AWS omics high security documentation change
Summary
Restructured documentation with updated service description emphasizing HIPAA eligibility, compliance features, and clinical use cases. Added GitHub connections integration and reorganized sections.
Security assessment
The change explicitly states HealthOmics is HIPAA-eligible and adds a 'Maintain compliance' section mentioning audit trails, data provenance tracking, and HIPAA-ready infrastructure. These are concrete security/compliance enhancements for handling protected health information.
Diff
diff --git a/omics/latest/dev/what-is-healthomics.md b/omics/latest/dev/what-is-healthomics.md index bab7e1a76..c3a977b69 100644 --- a//omics/latest/dev/what-is-healthomics.md +++ b//omics/latest/dev/what-is-healthomics.md @@ -5 +5 @@ -Important noticeConceptsHealthOmics featuresRelated servicesRegions and endpoints for AWS HealthOmicsHow to access HealthOmicsLearn more +Important noticeHealthOmics featuresConceptsRelated servicesHow to access HealthOmicsRegions and endpoints for AWS HealthOmicsLearn more @@ -9,3 +9 @@ Important noticeConceptsHealthOmics featuresRelated servicesRegions and endpoint -AWS HealthOmics is an AWS service that helps users such as bioinformaticians, researchers, and scientists to store, query, analyze, and generate insights from genomics and other biological data. It simplifies and accelerates the process of storing and analyzing genomic information for research and clinical organizations, and makes scientific discovery and insight generation faster. - -HealthOmics has three primary components. HealthOmics Storage helps you store and share petabytes of genomics data efficiently and at low cost per gigabase. HealthOmics Analytics simplifies how you prepare genomics data for multiomics and multimodal analyses. HealthOmics Workflows automatically provisions and scales the underlying infrastructure for your bioinformatics computation. +AWS HealthOmics is a HIPAA-eligible service that accelerates clinical diagnostic testing, drug discovery, and agriculture research by fully managing the complex infrastructure behind your bioinformatics workflows. HealthOmics supports industry-standard workflow languages (WDL, Nextflow, CWL) and seamlessly scales bioinformatics infrastructure to support data from tens of thousands of tests per day—all with predictable cost per-sample. HealthOmics handles the technical complexities like managing compute resources and maintaining workflow engines so you can focus entirely on scientific breakthroughs. @@ -17,2 +14,0 @@ HealthOmics has three primary components. HealthOmics Storage helps you store an - * HealthOmics concepts - @@ -21 +17 @@ HealthOmics has three primary components. HealthOmics Storage helps you store an - * Related services + * HealthOmics concepts @@ -23 +19 @@ HealthOmics has three primary components. HealthOmics Storage helps you store an - * Regions and endpoints for AWS HealthOmics + * Related services @@ -26,0 +23,2 @@ HealthOmics has three primary components. HealthOmics Storage helps you store an + * Regions and endpoints for AWS HealthOmics + @@ -38,5 +36 @@ HealthOmics is intended only for the transferring, storing, formatting, or displ -## HealthOmics concepts - -This topic covers definitions for key concepts and terms that are specific to HealthOmics, to help you understand the terminology of HealthOmics used this guide. - -###### Topics +## HealthOmics features @@ -44 +38 @@ This topic covers definitions for key concepts and terms that are specific to He - * Storage +**Primary use cases for HealthOmics:** @@ -46 +40 @@ This topic covers definitions for key concepts and terms that are specific to He - * Analytics + * _Clinical diagnostics_ – Build and scale diagnostic testing workflows with predictable costs and fully managed infrastructure that grows with your testing volume. @@ -48 +42 @@ This topic covers definitions for key concepts and terms that are specific to He - * Workflows + * _Drug discovery_ – Accelerate therapeutic research by orchestrating biological foundation models at scale, enabling rapid iteration across millions of potential candidates. @@ -49,0 +44 @@ This topic covers definitions for key concepts and terms that are specific to He + * _Agricultural research_ – Enhance crop traits like drought tolerance and pest resistance through AI-powered workflows that improve food security and agricultural productivity. @@ -53 +47,0 @@ This topic covers definitions for key concepts and terms that are specific to He -### Storage @@ -55 +49 @@ This topic covers definitions for key concepts and terms that are specific to He -Data storage is separated into sequence stores, for your genomics sequences and related information, and a reference store, for all of your reference genomes. The following terms describe the implementations that are specific to HealthOmics. +**Key benefits of HealthOmics:** @@ -57 +51 @@ Data storage is separated into sequence stores, for your genomics sequences and - * _Sequence store_ – A data store for the storage of genomics files. You can have one or more sequence stores within HealthOmics. Access permissions and AWS KMS encryption can be set on a sequence store to control who has access to the data. + * _Scalability_ – Scale workflows across 100,000+ concurrent vCPUs to support tens of thousands of tests daily with zero infrastructure management and predictable cost-per sample. @@ -59 +53 @@ Data storage is separated into sequence stores, for your genomics sequences and - * _Read set_ – A read set is an abstraction of genomics reads, which are stored in FASTQ, BAM, or CRAM formats. Read sets can be imported into sequence stores and annotated with metadata. You can apply permissions to read sets using attribute based access control (ABAC). + * _Focus on science, not infrastructure_ – Use familiar workflow languages and APIs while AWS automatically handles infrastructure orchestration and data management behind the scenes. @@ -61 +55 @@ Data storage is separated into sequence stores, for your genomics sequences and - * _Reference_ – A genome reference is used with reads to identify where in a genome a specific read, or group of reads, is mapped to. These are in FASTA format and stored in the reference store. + * _Maintain compliance_ – Comprehensive audit trails, data provenance tracking, and HIPAA-eligible infrastructure designed for clinical workflows—all out-of-the-box—support development of solutions that meet regulatory requirements. @@ -63 +56,0 @@ Data storage is separated into sequence stores, for your genomics sequences and - * _Reference store_ – A data store for the storage of reference genomes. You can have a single reference store in each account and region. @@ -66,0 +60 @@ Data storage is separated into sequence stores, for your genomics sequences and +HealthOmics consists of three main components: @@ -68 +62 @@ Data storage is separated into sequence stores, for your genomics sequences and -### Analytics + * [HealthOmics workflows](https://docs.aws.amazon.com/omics/latest/dev/private-workflows.html) — Run bioinformatics computations on automatically provisioned and scaled infrastructure. @@ -70 +64 @@ Data storage is separated into sequence stores, for your genomics sequences and -You can transform and analyze your genomics data with HealthOmics Analytics. Create a variant store or annotation store to include additional information for your queries. + * [HealthOmics storage](https://docs.aws.amazon.com/omics/latest/dev/sequence-stores.html) — Store and share petabytes of genomics data efficiently at a low cost per gigabase. @@ -72 +66 @@ You can transform and analyze your genomics data with HealthOmics Analytics. Cre - * _Variant store_ – data store that stores variant data at a population scale. Variant stores support both genomic Variant Call Format (gVCF) and VCF inputs. + * [HealthOmics analytics](https://docs.aws.amazon.com/omics/latest/dev/omics-analytics.html) — Prepare genomics data for multiomics and multimodal analyses. @@ -74 +67,0 @@ You can transform and analyze your genomics data with HealthOmics Analytics. Cre - * _Annotation store_ – A data store representing an annotation database, such as one from a TSV/CSV, VCF, or General Feature Format (GFF3) file. Annotation Stores are mapped to the same coordinate system as variant stores during an import. @@ -77,0 +71 @@ You can transform and analyze your genomics data with HealthOmics Analytics. Cre +Use these components independently or combine them for an end-to-end solution. @@ -79 +73 @@ You can transform and analyze your genomics data with HealthOmics Analytics. Cre -### Workflows +## HealthOmics concepts @@ -81 +75 @@ You can transform and analyze your genomics data with HealthOmics Analytics. Cre -With HealthOmics Workflows, you can process and analyze your genomics data. +This topic covers definitions for key concepts and terms that are specific to HealthOmics, to help you understand the terminology of HealthOmics used this guide. @@ -83 +77 @@ With HealthOmics Workflows, you can process and analyze your genomics data. - * _Workflow_ – The overall definition of an end to end process including parameters and references to tools. Workflow definitions can be expressed as WDL, Nextflow, or CWL. Each created workflow has a unique identifier. +###### Topics @@ -85 +79 @@ With HealthOmics Workflows, you can process and analyze your genomics data. - * _Run_ – A single invocation of a workflow. An individual run uses your defined input data and produces an output. Each created run has a unique identifier. + * Workflows @@ -87 +81 @@ With HealthOmics Workflows, you can process and analyze your genomics data. - * _Task_ – The individual processes within a run. HealthOmics Workflows use these defined compute specifications to run your task. Each task has a unique identifier. + * Storage @@ -89 +83 @@ With HealthOmics Workflows, you can process and analyze your genomics data. - * _Run group_ – A group of runs for which you can set the max vCPU, max duration, or max concurrent runs to help limit the compute resources used per run. You can specify and configure priorities for your runs within a run group. For example, you can specify that a high priority run will be performed before one that's lower priority, creating a priority queue. It is optional to use a Run Group, and each Run Group has a unique identifier. + * Analytics @@ -94 +88 @@ With HealthOmics Workflows, you can process and analyze your genomics data. -## HealthOmics features +### Workflows @@ -96 +90 @@ With HealthOmics Workflows, you can process and analyze your genomics data. -HealthOmics offers the following features. +With HealthOmics Workflows, you can process and analyze your genomics data. @@ -98 +92 @@ HealthOmics offers the following features. - * HealthOmics Storage — helps you store and share petabytes of raw genomics data efficiently and at low cost per gigabase. + * _Workflow_ – The overall definition of an end to end process including parameters and references to tools. Workflow definitions can be expressed as WDL, Nextflow, or CWL. Each created workflow has a unique identifier. @@ -100 +94 @@ HealthOmics offers the following features. - * HealthOmics Analytics — simplifies how you prepare genomics data for multiomics and multimodal analyses. + * _Run_ – A single invocation of a workflow. An individual run uses your defined input data and produces an output. Each created run has a unique identifier. @@ -102 +96 @@ HealthOmics offers the following features. - * HealthOmics Workflows — automatically provisions and scales the underlying infrastructure for your bioinformatics workflows. + * _Task_ – The individual processes within a run. HealthOmics Workflows use these defined compute specifications to run your task. Each task has a unique identifier. @@ -103,0 +98 @@ HealthOmics offers the following features. + * _Run group_ – A group of runs for which you can set the max vCPU, max duration, or max concurrent runs to help limit the compute resources used per run. You can specify and configure priorities for your runs within a run group. For example, you can specify that a high priority run will be performed before one that's lower priority, creating a priority queue. It is optional to use a Run Group, and each Run Group has a unique identifier. @@ -107 +101,0 @@ HealthOmics offers the following features. -You can use each component independently, or as part of an integrated end-to-end solution. @@ -109 +103 @@ You can use each component independently, or as part of an integrated end-to-end -HealthOmics offers you the following benefits. +### Storage @@ -111 +105 @@ HealthOmics offers you the following benefits. - * Securely store and combine genomic data — HealthOmics integrates with other AWS services such as AWS Lake Formation and Amazon Athena. You can securely store your genomics data and then query or combine it with medical history data for better diagnoses and personalized treatment plans. +Data storage is separated into sequence stores, for your genomics sequences and related information, and a reference store, for all of your reference genomes. The following terms describe the implementations that are specific to HealthOmics. @@ -113 +107 @@ HealthOmics offers you the following benefits. - * Protect patient privacy — HealthOmics is HIPAA eligible. It also integrates with IAM and Amazon CloudWatch so that you can control and log data access, and track how the data is used in analyses. + * _Sequence store_ – A data store for the storage of genomics files. You can have one or more sequence stores within HealthOmics. Access permissions and AWS KMS encryption can be set on a sequence store to control who has access to the data. @@ -115 +109 @@ HealthOmics offers you the following benefits. - * Built to scale — Support large population data analyses with simplified billing and new collaboration tools. + * _Read set_ – A read set is an abstraction of genomics reads, which are stored in FASTQ, BAM, or CRAM formats. Read sets can be imported into sequence stores and annotated with metadata. You can apply permissions to read sets using attribute based access control (ABAC). @@ -117 +111 @@ HealthOmics offers you the following benefits. - * Maximize efficiency — Use automated workflows and integrated tools to streamline data processing and analysis. + * _Reference_ – A genome reference is used with reads to identify where in a genome a specific read, or group of reads, is mapped to. These are in FASTA format and stored in the reference store. @@ -118,0 +113 @@ HealthOmics offers you the following benefits. + * _Reference store_ – A data store for the storage of reference genomes. You can have a single reference store in each account and region. @@ -122 +116,0 @@ HealthOmics offers you the following benefits. -You can use HealthOmics for the following biomedical applications: @@ -124 +118 @@ You can use HealthOmics for the following biomedical applications: - * Population sequencing — Query thousands of genomes at once to understand how genomic variation maps to phenotypes across a population. +### Analytics @@ -126 +120 @@ You can use HealthOmics for the following biomedical applications: - * Clinical genomics — Build reproducible genomics workflows from sequencer output to reportable data. You can also optimize for high volume throughput and set the compute requirements for high-priority clinical samples to reduce turnaround time. +You can transform and analyze your genomics data with HealthOmics Analytics. Create a variant store or annotation store to include additional information for your queries. @@ -128 +122 @@ You can use HealthOmics for the following biomedical applications: - * Clinical trials — Integrate genome analysis into clinical trials to better understand the efficacy of new drug candidates. Simplify and accelerate clinical trials with long-term cost savings and data provenance to meet regulations from governing bodies. + * _Variant store_ – data store that stores variant data at a population scale. Variant stores support both genomic Variant Call Format (gVCF) and VCF inputs. @@ -130 +124 @@ You can use HealthOmics for the following biomedical applications: - * Enhance research and innovation — Streamline and control storage, access, and analysis of anonymized genomics data with built-in row and column-based access control. + * _Annotation store_ – A data store representing an annotation database, such as one from a TSV/CSV, VCF, or General Feature Format (GFF3) file. Annotation Stores are mapped to the same coordinate system as variant stores during an import. @@ -148,0 +143 @@ The following services work with HealthOmics. + * [GitHub connections](https://docs.aws.amazon.com/codepipeline/latest/userguide/connections-github.html) – Use connections to connect your external code respoitories to your HealthOmics workflows. @@ -152,5 +146,0 @@ The following services work with HealthOmics. -## Regions and endpoints for AWS HealthOmics - -For a full list of regions and endpoints, see the [AWS General Reference](https://docs.aws.amazon.com/general/latest/gr/healthomics-quotas.html). - -In addition to the AWS regions that are active by default, there are also _Opt-in Regions_ which need to be activated. To learn more about how to activate or deactivate a Region, see [Specify which AWS Regions your account can use](https://docs.aws.amazon.com/accounts/latest/reference/manage-acct-regions.html#manage-acct-regions-enable-standalone) in the AWS Account Management guide. @@ -172,0 +163,6 @@ You can access AWS HealthOmics features using the management console, CLI, SDKs +## Regions and endpoints for AWS HealthOmics + +For a full list of regions and endpoints, see the [AWS General Reference](https://docs.aws.amazon.com/general/latest/gr/healthomics-quotas.html). + +In addition to the AWS regions that are active by default, there are also _Opt-in Regions_ which need to be activated. To learn more about how to activate or deactivate a Region, see [Specify which AWS Regions your account can use](https://docs.aws.amazon.com/accounts/latest/reference/manage-acct-regions.html#manage-acct-regions-enable-standalone) in the AWS Account Management guide. +