discussion/information-architecture

[bwalsh]

CALYPR Information Architecture Reviewer's Guide

Purpose of This Guide

This guide is intended to help reviewers evaluate the proposed documentation and website structure for the CALYPR platform.

The proposed approach reorganizes the site around:

1. Solutions
2. Personas
3. Use Cases
4. Tool Launch Pages
5. Standardized Tool Documentation

The objective is to help sophisticated researchers, bioinformaticians, engineers, and standards architects quickly understand:

• What problems CALYPR solves
• Which capabilities are relevant to them
• How those capabilities map to specific tools
• Where to begin using each tool

---

What Is Information Architecture?

Information Architecture (IA) is the practice of organizing, labeling, and structuring content so users can find information efficiently and understand how concepts relate to one another.

In practical terms, Information Architecture answers four questions:

1. What information exists?
2. How is it grouped?
3. How do users navigate between groups?
4. How do users know where they are and where to go next?

A well-designed Information Architecture:

• Reflects how users think about their goals
• Reduces cognitive load
• Makes navigation intuitive
• Supports discovery and reuse
• Scales as content grows

For CALYPR, Information Architecture determines how users move from high-level problems such as "Manage Data" to concrete documentation for tools such as Syphon or git-drs.

---

Why This Matters for CALYPR

CALYPR contains multiple powerful tools implementing open standards such as:

• GA4GH DRS
• GA4GH TES / WES
• GA4GH Passports
• FHIR
• GraphQL

Today, documentation is largely organized by tool repository.

This is useful for developers who already know which tool they need, but less effective for:

• Researchers trying to solve a scientific problem
• Bioinformaticians looking for workflow integrations
• Architects evaluating standards compliance
• Platform engineers comparing deployment options

The proposed Information Architecture starts with user goals rather than product names.

---

Design Principle

Lead with outcomes, not tools.

Users typically begin with questions such as:

• How do I register and share research data?
• How do I run workflows across institutions?
• How do I integrate clinical and omics data?
• How do I benchmark machine learning models?

The site should answer these questions first and then introduce the relevant tools.

---

Proposed Navigation Hierarchy

Home
├── Solutions
│   ├── Manage Data
│   ├── Manage Compute
│   ├── Integrate Data
│   └── Manage Models
├── Personas
│   ├── Researchers and Bioinformaticians
│   ├── Workflow Engineers
│   ├── Platform Engineers
│   ├── Data Stewards
│   └── Standards and Architecture Leads
├── Use Cases
│   ├── Register and Share Research Data
│   ├── Run Portable Workflows
│   ├── Integrate Biomedical Data
│   └── Benchmark Models Across Institutions
└── Tools
    ├── Syphon
    ├── git-drs
    ├── Funnel
    ├── GRIP
    ├── data-client
    ├── Sifter
    └── Forge

---

How the Structure Works

Solutions

Solutions are the highest-level categories and describe major problem domains.

Examples:

• Manage Data
• Manage Compute
• Integrate Data
• Manage Models

Personas

Persona pages help users identify where to start based on their professional role.

Examples:

• Researcher / Bioinformatician
• Workflow Engineer
• Platform Engineer
• Data Steward
• Standards Architect

Use Cases

Use cases describe concrete workflows and link to the tools that support them.

Examples:

• Register and Share Research Data
• Run Portable Workflows
• Integrate Biomedical Data
• Benchmark Models Across Institutions

Tool Launch Pages

Tool launch pages provide concise product introductions and route users into standardized technical documentation.

---

What Is a Tool Launch Page?

A Tool Launch Page is the entry point into a specific product.

It is not intended to contain all documentation.

Instead, it answers:

1. What does this tool do?
2. Why does it matter?
3. Who uses it?
4. What use cases does it support?
5. Which standards does it implement?
6. Where should I start?

The page then links to a standard documentation table of contents.

---

Standardized Tool Documentation

Each tool should expose a consistent documentation structure:

1. Overview
2. Quickstart
3. Installation
4. Configuration
5. Commands / API
6. Integrations
7. Examples
8. Troubleshooting
9. Developer Documentation

This consistency reduces friction and makes every tool feel part of a coherent platform.

---

Example User Journey

Researcher Wants to Share Data

1. Visits Home page
2. Selects Manage Data
3. Reads Register and Share Research Data use case
4. Launches Syphon or git-drs
5. Opens Quickstart
6. Successfully registers and accesses data

Platform Engineer Evaluating Infrastructure

1. Visits Home page
2. Selects Platform Engineer persona
3. Reviews Deploy Standards-Based Infrastructure use case
4. Launches Syphon or Funnel
5. Opens Installation and Configuration guides

---

Benefits of This Approach

Better First Impressions

The site communicates value before exposing technical detail.

Faster User Onboarding

Users reach relevant documentation with fewer decisions.

Clearer Product Positioning

Tools are presented as both standalone components and parts of a unified platform.

Improved Standards Visibility

Each page highlights implemented open standards.

Consistent Documentation Experience

All tools share predictable structure and navigation.

Scalable Architecture

New tools, use cases, and solutions can be added without restructuring the site.

---

Relationship to Marketing and UX

This approach combines:

• Information Architecture
• User Experience Design
• Product Marketing
• Technical Documentation

Marketing communicates why CALYPR matters.

UX ensures users can find the right information quickly.

Documentation provides the technical depth required by advanced audiences.

---

Review Questions

Strategic Fit

• Does the structure accurately reflect CALYPR's capabilities?
• Does it present CALYPR as a coherent platform?
• Does it balance modular tools and integrated solutions?

Audience Fit

• Will researchers understand where to begin?
• Will engineers find technical depth quickly?
• Will standards groups see explicit compliance and interoperability?

Navigation Fit

• Is the Solutions → Personas → Use Cases → Tools flow intuitive?
• Are category names clear and concise?

Documentation Fit

• Does the standardized table of contents make sense?
• Are any sections missing or unnecessary?

Messaging Fit

• Is the tone precise and sophisticated?
• Does the site avoid unnecessary marketing hype?

---

Recommended Review Method

1. Read the homepage and Solutions sections.
2. Follow one persona relevant to your role.
3. Select a use case you care about.
4. Launch a tool page.
5. Open the Quickstart.
6. Assess whether the path feels natural and efficient.

---

Success Criteria

The Information Architecture will be successful if users can answer:

• What does CALYPR do?
• Which solution area applies to me?
• Which tools are relevant?
• How do I get started quickly?
• How does this align with open standards?

---

Key Positioning Statement

CALYPR provides modular tools and an integrated platform for managing biomedical data, compute, integration, and model workflows using open standards.

---

Closing Perspective

The proposed Information Architecture is designed to present CALYPR in a way that is:

• Technically rigorous
• Strategically coherent
• Easy to navigate
• Scalable over time
• Credible to sophisticated technical audiences

By organizing content around solutions, personas, and use cases, CALYPR can communicate both immediate practical value and a broader architectural vision.

[bwalsh]

---

title: "CALYPR Information Architecture"
description: "Front-matter-driven site architecture organized by solutions, personas, use cases, and tool launch pages."
status: "draft"
audience:

• sophisticated researchers
• bioinformaticians
• platform engineers
• academic consortia
• industry partners
• standards groups
  tone: "simple, sophisticated, standards-aware"

---

CALYPR Information Architecture

CALYPR should present itself as a standards-based biomedical data platform: modular enough for engineers to adopt individual tools, integrated enough for institutions and consortia to deploy a coherent research infrastructure.

The site should flow from solutions to personas to use cases, and finally into tool launch pages that provide consistent, practical documentation.

---

1. Top-Level Site Flow

Home
├── Solutions
│   ├── Manage Data
│   ├── Manage Compute
│   ├── Integrate Data
│   └── Manage Models
├── Personas
│   ├── Researcher / Bioinformatician
│   ├── Workflow Engineer
│   ├── Platform Engineer
│   ├── Data Steward
│   ├── Standards / Architecture Lead
│   └── Security / Compliance Reviewer
├── Use Cases
│   ├── Register and share research data
│   ├── Run portable workflows
│   ├── Integrate biomedical datasets
│   ├── Query graph-linked data
│   ├── Benchmark models across institutions
│   └── Deploy standards-based infrastructure
└── Tools
    ├── Syphon
    ├── git-drs
    ├── Funnel
    ├── GRIP
    ├── data-client
    ├── Sifter
    └── Forge

---

2. Front Matter Model

Each page should declare how it fits into the site. This enables generated navigation, cross-links, cards, and persona-specific landing pages.

Common Front Matter

---
title: "Page Title"
summary: "One-sentence summary for cards, lists, and search."
category: "solution | persona | use_case | tool"
solution:
  - manage-data
persona:
  - bioinformatician
  - platform-engineer
use_cases:
  - register-data
  - run-workflows
tools:
  - syphon
  - git-drs
standards:
  - GA4GH DRS
  - TES
  - WES
  - FHIR
status: "draft | stable | experimental"
priority: 1
---

---

3. Solutions

Solutions are the highest-level product categories. They should describe outcomes, not implementation details.

3.1 Manage Data

---
title: "Manage Data"
category: "solution"
slug: "manage-data"
summary: "Register, version, locate, and share biomedical data using open standards."
personas:
  - bioinformatician
  - data-steward
  - platform-engineer
  - standards-architect
use_cases:
  - register-data
  - version-large-files
  - resolve-drs-objects
  - govern-controlled-access-data
tools:
  - syphon
  - git-drs
  - data-client
standards:
  - GA4GH DRS
  - GA4GH Passports
status: "draft"
---

Page Intent

Help users understand how CALYPR supports durable data registration, access, metadata, version-aware workflows, and standards-based interoperability.

Primary Message

CALYPR helps teams manage research data as addressable, governed, reusable digital objects.

---

3.2 Manage Compute

---
title: "Manage Compute"
category: "solution"
slug: "manage-compute"
summary: "Run portable workflows and tasks across local, cloud, and federated environments."
personas:
  - workflow-engineer
  - bioinformatician
  - platform-engineer
use_cases:
  - run-portable-workflows
  - execute-federated-compute
  - connect-data-to-analysis
tools:
  - funnel
  - git-drs
  - data-client
standards:
  - GA4GH TES
  - GA4GH WES
status: "draft"
---

Primary Message

CALYPR supports reproducible biomedical compute by connecting workflow engines, data access, and task execution infrastructure.

---

3.3 Integrate Data

---
title: "Integrate Data"
category: "solution"
slug: "integrate-data"
summary: "Connect heterogeneous biomedical datasets into queryable, graph-linked structures."
personas:
  - analyst
  - data-engineer
  - standards-architect
  - bioinformatician
use_cases:
  - integrate-clinical-and-omics-data
  - query-linked-data
  - transform-tabular-data
  - expose-graph-apis
tools:
  - grip
  - sifter
  - forge
standards:
  - FHIR
  - GraphQL
status: "draft"
---

Primary Message

CALYPR helps transform fragmented biomedical data into linked, queryable, analysis-ready structures.

---

3.4 Manage Models

---
title: "Manage Models"
category: "solution"
slug: "manage-models"
summary: "Package, share, benchmark, and govern portable biomedical models across institutions."
personas:
  - researcher
  - bioinformatician
  - workflow-engineer
  - platform-engineer
  - standards-architect
  - clinical-informatics-lead
use_cases:
  - package-containerized-models
  - register-model-artifacts
  - benchmark-models-federated
  - generate-synthetic-data
  - curate-model-registries
  - validate-clinical-algorithms
  - deploy-regulated-models
tools:
  - funnel
  - syphon
  - data-client
  - sifter
standards:
  - OCI Containers
  - GA4GH DRS
  - GA4GH TES
  - GA4GH WES
status: "concept"
---

Manage Models

CALYPR supports the emerging discipline of model management for biomedical research and clinical informatics.

The goal is to treat predictive models as governed, portable, and reproducible research assets that can be packaged, registered, benchmarked, and deployed across institutions.

Why it matters

Biomedical organizations increasingly rely on machine learning and statistical models to:

• Predict disease risk
• Interpret genomic variation
• Classify medical images
• Generate synthetic datasets
• Support clinical decision-making

These models are valuable scientific assets. Like data and workflows, they require standardized packaging, metadata, governance, benchmarking, and reproducible execution.

Strategic Vision

The CALYPR platform is designed to support a comprehensive model lifecycle, including:

Portable Containerized Models

Models are packaged with all runtime dependencies using container technologies, enabling reproducible execution across local, cloud, and federated environments.

Federated Benchmarking Across Hospitals

Models can be dispatched to participating institutions, evaluated against local benchmark datasets, and scored without requiring raw data to leave institutional boundaries.

Synthetic Data Generation

Generative models can create privacy-preserving synthetic datasets for software testing, workflow development, and preliminary analysis.

Model Registries ("Model Zoos")

Curated repositories provide versioned storage, metadata, provenance, and discoverability for reusable research and production models.

Regulated Clinical Algorithms

The platform can support validated and potentially regulated algorithms that require strict provenance, reproducibility, and continuous performance monitoring.

Common Use Cases

• Submit containerized models to research challenges such as DREAM.
• Benchmark algorithms across multiple hospitals.
• Compare competing models using common evaluation datasets.
• Publish reusable model artifacts with metadata and provenance.
• Generate synthetic cohorts for development and testing.
• Monitor model drift and revalidate clinical algorithms over time.

Conceptual Workflow

Model code and weights
→ Container packaging
→ Model registration
→ Metadata and provenance capture
→ Federated execution and benchmarking
→ Performance reporting
→ Approval and publication
→ Operational deployment
→ Ongoing monitoring and revalidation

How it fits into CALYPR

• Syphon stores model artifacts, metadata, and benchmark outputs.
• Funnel executes containerized models and orchestrates benchmarking workflows.
• data-client automates registration and retrieval.
• Sifter can support synthetic data generation and transformation workflows.

Together, these tools create a foundation for reproducible, portable, and governed model lifecycle management.

Target Audiences

• Researchers and data scientists
• Bioinformaticians
• Workflow engineers
• Platform engineers
• Clinical informatics leaders
• Standards architects
• Research consortia and challenge organizers

Relationship to Research Challenges

This capability aligns naturally with initiatives such as:

• DREAM Challenges
• Federated learning consortia
• Multi-institution benchmarking studies
• Translational and clinical research programs

Participants can package models as containers, submit them for standardized execution, and receive comparable benchmark results across institutions.

Long-Term Vision

The long-term vision is to make predictive models as portable and governable as datasets and workflows.

Organizations should be able to:

• Discover validated models
• Execute them reproducibly
• Benchmark them against local data
• Compare results across institutions
• Govern their lifecycle
• Deploy them confidently in research and clinical environments

Positioning Statement

Manage Models extends CALYPR's standards-based platform to the full lifecycle of biomedical models—from research prototypes to federated benchmarking and clinically governed deployment.

4. Personas

Persona pages should make users feel recognized without over-segmenting the site. They should answer: “Where do I start?”

4.1 Researcher / Bioinformatician

---
title: "For Researchers and Bioinformaticians"
category: "persona"
slug: "bioinformatician"
summary: "Find data, run analyses, and integrate CALYPR tools into scientific workflows."
solutions:
  - manage-data
  - manage-compute
  - integrate-data
use_cases:
  - register-data
  - run-portable-workflows
  - query-linked-data
tools:
  - git-drs
  - syphon
  - funnel
  - grip
---

Needs

• Find and access data reliably.
• Move large files into workflows.
• Run reproducible analyses.
• Avoid infrastructure complexity.

Entry Points

• Register data with Syphon.
• Track large files with git-drs.
• Run tasks with Funnel.
• Query integrated datasets with GRIP.

---

4.2 Workflow Engineer

---
title: "For Workflow Engineers"
category: "persona"
slug: "workflow-engineer"
summary: "Connect data access, task execution, and workflow systems."
solutions:
  - manage-compute
  - manage-data
use_cases:
  - run-portable-workflows
  - connect-drs-to-workflows
  - execute-federated-compute
tools:
  - funnel
  - git-drs
  - syphon
  - data-client
---

Needs

• Portable execution.
• Clear resource configuration.
• Data access by URI or DRS object.
• Compatibility with Nextflow, Snakemake, Cromwell, or custom systems.

---

4.3 Platform Engineer

---
title: "For Platform Engineers"
category: "persona"
slug: "platform-engineer"
summary: "Deploy, operate, secure, and scale CALYPR services."
solutions:
  - manage-data
  - manage-compute
  - integrate-data
use_cases:
  - deploy-standards-based-infrastructure
  - operate-controlled-access-services
  - monitor-platform-health
tools:
  - syphon
  - funnel
  - grip
---

Needs

• Deployment guides.
• Helm or Kubernetes patterns.
• Monitoring and logging.
• Authentication and authorization.
• Upgrade and troubleshooting guidance.

---

4.4 Data Steward

---
title: "For Data Stewards"
category: "persona"
slug: "data-steward"
summary: "Register, curate, govern, and share project data."
solutions:
  - manage-data
  - integrate-data
use_cases:
  - register-data
  - attach-metadata
  - govern-controlled-access-data
tools:
  - syphon
  - data-client
  - git-drs
---

---

4.5 Standards / Architecture Lead

---
title: "For Standards and Architecture Leads"
category: "persona"
slug: "standards-architect"
summary: "Understand how CALYPR implements and composes open biomedical standards."
solutions:
  - manage-data
  - manage-compute
  - integrate-data
use_cases:
  - evaluate-standards-compliance
  - compose-ga4gh-services
  - design-federated-architecture
tools:
  - syphon
  - funnel
  - grip
standards:
  - GA4GH DRS
  - GA4GH TES
  - GA4GH WES
  - GA4GH Passports
  - FHIR
---

---

5. Use Cases

Use cases bridge high-level solutions and tool documentation. Each use case should explain the workflow, then link users to the relevant tools.

5.1 Register and Share Research Data

---
title: "Register and Share Research Data"
category: "use_case"
slug: "register-data"
summary: "Create durable, standards-based records for research files and datasets."
solution: "manage-data"
personas:
  - bioinformatician
  - data-steward
  - platform-engineer
tools:
  - syphon
  - git-drs
  - data-client
standards:
  - GA4GH DRS
---

Flow

Research file
→ register object
→ attach metadata
→ resolve by DRS ID
→ share with workflows or collaborators

Launch Tools

• Syphon: Register and resolve data objects.
• git-drs: Track data objects alongside code.
• data-client: Script registration and access workflows.

---

5.2 Run Portable Workflows

---
title: "Run Portable Workflows"
category: "use_case"
slug: "run-portable-workflows"
summary: "Execute reproducible computational tasks across local, cloud, or federated environments."
solution: "manage-compute"
personas:
  - bioinformatician
  - workflow-engineer
  - platform-engineer
tools:
  - funnel
  - git-drs
  - syphon
standards:
  - GA4GH TES
  - GA4GH WES
---

Flow

Workflow definition
→ task execution request
→ input resolution
→ container execution
→ output registration

---

5.3 Integrate Biomedical Data

---
title: "Integrate Biomedical Data"
category: "use_case"
slug: "integrate-biomedical-data"
summary: "Connect clinical, omics, and project metadata into queryable structures."
solution: "integrate-data"
personas:
  - researcher
  - analyst
  - data-engineer
  - standards-architect
tools:
  - grip
  - sifter
  - forge
standards:
  - FHIR
  - GraphQL
---

Flow

Source datasets
→ mapping and transformation
→ graph representation
→ query and export
→ downstream analysis

---

5.4 Benchmark Models Across Institutions

---
title: "Benchmark Models Across Institutions"
category: "use_case"
slug: "benchmark-models"
summary: "Package and evaluate models across independent datasets and institutions."
solution: "manage-models"
personas:
  - researcher
  - workflow-engineer
  - platform-engineer
tools:
  - funnel
  - syphon
  - data-client
status: "concept"
---

Flow

Containerized model
→ controlled execution environment
→ institutional benchmark dataset
→ performance report
→ model comparison

---

6. Tool Launch Pages

Tool pages are not the top of the funnel. They are launch points for users who already know which tool they need, or who arrived from a solution, persona, or use-case page.

Each tool launch page should include:

1. What this tool does
2. Who it is for
3. When to use it
4. How it fits into CALYPR
5. Standards and integrations
6. Links into the standardized documentation table of contents

---

6.1 Standard Tool Front Matter

---
title: "Tool Name"
category: "tool"
slug: "tool-name"
summary: "Short description of the tool."
solution:
  - manage-data
personas:
  - bioinformatician
  - platform-engineer
use_cases:
  - register-data
standards:
  - GA4GH DRS
repository: "https://github.com/calypr/tool-name"
status: "stable"
nav:
  - Overview: docs/index.md
  - Quickstart: docs/quickstart.md
  - Installation: docs/installation.md
  - Configuration: docs/configuration.md
  - Commands/API: docs/commands.md
  - Integrations: docs/integrations.md
  - Examples: docs/examples.md
  - Troubleshooting: docs/troubleshooting.md
  - Developer: docs/developer/
---

---

6.2 Standard Tool Launch Page Body

# Tool Name

One clear sentence describing what the tool does.

## Why it matters

Explain the problem this tool solves in plain, precise language.

## Who uses it

- Researchers and bioinformaticians
- Workflow engineers
- Platform engineers
- Data stewards

## Common use cases

- Use case one
- Use case two
- Use case three

## How it fits into CALYPR

Explain whether the tool can be used independently, as part of the full platform, or both.

## Standards and integrations

- GA4GH DRS
- GA4GH TES
- FHIR
- GraphQL

## Start here

- [Overview](docs/index.md)
- [Quickstart](docs/quickstart.md)
- [Installation](docs/installation.md)
- [Configuration](docs/configuration.md)
- [Commands/API](docs/commands.md)
- [Integrations](docs/integrations.md)
- [Examples](docs/examples.md)
- [Troubleshooting](docs/troubleshooting.md)
- [Developer Documentation](docs/developer/)

---

7. Example Tool Launch Pages

7.1 Syphon

---
title: "Syphon"
category: "tool"
slug: "syphon"
summary: "A standards-based data repository service for registering, resolving, and governing biomedical data objects."
solution:
  - manage-data
personas:
  - data-steward
  - platform-engineer
  - bioinformatician
  - standards-architect
use_cases:
  - register-data
  - resolve-drs-objects
  - govern-controlled-access-data
standards:
  - GA4GH DRS
  - GA4GH Passports
status: "draft"
repository: "https://github.com/calypr/syphon"
---

Syphon

Syphon is a data repository service for registering, resolving, and governing biomedical data objects using GA4GH DRS patterns.

Why it matters

Biomedical data needs stable identifiers, resolvable access paths, metadata, and access-aware governance. Syphon provides the repository layer for those workflows.

Who uses it

• Data stewards registering project data
• Platform engineers operating data services
• Bioinformaticians resolving data into workflows
• Standards architects evaluating DRS-based infrastructure

Common use cases

• Register files and datasets as durable data objects
• Resolve DRS identifiers to access methods
• Attach metadata and provenance
• Integrate data access with workflow systems

How it fits into CALYPR

Syphon can run as an independent DRS-oriented service or as part of the integrated CALYPR platform.

Start here

• Overview
• Quickstart
• Installation
• Configuration
• Commands/API
• Integrations
• Examples
• Troubleshooting
• Developer Documentation

---

7.2 git-drs

---
title: "git-drs"
category: "tool"
slug: "git-drs"
summary: "A Git-integrated client for tracking large research data objects using DRS-aware workflows."
solution:
  - manage-data
personas:
  - bioinformatician
  - workflow-engineer
  - data-steward
  - developer
use_cases:
  - version-large-files
  - register-data
  - connect-drs-to-workflows
standards:
  - GA4GH DRS
status: "draft"
repository: "https://github.com/calypr/git-drs"
---

git-drs

git-drs helps researchers track large data objects alongside code without forcing large files directly into Git history.

Why it matters

Scientific workflows often combine code, configuration, and large datasets. git-drs keeps those relationships explicit while allowing the data itself to live in managed object storage or a DRS-compatible service.

Who uses it

• Bioinformaticians versioning analysis inputs
• Workflow engineers connecting repositories to execution environments
• Data stewards coordinating project data
• Developers building DRS-aware tooling

Common use cases

• Track large files as data objects
• Fetch inputs on compute nodes
• Pair code revisions with data revisions
• Register external data references

How it fits into CALYPR

git-drs complements Syphon by giving users a Git-native way to work with DRS-managed data.

Start here

• Overview
• Quickstart
• Installation
• Configuration
• Commands/API
• Integrations
• Examples
• Troubleshooting
• Developer Documentation

---

7.3 Funnel

---
title: "Funnel"
category: "tool"
slug: "funnel"
summary: "A task execution service for portable biomedical compute."
solution:
  - manage-compute
personas:
  - workflow-engineer
  - bioinformatician
  - platform-engineer
use_cases:
  - run-portable-workflows
  - execute-federated-compute
  - connect-data-to-analysis
standards:
  - GA4GH TES
status: "draft"
repository: "https://github.com/calypr/funnel"
---

Funnel

Funnel provides a standards-aligned execution layer for running portable computational tasks.

Why it matters

Biomedical workflows often need to run across heterogeneous infrastructure. Funnel helps separate the task definition from the execution environment.

Who uses it

• Workflow engineers
• Bioinformaticians
• Platform engineers
• Federated compute operators

Common use cases

• Execute workflow tasks
• Connect task execution to data access
• Support federated compute
• Run containerized analysis workloads

How it fits into CALYPR

Funnel is the compute execution layer of the CALYPR platform and can also be adopted independently.

Start here

• Overview
• Quickstart
• Installation
• Configuration
• Commands/API
• Integrations
• Examples
• Troubleshooting
• Developer Documentation

---

7.4 GRIP

---
title: "GRIP"
category: "tool"
slug: "grip"
summary: "A graph-oriented platform for querying integrated biomedical data."
solution:
  - integrate-data
personas:
  - analyst
  - bioinformatician
  - data-engineer
  - standards-architect
use_cases:
  - integrate-biomedical-data
  - query-linked-data
  - expose-graph-apis
standards:
  - GraphQL
  - FHIR
status: "draft"
repository: "https://github.com/calypr/grip"
---

GRIP

GRIP helps teams represent and query linked biomedical data using graph-oriented patterns.

Why it matters

Biomedical data often spans studies, samples, files, phenotypes, clinical records, and derived results. GRIP helps expose those relationships for discovery and analysis.

Who uses it

• Analysts exploring integrated datasets
• Bioinformaticians linking files to metadata
• Data engineers building graph-backed APIs
• Standards architects evaluating graph and FHIR patterns

Common use cases

• Query linked metadata
• Integrate clinical and omics data
• Expose graph APIs
• Support exploratory analysis

How it fits into CALYPR

GRIP supports CALYPR’s integrated-data solution area and can serve as a graph interface for platform data.

Start here

• Overview
• Quickstart
• Installation
• Configuration
• Commands/API
• Integrations
• Examples
• Troubleshooting
• Developer Documentation

---

8. Recommended MkDocs Navigation

nav:
  - Home: index.md
  - Solutions:
      - Overview: solutions/index.md
      - Manage Data: solutions/manage-data.md
      - Manage Compute: solutions/manage-compute.md
      - Integrate Data: solutions/integrate-data.md
      - Manage Models: solutions/manage-models.md
  - Personas:
      - Overview: personas/index.md
      - Researchers and Bioinformaticians: personas/bioinformaticians.md
      - Workflow Engineers: personas/workflow-engineers.md
      - Platform Engineers: personas/platform-engineers.md
      - Data Stewards: personas/data-stewards.md
      - Standards and Architecture Leads: personas/standards-architects.md
  - Use Cases:
      - Overview: use-cases/index.md
      - Register and Share Research Data: use-cases/register-data.md
      - Run Portable Workflows: use-cases/run-portable-workflows.md
      - Integrate Biomedical Data: use-cases/integrate-biomedical-data.md
      - Benchmark Models Across Institutions: use-cases/benchmark-models.md
  - Tools:
      - Overview: tools/index.md
      - Syphon: tools/syphon/index.md
      - git-drs: tools/git-drs/index.md
      - Funnel: tools/funnel/index.md
      - GRIP: tools/grip/index.md
      - data-client: tools/data-client/index.md
      - Sifter: tools/sifter/index.md
      - Forge: tools/forge/index.md

---

9. UX Principles

Lead with outcomes

Do not start with tools. Start with what users are trying to accomplish.

Let users self-identify

Avoid overly rigid persona labels. Use subtle phrasing: “If you need to…”, “Start here when…”

Keep the tone precise

The audience is technical and sophisticated. Avoid hype. Prefer clear claims about standards, interoperability, and workflows.

Make tools discoverable but not dominant

Tools should be reachable from every relevant solution, persona, and use-case page, but the homepage should emphasize platform value.

Support both adoption paths

Every tool page should make clear that the tool can be used independently or as part of the integrated platform, where applicable.

---

10. Recommended Homepage Copy

Build Biomedical Data Platforms on Open Standards

CALYPR provides modular tools and an integrated platform for managing biomedical data, compute, integration, and model workflows.

Use individual components where they fit. Deploy the full platform when you need a coherent research infrastructure.

Solution Areas

• Manage Data — Register, version, govern, and resolve research data objects.
• Manage Compute — Run portable workflows across local, cloud, and federated environments.
• Integrate Data — Link clinical, omics, and project metadata into queryable structures.
• Manage Models — Package, share, and benchmark portable biomedical models.

Built for

• Researchers and bioinformaticians
• Workflow engineers
• Platform engineers
• Data stewards
• Academic and industry consortia
• Standards groups and infrastructure architects

Built on open standards

• GA4GH DRS
• GA4GH TES / WES
• GA4GH Passports
• FHIR
• GraphQL

---

11. Implementation Notes

A practical implementation can begin with:

1. Create solutions/, personas/, and use-cases/ sections.
2. Add front matter to all pages.
3. Create tool launch pages using the standard template.
4. Add generated card grids based on front matter.
5. Prioritize launch pages for Syphon, git-drs, Funnel, and GRIP.
6. Add missing standard documentation pages for priority tools.
7. Run documentation audit in CI.

---

12. Priority Rollout

Phase 1

• Homepage rewrite
• Solutions overview
• Persona overview
• Use-case overview
• Tool launch pages for Syphon, git-drs, Funnel, and GRIP

Phase 2

• Standardized documentation pages for priority tools
• TL;DR quickstarts
• Bioinformatician examples
• MkDocs navigation updates

Phase 3

• Generated cross-linking from front matter
• Documentation completeness audit in CI
• Standards compliance pages
• Case studies and institutional adoption pages

[bwalsh]

calypr_visual_assets.zip

CALYPR Visual Asset Pack

Original SVG assets for the CALYPR information architecture.

Contents

• solutions/ — one image per solution area
• personas/ — one image per persona
• manifest.json — metadata and suggested license notes

Design Intent

These assets are designed to fit the current CALYPR documentation style:

• clean technical cards
• light background
• restrained biomedical/platform iconography
• teal, cyan, blue, violet, amber, and slate palette
• suitable for hero sections, cards, and landing pages

Suggested Usage

Use solution assets on solutions/*.md landing pages and persona assets on personas/*.md.

Example:

![Manage Data](../assets/solutions/manage-data.svg)

Licensing

These are original generated assets created for CALYPR. Suggested licensing: CC BY 4.0, Apache-2.0, or the same license used for CALYPR documentation.

Solutions

Personas