Merge pull request #1074 from FredHutch/link-fixes

Link fixes

_compdemos/AWSCLI_WSL.md

@@ -41,7 +41,7 @@ Open the WSL and copy/paste these commands (you may have to use CTRL+SHIFT+V or
 
 This should install the latest version of the CLI on your machine. When it is complete, you should be able to type `aws –version` in the WSL terminal and verify that it is installed (step by step [here](https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html)).
 
-To interact with a specific AWS account or S3 bucket, you will need a few pieces of information first. When interacting with the CLI, rather than using a username and password, you use an access key (AK) and a secret access key (SAK). In addition, you’ll need the region the account lives in (FHCC uses us-west-2 for almost everything), and the output (json or text depending on preference and need). You can contact the Helpdesk to get an AK and SAK generated for you. These keys generally expire after 6 months and are specific to your level of permissions. **Do not share keys with anyone.**
+To interact with a specific AWS account or S3 bucket, you will need a few pieces of information first. When interacting with the CLI, rather than using a username and password, you use an access key (AK) and a secret access key (SAK). In addition, you’ll need the region the account lives in (Fred Hutch Cancer Center uses us-west-2 for almost everything), and the output (json or text depending on preference and need). You can contact the Helpdesk to get an AK and SAK generated for you. These keys generally expire after 6 months and are specific to your level of permissions. **Do not share keys with anyone.**
 
 Type `aws configure` to start the process and follow the prompts. More detailed instructions are [here](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-quickstart.html#cli-configure-quickstart-config). Once this is done, you are all set to perform operations within a specific AWS account.
 

_dasldemos/computational_rank.md

@@ -59,7 +59,7 @@ The next section talks about basic best practices when running software using ea
 
 ## General Advice
 
-- Before reinventing the wheel, check out the [WILDS Docker Repository](https://getwilds.org/packages.html#docker) to see if there’s a similar workflow to what you need. You may just need to [fork an existing workflow](https://getwilds.org/packages.html#wdls) (make your own version) to get started.
+- Before reinventing the wheel, check out the [WILDS Docker Repository](https://getwilds.org/projects.html#docker-recipes) to see if there’s a similar workflow to what you need. You may just need to [fork an existing workflow](https://getwilds.org/projects.html#wdls) (make your own version) to get started.
 - Avoid mixing and matching your software environments and loading them all at once to avoid dependency conflicts. In practice, this means sticking to either environment modules or Docker containers if possible.
 - Pick a version number for your software. This practice will keep your workflow reproducible if the latest version of the software changes. For easymodules, you can see the versions using `module avail <module-name>`, such as `module avail samtools`.
 - For Docker containers, pick a tagged container from the container image library. For example:  [`biocontainers/samtools:v1.9-4-deb_cv1`](https://hub.docker.com/layers/biocontainers/samtools/v1.9-4-deb_cv1/images/sha256-da61624fda230e94867c9429ca1112e1e77c24e500b52dfc84eaf2f5820b4a2a?context=explore)
@@ -231,7 +231,7 @@ This also has the advantage of being the first step in transforming your script
 
 ## How do I transform a snakemake script to WDL?
 
-This assumes that nothing similar exists in [WILDS WDL Workflows](https://getwilds.org/packages.html#wdls). If something does, then fork that workflow and start from there.
+This assumes that nothing similar exists in [WILDS WDL Workflows](https://getwilds.org/projects.html#wdls). If something does, then fork that workflow and start from there.
 
 1. Start with the Bash code: separate each step into its own task. See above example.
 2. For each task, identify the inputs needed for that task and their formats. This might be an output from a previous task.

_datascience/patient-data.md

@@ -1,13 +1,13 @@
 ---
-title: FHCC Patient Clinical Data for Research
+title: Fred Hutch Cancer Center Patient Clinical Data for Research
 last_modified_at: 2020-05-06
 main_authors: Monica Gerber, Rachel Galbraith
 primary_reviewers: vortexing
 ---
 
 Access to clinical data for Fred Hutch Cancer Center’s patient population is
-critical for research activities at FHCC. This page outlines the clinical data
-systems at FHCC that can be used for research. 
+critical for research activities at Fred Hutch Cancer Center. This page outlines the clinical data
+systems at Fred Hutch Cancer Center that can be used for research. 
 
 ## Upcoming Opportunities
 
@@ -22,11 +22,11 @@ across the institution. In April 2023, the Data Science Lab team, along with
 Legal, Compliance, and IT, finalized a new agreement with University of
 Washington that enables comprehensive data access and use. 
 
-These exciting new opportunities for use of FHCC’s patient clinical data depend
+These exciting new opportunities for use of Fred Hutch Cancer Center’s patient clinical data depend
 on the development of expanded data infrastructure and new data governance and
-stewardship policies. DaSL and its partners at FHCC have initiated a new data
+stewardship policies. DaSL and its partners at Fred Hutch Cancer Center have initiated a new data
 infrastructure approach and a new data governance approach for clinical data.
-This new approach envisions a future FHCC with multimodal data integration and
+This new approach envisions a future Fred Hutch Cancer Center with multimodal data integration and
 democratized data access. For more information and to stay up-to-date with new
 developments, visit DaSL’s [home page](https://hutchdatascience.org) and [CenterNet page](https://centernet.fredhutch.org/u/data-science-lab.html). 
 
@@ -44,11 +44,11 @@ radiation oncology, and a variety of unstructured radiology, pathology, and
 clinical narrative reports.  Currently, to request access to these data, go to
 the [Fred Hutch Patient Data for Research](https://centernet.fredhutch.org/u/data-science-lab/patient-data.html) page on CenterNet.
 
-*FHCC patient population*
+*Fred Hutch Cancer Center patient population*
 
 The patient population included in HIDRA is created by filtering for patients
-across FHCC and UW Medicine in Clarity. Clarity is the name of the database that
-contains the unified Epic medical record for FHCC and UW Medicine. Patients are
+across Fred Hutch Cancer Center and UW Medicine in Clarity. Clarity is the name of the database that
+contains the unified Epic medical record for Fred Hutch Cancer Center and UW Medicine. Patients are
 included if they have at least one oncology-related base record in any of
 Clarity’s data domains (encounters, hospital billing account, professional
 billing, referral). A base record is defined as the most relevant unit of
@@ -57,7 +57,7 @@ least one oncology-related base record in any data domain is identified, records
 for all care for those patients are brought in (not just care directly related
 to cancer).
 
-Oncology-related records are defined in a MOU between the UW and FHCC:
+Oncology-related records are defined in a MOU between the UW and Fred Hutch Cancer Center:
 
 >1.1 Cancer-Related Care: Includes,
 >
@@ -109,4 +109,4 @@ There are 12 programs with data abstracted into Caisis:
 Data abstracted into Caisis is still available to any Cancer Consortium
 investigator, with valid IRB approval or for activities preparatory to research.
 Currently, STTR is developing new tools for data abstraction. See STTR’s
-newsletter to stay informed about new data abstraction tools.
+newsletter to stay informed about new data abstraction tools.

_datascience/stewardship.md

@@ -3,7 +3,7 @@ title: Research Data Stewardship
 primary_reviewers: vortexing
 ---
 
-As research increasingly relies on effective and large scale use of data, our skills and attention around data stewardship become increasingly important.  The Data Science Lab will be kicking off a series of efforts focusing on training, documentation and support for research data stewardship over the coming year that we hope will help all FHCC researchers do more research with more data in a financially sustainable and responsible way.  If you're interested in discussing these topics or contributing to the effort, please schedule a [Data House Call](https://hutchdatascience.org/datahousecalls/) to get a consultation with a Data Science Lab member. 
+As research increasingly relies on effective and large scale use of data, our skills and attention around data stewardship become increasingly important.  The Data Science Lab will be kicking off a series of efforts focusing on training, documentation and support for research data stewardship over the coming year that we hope will help all Fred Hutch Cancer Center researchers do more research with more data in a financially sustainable and responsible way.  If you're interested in discussing these topics or contributing to the effort, please schedule a [Data House Call](https://hutchdatascience.org/datahousecalls/) to get a consultation with a Data Science Lab member. 
 
 ## Data Management Guidance
 

_scicomputing/access_aws.md

@@ -27,11 +27,11 @@ Then you can read more about [AWS Storage](/scicomputing/store_objectstore/) and
 Unless otherwise specified, all accounts follow the same pricing model:
 •	S3 usage (sometimes called Economy Cloud) is free up to 100TBs.
 •	After 100TB, the cost is $3/TB/Month. 
-•	There is a free tier for compute that comes standard with every AWS account. After that free tier, charges are pay-as-you-go (minus an 11% discount FHCC has negotiated with AWS). 
+•	There is a free tier for compute that comes standard with every AWS account. After that free tier, charges are pay-as-you-go (minus an 11% discount Fred Hutch Cancer Center has negotiated with AWS). 
 
 In the background, IT pays all AWS charges up front and then bills back to researchers; this is done to maximize the institutional discount. Any credits that get issued to a researcher are redeemed with IT; IT tracks them on researchers’ behalf and subtracts them from monthly bills until the credits have been used. When a researcher begins to use AWS services, they will receive a monthly invoice from IT BizOps with itemized charges; those charges are assigned to grants (Project IDs) and the amounts deducted accordingly. 
 
-Here are some links to learn more. Keep in mind that tools provided by AWS will not reflect FHCC institutional discounts or offerings. However, they can be used to get a general idea of costs):
+Here are some links to learn more. Keep in mind that tools provided by AWS will not reflect Fred Hutch Cancer Center institutional discounts or offerings. However, they can be used to get a general idea of costs):
 •	[AWS Pricing 101](https://aws.amazon.com/pricing/?aws-products-pricing.sort-by=item.additionalFields.productNameLowercase&aws-products-pricing.sort-order=asc&awsf.Free%20Tier%20Type=*all&awsf.tech-category=*all)
 •	[AWS Pricing Calculator](https://calculator.aws/#/?nc2=pr)