you in St. Jude Cloud: -* **Cloud access**. You can choose to work with the data in DNAnexus' genomics cloud ecosystem. This is our suggested method of interaction, as you can avoid downloading the data to your local servers (which both takes time and is error prone). If you choose to leverage this approach, you can either wrap your own analysis pipeline as a cloud app (see [our guide](../analyzing-data/creating-a-cloud-app.md)) or leverage any of DNAnexus' publicly available apps (see [DNAnexus' guide](https://documentation.dnanexus.com/user/running-apps-and-workflows). -* **Download the data** (*not suggested*). The second way to interact with data vended to you in St. Jude Cloud is by downloading the data to your local servers. If you wish to do this, you can download the data on the command line (see [our guide](../analyzing-data/command-line.md)). **Note that you must have indicated you wish to download the data in your [data access agreement](../requesting-data/how-to-fill-out-DAA.md#the-data-access-agreement).** +* **Cloud access**. You can choose to work with the data in DNAnexus' genomics cloud ecosystem. This is our suggested method of interaction, as you can avoid downloading the data to your local servers (which both takes time and is error prone). If you choose to leverage this approach, you can either wrap your own analysis pipeline as a cloud app (see [our guide](../../analyzing-data/creating-a-cloud-app)) or leverage any of DNAnexus' publicly available apps (see [DNAnexus' guide](https://documentation.dnanexus.com/user/running-apps-and-workflows)). +* **Download the data** (*not suggested*). The second way to interact with data vended to you in St. Jude Cloud is by downloading the data to your local servers. If you wish to do this, you can download the data on the command line (see [our guide](../../analyzing-data/command-line)). **Note that you must have indicated you wish to download the data in your [data access agreement](../../requesting-data/how-to-fill-out-daa/#the-data-access-agreement).** ## Similar Topics -[About our Data](../requesting-data/about-our-data.md) -[Making a Data Request](../requesting-data/data-request.md) -[Upload/Download Data (local)](../managing-data/upload-local.md) +[About our Data](../../requesting-data/about-our-data) +[Making a Data Request](../../requesting-data/making-a-data-request) +[Upload/Download Data (local)](../upload-local) diff --git a/docs/genomics-platform/requesting-data/about-our-data/index.md b/docs/genomics-platform/requesting-data/about-our-data/index.md index c1b75338..1dc85252 100644 --- a/docs/genomics-platform/requesting-data/about-our-data/index.md +++ b/docs/genomics-platform/requesting-data/about-our-data/index.md @@ -120,7 +120,7 @@ RNA-Seq BAM files are mapped to HG38. For alignment, `STAR` v2.7.1a 2-pass mappi ``` ## Data Access Units -We currently have the five [Data Access Units (DAU)](../requesting-data/glossary.md#data-access-unit) listed below. [Basic clinical data](#clinical-and-phenotypic-information) is available for relevant subjects in each DAU. Click on the DAU's abbreviation below to navigate directly to that DAU's [Study page](../../../guides/studies/index.md) for more detailed information. +We currently have the five [Data Access Units (DAU)](../glossary/#data-access-unit) listed below. [Basic clinical data](#clinical-and-phenotypic-information) is available for relevant subjects in each DAU. Click on the DAU's abbreviation below to navigate directly to that DAU's [Study page](../../studies/) for more detailed information. ### Pediatric Cancer Genome Project (PCGP) **[PCGP](https://stjude.cloud/studies/pediatric-cancer-genome-project) is a paired-tumor normal dataset focused on discovering the genetic origins of pediatric cancer.** @@ -172,14 +172,14 @@ Each data request includes a text file called `SAMPLE_INFO.txt` that provides a | sample_name | A unique sample identifier assigned internally at St. Jude. | | sample_type | One of Autopsy, Cell line, Diagnosis, Germline, Metastasis, Relapse, or Xenograft. | | sequencing_type | Whether the file was generated from Whole Genome (WGS), Whole Exome (WES), or RNA-Seq. | -| file_type | One of the [file types](../../guides/data/types-of-data) available in St. Jude Cloud. | +| file_type | One of the file types available in St. Jude Cloud. | | description | Optional field that may contain additional file information. | | sj_diseases | If your data request was process after August 18, 2020, the field should be interpreted as the harmonized St. Jude Cloud diagnosis based on the best available information (data provided by the lab or PI and followup by scientists on the St. Jude Cloud team). If your data request was processed before August 18, 2020, this field should be interpreted as the disease identifier assigned at the time of genomic sequencing (keyly, the diagnosis known at the time of genomic testing may not be the best available information). **If your data request was processed after August 18, 2020 and you'd like to use the most up to date, harmonized diagnosis**, we recommend using `sj_diseases` when including diagnosis in your analysis. If your data request was made before this time *or* if you wish to use the values exactly as provided by the lab or PI, we recommend using the lab-provided value in `attr_diagnosis`. | | sj_datasets | If present, the datasets in the data browser which this file is associated with. | | sj_pmid_accessions | If the file was associated with a paper, the related [Pubmed][pubmed] accession number. | | sj_ega_accessions | If the file was associated with a paper, the related [EGA][ega] accession number. | | sj_dataset_accession | If present, the permanent accession number assigned in St. Jude Cloud. | -| sj_embargo_date | The [embargo date](glossary.md#embargo-date), which specifies the first date which the files can be used in a publication. | +| sj_embargo_date | The [embargo date](../glossary/#embargo-date), which specifies the first date which the files can be used in a publication. | ### Clinical and Phenotypic Information diff --git a/docs/genomics-platform/requesting-data/glossary/index.md b/docs/genomics-platform/requesting-data/glossary/index.md index b73838c7..b6065fe1 100644 --- a/docs/genomics-platform/requesting-data/glossary/index.md +++ b/docs/genomics-platform/requesting-data/glossary/index.md @@ -5,16 +5,16 @@ title: About Our Decision Process and Terminology ### Data Access Unit -A St. Jude Cloud **Data Access Unit (DAU)** is a grouping of data that typically corresponds to a project, study, or dataset generated at the same time at the same institution. Each DAU has its own governing body of researchers, the [Data Access Committee](#data-access-committee), who preside over the data and who may grant or deny access. Each Data Access Committee has its own protocols for approving access to their DAU. Please [contact us](mailto:support@stjude.cloud) if you have questions about committee approval protocols. We currently have 5 DAUs: Pediatric Cancer Genome Project (PCGP), St. Jude Lifetime Cohort Study (SJLIFE), Genomes for Kids (G4K) and Clinical Genomics, Sickle Cell Genome Project (SGP), and Childhood Cancer Survivor Study (CCSS). For a brief description of each DAU see the [Studies page](about-our-data.md#data-access-units). For a more detailed description please see the respective [Schedule 1(s)](../../../citing-stjude-cloud.md#dataset-reference-table). +A St. Jude Cloud **Data Access Unit (DAU)** is a grouping of data that typically corresponds to a project, study, or dataset generated at the same time at the same institution. Each DAU has its own governing body of researchers, the [Data Access Committee](#data-access-committee), who preside over the data and who may grant or deny access. Each Data Access Committee has its own protocols for approving access to their DAU. Please [contact us](mailto:support@stjude.cloud) if you have questions about committee approval protocols. We currently have 5 DAUs: Pediatric Cancer Genome Project (PCGP), St. Jude Lifetime Cohort Study (SJLIFE), Genomes for Kids (G4K) and Clinical Genomics, Sickle Cell Genome Project (SGP), and Childhood Cancer Survivor Study (CCSS). For a brief description of each DAU see the [Studies page](../about-our-data/#data-access-units). For a more detailed description please see the respective [Schedule 1(s)](../../../citing-stjude-cloud.md#dataset-reference-table). ### Data Access Agreement A St. Jude Cloud **Data Access Agreement (DAA)** is a legally binding document outlining a number of terms and conditions to which anyone working with St. Jude Cloud data must agree. -We do not negotiate the terms of this document unless terms are found to be in conflict with the institution's state law. Filling out the Data Access Agreement carefully and completely is crucial to having your request approved promptly. [Click Here](../../../files/DAA_v4_10-1-2019.pdf) to download a copy of the DAA. [Click Here](how-to-fill-out-DAA.md) for a step by step guide on how to fill out the DAA. +We do not negotiate the terms of this document unless terms are found to be in conflict with the institution's state law. Filling out the Data Access Agreement carefully and completely is crucial to having your request approved promptly. [Click Here](../../../files/DataAccessAgreement_v4.2_10.13.20.pdf) to download a copy of the DAA. [Click Here](../how-to-fill-out-daa) for a step by step guide on how to fill out the DAA. -If you have incompletely or incorrectly filled out your DAA and would like to upload a revised form, [Click Here](how-to-fill-out-DAA.md#uploading-a-revised-daa) for instructions. +If you have incompletely or incorrectly filled out your DAA and would like to upload a revised form, [Click Here](../how-to-fill-out-daa/#uploading-a-revised-daa) for instructions. -Once you have submitted a correctly filled out DAA and have been granted access to one or more [Data Access Units (DAUs)](#data-access-unit), you can continue checking out files from those DAUs until your access expires. Access is generally granted for 1 year, at which point you must submit an Extension Addendum to continue using the data. [Click Here](../managing-data/how-to-fill-out-Extension.md) for a step-by-step guide on how to fill out the Extension Addendum. +Once you have submitted a correctly filled out DAA and have been granted access to one or more [Data Access Units (DAUs)](#data-access-unit), you can continue checking out files from those DAUs until your access expires. Access is generally granted for 1 year, at which point you must submit an Extension Addendum to continue using the data. [Click Here](../../managing-data/how-to-fill-out-extension) for a step-by-step guide on how to fill out the Extension Addendum. ### Data Access Committee @@ -46,7 +46,8 @@ The **Embargo Date** specifies the date that a publishing embargo on the file in | Clinical Genomics | Rolling based on release date | | Sickle Cell Genome Project | September 1, 2019 | | Childhood Cancer Survivor Study | November 1, 2019 | +| Pan-Acute Lymphoblastic Leukemia | January 14, 2019 | ### Similar Topics -[About our Data](about-our-data.md) \ No newline at end of file +[About our Data](../about-our-data) \ No newline at end of file diff --git a/docs/genomics-platform/requesting-data/how-to-fill-out-daa/index.md b/docs/genomics-platform/requesting-data/how-to-fill-out-daa/index.md index 56ebb94d..cf742a93 100644 --- a/docs/genomics-platform/requesting-data/how-to-fill-out-daa/index.md +++ b/docs/genomics-platform/requesting-data/how-to-fill-out-daa/index.md @@ -19,7 +19,7 @@ If you reside outside of the US, you must fill out the Data Access Agreement man ### Data Access Units -A St. Jude Cloud **Data Access Unit (DAU)** is a grouping of data that typically corresponds to a project, study, or dataset generated at the same time at the same institution. To learn more, see our section on [Data Access Units](about-our-data.md#data-access-units). +A St. Jude Cloud **Data Access Unit (DAU)** is a grouping of data that typically corresponds to a project, study, or dataset generated at the same time at the same institution. To learn more, see our section on [Data Access Units](../about-our-data/#data-access-units). On page 7 of the DAA, you must mark all Data Access Units for which you are applying. The DAU(s) associated to the data you requested are listed in the Controlled Access Data section, directly above the Download Data Access Agreement button. This can be found on the Request Data webpage which immediately follows your selection of data from the data browser. @@ -29,7 +29,7 @@ If you mark the incorrect datasets, you will be required to resubmit your agreem ### Contemplated Use -On page 8 of the DAA, you must submit a description of your research project. Please specifically describe the intended role of St. Jude’s data in your research project. Your contemplated use can be anywhere from a paragraph to a few pages long, although a typical contemplated use is 1-2 paragraphs. Each [Data Access Committee](glossary.md#data-access-committee) will evaluate your contemplated use case and decide whether to approve or deny your application for data access based on their own set of protocols. Please [contact us](https://stjude.cloud/contact) if you have any questions regarding the protocols of the approval process. +On page 8 of the DAA, you must submit a description of your research project. Please specifically describe the intended role of St. Jude’s data in your research project. Your contemplated use can be anywhere from a paragraph to a few pages long, although a typical contemplated use is 1-2 paragraphs. Each [Data Access Committee](../glossary/#data-access-committee) will evaluate your contemplated use case and decide whether to approve or deny your application for data access based on their own set of protocols. Please [contact us](https://stjude.cloud/contact) if you have any questions regarding the protocols of the approval process. ![](./docs-CU-short.png) @@ -55,7 +55,7 @@ Pages 10 and 11 of the DAA must be signed by any additional person(s) who will h ### Institutional Authority Page 12 of the agreement must be filled out and signed by your Institutional or Administrative Authority. The institutional authority is an individual who has the authority to sign for a grant application. This individual cannot be the same as the Principal Investigator that signed on page 9, as this additional signature provides a second-party authority of the institution to ensure that the institution will uphold the terms of this agreement. - ![](./requesting-data/docs-IA.png) + ![](./docs-IA.png) ### Information Security Officer @@ -73,14 +73,14 @@ Users who live in the United States will be given the option to complete the Dat After submitting the required information, the Data Access Agreement will be sent via email to each individual entered through the setup wizard. Each individual must follow the link in their email to sign the appropriate page of the agreement via DocuSign. If any individual rejects or declines to sign the agreement, you will need to start a new data request from the data browser. -Once you start the Electronic Data Access Agreement process, you will have a draft autosaved for you on your [My Dashboard](https://platform.stjude.cloud/requests/manage) page, accessible at any time. Learn how to [check your Request Status](../managing-data/working-with-our-data.md#managing-your-data-requests) +Once you start the Electronic Data Access Agreement process, you will have a draft autosaved for you on your [My Dashboard](https://platform.stjude.cloud/requests/manage) page, accessible at any time. Learn how to [check your Request Status](../../managing-data/working-with-our-data/#managing-your-data-requests) -Once all signatures have been collected, your data access request will be submitted to St. Jude Cloud. A St. Jude Cloud administrator will forward your Data Access Agreement and intended use to the appropriate [Data Access Committee(s)](glossary.md#data-access-committee) for approval. Upon approval from the DAC(s), you will receive an email with a link to the approved data, which will be hosted through DNAnexus. +Once all signatures have been collected, your data access request will be submitted to St. Jude Cloud. A St. Jude Cloud administrator will forward your Data Access Agreement and intended use to the appropriate [Data Access Committee(s)](../glossary/#data-access-committee) for approval. Upon approval from the DAC(s), you will receive an email with a link to the approved data, which will be hosted through DNAnexus. ### Similar Topics -[Studies](about-our-data.md#data-access-units) -[Making a Data Request](data-request.md) -[Renewing your Data Access](../managing-data/how-to-fill-out-Extension.md) -[Managing Data Overview](../managing-data/working-with-our-data.md) +[Studies](../about-our-data/#data-access-units) +[Making a Data Request](../making-a-data-request) +[Renewing your Data Access](../../managing-data/how-to-fill-out-extension) +[Managing Data Overview](../../managing-data/working-with-our-data) diff --git a/docs/genomics-platform/requesting-data/making-a-data-request/index.md b/docs/genomics-platform/requesting-data/making-a-data-request/index.md index ae2a56dc..76d356de 100644 --- a/docs/genomics-platform/requesting-data/making-a-data-request/index.md +++ b/docs/genomics-platform/requesting-data/making-a-data-request/index.md @@ -12,9 +12,9 @@ St. Jude Cloud does not allow for-profit companies to access any restricted acce #### Helpful Things to Remember -1. Data in St. Jude Cloud is grouped into [Data Access Units (DAUs)](glossary.md#data-access-unit), which usually correspond to large-scale sequencing initiatives at St. Jude. -2. Individuals can [apply for access](glossary.md#data-access-agreement) to DAUs on a case-by-case basis for a specific amount of time (usually 1 year). -3. Access to data in a given DAU is assessed by the corresponding [Data Access Committee](glossary.md#data-access-committee) who reviews a variety of factors to grant access. +1. Data in St. Jude Cloud is grouped into [Data Access Units (DAUs)](../glossary/#data-access-unit), which usually correspond to large-scale sequencing initiatives at St. Jude. +2. Individuals can [apply for access](../glossary/#data-access-agreement) to DAUs on a case-by-case basis for a specific amount of time (usually 1 year). +3. Access to data in a given DAU is assessed by the corresponding [Data Access Committee](../glossary/#data-access-committee) who reviews a variety of factors to grant access. 4. There are a number of terms of use and restrictions outlined in the [Data Access Agreement](https://platform.stjude.cloud/access_form). Everyone who will be working with the data must understand and agree to these terms. ## Selecting Data @@ -28,12 +28,12 @@ As you filter and make selections, the data summary panel in the upper left hand ![](./request-data-select-data.gif) !!!note -You must have [created an account](../accounts-and-billing.md) and be logged in to submit a data request. If you have not yet created an account or you are not logged in, the submit button will say *Log In* rather than *Request Data*. +You must have [created an account](../../accounts-and-billing) and be logged in to submit a data request. If you have not yet created an account or you are not logged in, the submit button will say *Log In* rather than *Request Data*. !!! -Alternatively, you may be directed to the Genomics Platform Data Browser through another App to request specific samples. The [PeCan homepage](../../pecan/index.md#requesting-raw-genomics-through-pecan) is one such app that allows you to select data through an interactive visualization. +Alternatively, you may be directed to the Genomics Platform Data Browser through another App to request specific samples. The [PeCan homepage](../../../pecan/#requesting-raw-genomics-through-pecan) is one such app that allows you to select data through an interactive visualization. -After clicking on *Request Data*, we ask that you review your selection and make sure that the [DAUs](glossary.md#data-access-unit) corresponding to the set of data you have selected is indeed the data you want to request. +After clicking on *Request Data*, we ask that you review your selection and make sure that the [DAUs](../glossary/#data-access-unit) corresponding to the set of data you have selected is indeed the data you want to request. ![](./request-data-select-DAUs.png) @@ -52,21 +52,21 @@ If you already have access to the data or are requesting open-access data, you w !!! -Every person who requests access to our controlled-access data must sign the [Data Access Agreement (DAA)](glossary.md#data-access-agreement). If you are located in the United States of America, you can opt in to completing the DAA through an electronic setup wizard. If you are not located in the USA, or would like to complete the form manually, you can follow our instructions on [Filling Out The Data Access Agreement](how-to-fill-out-DAA.md). +Every person who requests access to our controlled-access data must sign the [Data Access Agreement (DAA)](../glossary/#data-access-agreement). If you are located in the United States of America, you can opt in to completing the DAA through an electronic setup wizard. If you are not located in the USA, or would like to complete the form manually, you can follow our instructions on [Filling Out The Data Access Agreement](../how-to-fill-out-daa). -If you opt to do the process through the setup wizard, the necessary information will be collected and added automatically to your agreement. Once you have completed the setup wizard, the form will be sent to you and necessary signatories through email via [DocuSign](https://www.docusign.com). You can learn more about our electronic data access agreement process [here](how-to-fill-out-DAA.md#the-electronic-data-access-agreement-process). +If you opt to do the process through the setup wizard, the necessary information will be collected and added automatically to your agreement. Once you have completed the setup wizard, the form will be sent to you and necessary signatories through email via [DocuSign](https://www.docusign.com). You can learn more about our electronic data access agreement process [here](../how-to-fill-out-daa/#the-electronic-data-access-agreement-process). Request approval typically takes a week or two if your data access agreement is correctly and completely filled out. You will receive automated emails from notifications@stjude.cloud at the time that your request is approved. !!!tip -If you receive an email from us that your DAA is incomplete, you may edit your DAA and upload the revised copy using the 'Add a Form' button the on [My Dashboard](../managing-data/working-with-our-data.md#managing-your-data-requests) page. +If you receive an email from us that your DAA is incomplete, you may edit your DAA and upload the revised copy using the 'Add a Form' button the on [My Dashboard](../../managing-data/working-with-our-data/#managing-your-data-requests) page. !!! ## Managing your Data Request -Go to our [Managing Data Overview](../managing-data/working-with-our-data.md) documentation page to learn how to check the status of your data request, complete an EDAA draft, upload a revised DAA, and ultimately access your data from your [My Dashboard](https://platform.stjude.cloud/requests/manage) page. +Go to our [Managing Data Overview](../../managing-data/working-with-our-data) documentation page to learn how to check the status of your data request, complete an EDAA draft, upload a revised DAA, and ultimately access your data from your [My Dashboard](https://platform.stjude.cloud/requests/manage) page. !!!info -If you would like to download the data to local storage, there are extra steps you'll need to follow such as [getting additional signatures](how-to-fill-out-DAA.md#data-download-permission) on your data access agreement. We recommend that you work with the data in the cloud if it's feasible; the data provided by St. Jude is free, the compute charges are reasonable, and working in the cloud helps to eliminate the long, error-prone downloading process. Porting your tools to be run in the cloud is easy, as well. We recommend you follow [this guide](../analyzing-data/creating-a-cloud-app.md) to get started. +If you would like to download the data to local storage, there are extra steps you'll need to follow such as [getting additional signatures](../how-to-fill-out-daa/#data-download-permission) on your data access agreement. We recommend that you work with the data in the cloud if it's feasible; the data provided by St. Jude is free, the compute charges are reasonable, and working in the cloud helps to eliminate the long, error-prone downloading process. Porting your tools to be run in the cloud is easy, as well. We recommend you follow [this guide](../../analyzing-data/creating-a-cloud-app) to get started. !!! \ No newline at end of file