diff --git a/DEVELOPING.md b/DEVELOPING.md index 5f9a361..ca1a48d 100644 --- a/DEVELOPING.md +++ b/DEVELOPING.md @@ -49,6 +49,12 @@ zensical serve Navigation is fully defined in [zensical.toml](./zensical.toml). +The current information architecture is intentionally audience-based: + +- `Home`, `Platform`, and `Solutions` are the business-facing front of the site. +- `Developers` is the technical back of the site. +- Existing CALYPR product docs and open-source tool docs keep their URLs, but they should not be treated as the main marketing entry point. + If you want to: - rename a sidebar label @@ -69,11 +75,16 @@ These live in `docs/` and should be edited directly there. Examples: - `docs/index.md` +- `docs/platform/...` +- `docs/solutions/...` +- `docs/developers/index.md` - `docs/calypr/...` - `docs/tools/index.md` - `docs/tools/funnel/...` - `docs/tools/grip/...` +Business-facing pages should explain outcomes first and link to developer docs second. Avoid making command references, protocol names, or implementation components the first thing a non-technical reader has to understand. + ### Imported tool pages These are not authored in this repo anymore. diff --git a/docs/assets/personas/data-steward.svg b/docs/assets/personas/data-steward.svg new file mode 100644 index 0000000..826acfd --- /dev/null +++ b/docs/assets/personas/data-steward.svg @@ -0,0 +1,72 @@ + + Data Steward + Register, curate, govern, and share project data with confidence. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Persona + Data Steward + +
+ Register, curate, govern, and share project data with confidence. +
+
+ + + + + + + + + + + + + + + + + Open standards + + Modular tools + + Research-ready + +
+ + + + CALYPR biomedical platform + +
+
diff --git a/docs/assets/personas/platform-engineer.svg b/docs/assets/personas/platform-engineer.svg new file mode 100644 index 0000000..fe563d2 --- /dev/null +++ b/docs/assets/personas/platform-engineer.svg @@ -0,0 +1,76 @@ + + Platform Engineer + Deploy, secure, monitor, and scale standards-based research infrastructure. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Persona + Platform Engineer + +
+ Deploy, secure, monitor, and scale standards-based research infrastructure. +
+
+ + + + + + + + + + + + + + + + + + + + + Open standards + + Modular tools + + Research-ready + +
+ + + + CALYPR biomedical platform + +
+
diff --git a/docs/assets/personas/researcher-bioinformatician.svg b/docs/assets/personas/researcher-bioinformatician.svg new file mode 100644 index 0000000..eadf2ca --- /dev/null +++ b/docs/assets/personas/researcher-bioinformatician.svg @@ -0,0 +1,73 @@ + + Researcher / Bioinformatician + Find data, run analyses, and move from question to reproducible result. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Persona + Researcher / Bioinformatician + +
+ Find data, run analyses, and move from question to reproducible result. +
+
+ + + + + + + + + + + + + + + + + + Open standards + + Modular tools + + Research-ready + +
+ + + + CALYPR biomedical platform + +
+
diff --git a/docs/assets/personas/security-compliance-reviewer.svg b/docs/assets/personas/security-compliance-reviewer.svg new file mode 100644 index 0000000..51db950 --- /dev/null +++ b/docs/assets/personas/security-compliance-reviewer.svg @@ -0,0 +1,71 @@ + + Security / Compliance Reviewer + Review access, auditability, governance, and operational controls. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Persona + Security / Compliance Reviewer + +
+ Review access, auditability, governance, and operational controls. +
+
+ + + + + + + + + + + + + + + + Open standards + + Modular tools + + Research-ready + +
+ + + + CALYPR biomedical platform + +
+
diff --git a/docs/assets/personas/standards-architecture-lead.svg b/docs/assets/personas/standards-architecture-lead.svg new file mode 100644 index 0000000..4c90b8b --- /dev/null +++ b/docs/assets/personas/standards-architecture-lead.svg @@ -0,0 +1,75 @@ + + Standards / Architecture Lead + Evaluate interoperability, service composition, and standards alignment. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Persona + Standards / Architecture Lead + +
+ Evaluate interoperability, service composition, and standards alignment. +
+
+ + + + + + + + + + + + + + + + + + + + Open standards + + Modular tools + + Research-ready + +
+ + + + CALYPR biomedical platform + +
+
diff --git a/docs/assets/personas/workflow-engineer.svg b/docs/assets/personas/workflow-engineer.svg new file mode 100644 index 0000000..50dcda3 --- /dev/null +++ b/docs/assets/personas/workflow-engineer.svg @@ -0,0 +1,75 @@ + + Workflow Engineer + Connect data access, execution engines, and reproducible pipelines. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Persona + Workflow Engineer + +
+ Connect data access, execution engines, and reproducible pipelines. +
+
+ + + + + + + + + + + + + + + + + + + + Open standards + + Modular tools + + Research-ready + +
+ + + + CALYPR biomedical platform + +
+
diff --git a/docs/assets/solutions/integrate-data.svg b/docs/assets/solutions/integrate-data.svg new file mode 100644 index 0000000..efd9dea --- /dev/null +++ b/docs/assets/solutions/integrate-data.svg @@ -0,0 +1,77 @@ + + Integrate Data + Connect clinical, omics, and project metadata into queryable structures. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Solution Area + Integrate Data + +
+ Connect clinical, omics, and project metadata into queryable structures. +
+
+ + + + + + + + + + + + + + + + + + + + + + Open standards + + Modular tools + + Research-ready + +
+ + + + CALYPR biomedical platform + +
+
diff --git a/docs/assets/solutions/manage-compute.svg b/docs/assets/solutions/manage-compute.svg new file mode 100644 index 0000000..afddfe9 --- /dev/null +++ b/docs/assets/solutions/manage-compute.svg @@ -0,0 +1,75 @@ + + Manage Compute + Run portable workflows across local, cloud, and federated environments. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Solution Area + Manage Compute + +
+ Run portable workflows across local, cloud, and federated environments. +
+
+ + + + + + + + + + + + + + + + + + + + Open standards + + Modular tools + + Research-ready + +
+ + + + CALYPR biomedical platform + +
+
diff --git a/docs/assets/solutions/manage-data.svg b/docs/assets/solutions/manage-data.svg new file mode 100644 index 0000000..baebfdf --- /dev/null +++ b/docs/assets/solutions/manage-data.svg @@ -0,0 +1,73 @@ + + Manage Data + Register, version, govern, and resolve biomedical research data. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Solution Area + Manage Data + +
+ Register, version, govern, and resolve biomedical research data. +
+
+ + + + + + + + + + + + + + + + + + Open standards + + Modular tools + + Research-ready + +
+ + + + CALYPR biomedical platform + +
+
diff --git a/docs/assets/solutions/manage-models.svg b/docs/assets/solutions/manage-models.svg new file mode 100644 index 0000000..ec0f39d --- /dev/null +++ b/docs/assets/solutions/manage-models.svg @@ -0,0 +1,75 @@ + + Manage Models + Package, share, benchmark, and govern portable biomedical models. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Solution Area + Manage Models + +
+ Package, share, benchmark, and govern portable biomedical models. +
+
+ + + + + + + + + + + + + + + + + + + + Open standards + + Modular tools + + Research-ready + +
+ + + + CALYPR biomedical platform + +
+
diff --git a/docs/calypr/index.md b/docs/calypr/index.md index 1876a16..4b7b195 100644 --- a/docs/calypr/index.md +++ b/docs/calypr/index.md @@ -1,43 +1,39 @@ -# CALYPR Platform +# CALYPR Product Guide -Welcome to the **CALYPR Platform**. CALYPR is a next-generation genomic data science ecosystem designed to bridge the gap between massive, centralized data commons and the agile, distributed workflows of modern researchers. +CALYPR is the product layer of the CALYPR open platform. It turns the underlying data, compute, metadata, and access-control tools into a workspace experience that research programs can understand and operate. !!! info "Private Beta" - CALYPR platform is currently in a private beta phase. We are actively working with a select group of research partners to refine the platform. If you encounter any issues or have feature requests, please reach out to the team. The individual [tools](/tools/) are available for public use. - ---- - -## The CALYPR Philosophy - -Traditional data repositories often create data silos where information is easy to store but difficult to move, version, or integrate with external tools. CALYPR breaks these silos by embracing **Interoperability**, **Reproducibility**, and **Scalability**. - -### 1. Interoperability (GA4GH Standards) -CALYPR is built from the ground up on [GA4GH](https://www.ga4gh.org/) standards. By using the **Data Repository Service (DRS)** and **Task Execution Service (TES)**, CALYPR ensures that your data and workflows can move seamlessly between different cloud providers and on-premises high-performance computing (HPC) clusters. -The data system is based on the Fast Healthcare Interoperability Resources (FHIR) standard. - -### 2. Reproducibility (Git-like Data Management) -The core of the CALYPR experience is **Git-DRS**. We believe that data management should feel as natural as code management. Git-DRS allows you to track, version, and share massive genomic datasets using the familiar `git` commands, ensuring that every analysis is backed by a specific, immutable version of the data. - -### 3. Scalability (Hybrid Cloud Infrastructure) -Whether you are working with a few genomes or petabyte-scale cohorts, CALYPR's architecture—powered by **Gen3**—scales to meet your needs. Our hybrid cloud approach allows for secure data storage in AWS while leveraging your local compute resources when necessary. - ---- - -## How it Works: The Connected Commons - -CALYPR acts as the "connective tissue" between your research environment and the cloud: - -* **Data Commons ([Gen3](https://gen3.org)):** Provides the robust backend for metadata management, indexing, and authentication. -* **Data Service ([Syfon](/tools/syfon/)):** Implements the DRS-facing storage layer, handling object registration, presigned upload and download URLs, bucket routing, and server-side access control between clients and object storage. -* **Version Control ([Git-DRS](/tools/git-drs/)):** Manages the check-in and check-out operations for large files, allowing you to treat remote DRS objects as local files. -* **Metadata Orchestration ([Forge](/tools/forge/)):** Streamlines the validation, publishing, and harmonizing of genomic metadata. -* **Compute ([Funnel](/tools/funnel/)):** Executes complex pipelines across distributed environments using standardized task definitions. -* **Graph Insights ([GRIP](/tools/grip/)):** Enables high-performance queries across heterogeneous datasets once integrated. - ---- + CALYPR is currently in private beta. The platform is being refined with research partners. The underlying [open-source tools](../tools/index.md) remain available for public use. + +## What The Product Adds + +
+
+

Project-centered collaboration

+

Research programs need a shared place to organize datasets, metadata, users, approvals, and analysis context.

+
+
+

Governed data operations

+

CALYPR keeps controlled data movement visible through access workflows and DRS-native object references.

+
+
+

Technical depth when needed

+

Engineers can drop into Git-DRS, Syfon, Funnel, GRIP, Forge, and the data client without making those tools the default front door for everyone.

+
+
+ +## Platform Foundation + +CALYPR is built on standards-aligned components: + +- **Gen3-compatible commons patterns** for metadata, indexing, and authentication. +- **GA4GH DRS** for data references and access. +- **GA4GH TES** for portable workflow execution. +- **FHIR-oriented metadata** for connecting research files to biological and clinical context. +- **Open-source CALYPR tools** for versioning, storage mediation, metadata publishing, graph querying, and workflow execution. ## Next Steps -To get started: -1. **[Quick Start Guide](quick-start.md):** The fastest way to install tools and start tracking data. -2. **[Data & Metadata](data/managing-metadata.md):** Learn how to associate your biological metadata with the files you've uploaded. +1. Start with the [quick start guide](quick-start.md) if you are setting up or trying the platform. +2. Review [data and metadata](data/managing-metadata.md) if you are preparing datasets. +3. Use the [developer docs](../developers/index.md) when you need command references, deployment details, or component-level documentation. diff --git a/docs/developers/index.md b/docs/developers/index.md new file mode 100644 index 0000000..1c492b8 --- /dev/null +++ b/docs/developers/index.md @@ -0,0 +1,75 @@ +--- +body_class: marketing-page developers-page +hide: + - navigation + - toc +--- + +
+

Open-source tools

+
+
+ Data lake tools +

Versioned object pointers, DRS-native upload/download, and storage-layer services.

+ +
+
+ Workflow execution +

Portable TES-based task execution across local, cloud, and federated infrastructure.

+ +
+
+ Graph database +

Graph query, traversal, and API-facing discovery services for connected research data.

+ +
+
+ Data transformation +

Validation, transformation, and publication workflows for metadata and structured records.

+ +
+
+ Management software +

CLI workflows for access requests, data operations, and program-level user actions.

+ +
+
+
+ +
+

CALYPR platform docs

+
+ + CALYPR overview + Architecture, platform shape, and product-level technical orientation. + Platform + + + Quick start guide + First-run path for teams standing up CALYPR in a real environment. + Setup + + + Data and metadata + FHIR-oriented data modeling, metadata handling, and integration patterns. + Data + + + Project management + Project structure, customization, publishing, roles, and admin workflows. + Operations + +
+
diff --git a/docs/index.md b/docs/index.md index 1251523..4f0e91a 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,130 +1,102 @@ --- template: home.html -body_class: home +body_class: home business-home hide: - navigation - toc - header --- - - - -
-

CALYPR Platform

-

- A scalable, hybrid cloud infrastructure designed for the demands of modern genomics research. - Built on open-source standards, CALYPR provides GA4GH-compliant tools for seamless data integration, analysis, and biological insights. Based on the Gen3 Data Commons architecture, CALYPR empowers analysts to manage large-scale genomic datasets and integrate data to build new predictive models. -

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- 🚀 Get Started Quickly -
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- - -
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Built on Open Standards

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TES
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Task Execution Service. A GA4GH standard for distributed task execution to enable federated computing.
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DRS
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Data Reference System. A GA4GH standard for data discovery and access.
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FHIR
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Healthcare Interoperability. Exchanging patient health information.
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JSON Hyper-Schema
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JSON-Schema + Graph data. Represent complex and high quality data.
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+
+

Research data infrastructure

+

Govern biomedical data without slowing down research.

+

+ CALYPR helps research organizations control data access, run reproducible analysis, connect metadata, and prepare model-ready assets across cloud, on-prem, and federated environments. +

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