Doc reorg summary and listing (#4166)

Co-authored-by: Dr. Ernie Prabhakar <[email protected]>
Co-authored-by: Dr. Ernie Prabhakar <[email protected]>

docs/README.md

@@ -7,6 +7,30 @@ data integrity at scale.
 
 ---
 
+## How to Get Started
+
+Quilt consists of three main elements:
+
+- [Quilt Platform](#quilt-platform-overview) which is a cloud platform for
+  interacting with, visualizing, searching and querying Quilt Packages, which is
+  hosted in an organization's AWS Account.
+- [Quilt Python SDK](#quilt-python-sdk) which provides the ability to create,
+  push, install and delete Quilt Packages.
+- [Quilt Ecosystem](#quilt-ecosystem-and-integrations) which provide extension
+  of the core Quilt Capabilities to enable typical elements of life sciences
+  workflows, such as incorporating orchestration data, and connecting packages
+  to Electronic Lab Notebooks.
+
+To dive deeper into the capabilities of Quilt, start with our [Quick Start
+Guide](Quickstart.md) or explore the [Installation
+Instructions](Installation.md) for setting up your environment.
+
+If you have any questions or need help, join our [Slack
+community](https://slack.quiltdata.com/) or submit a support request to
+<[email protected]>.
+
+---
+
 ## Navigating the Documentation
 
 The Quilt documentation is structured to guide users through different layers of
@@ -24,8 +48,7 @@ capabilities like embeddable previews and metadata collection.
 **Core Sections:**
 
 - [Architecture](Architecture.md) - Learn how Quilt is architected.
-- [Mental Model](MentalModel.md) - Understand the guiding principles behind
-  Quilt.
+- [Mental Model](MentalModel.md) - Understand the guiding principles behind Quilt.
 - [Metadata Management](Catalog/Metadata.md) - Manage metadata at scale.
 
 For users of the Quilt Platform (often referred to as the Catalog):
@@ -40,11 +63,9 @@ For users of the Quilt Platform (often referred to as the Catalog):
 
 For administrators managing Quilt deployments:
 
-- [Admin Settings UI](Catalog/Admin.md) - Control platform settings and user
-  access.
+- [Admin Settings UI](Catalog/Admin.md) - Control platform settings and user access.
 - [Catalog Configuration](Catalog/Preferences.md) - Set platform preferences.
-- [Cross-Account Access](CrossAccount.md) - Manage multi-account access to S3
-  data.
+- [Cross-Account Access](CrossAccount.md) - Manage multi-account access to S3 data.
 
 ### Quilt Python SDK
 
@@ -58,18 +79,16 @@ flexibility needed for deeper integrations.
   managing data packages.
 - [Editing and Uploading Packages](walkthrough/editing-a-package.md) - Learn how
   to version, edit, and share data.
-- [API Reference](api-reference/api.md) - Detailed API documentation for
-  developers.
+- [API Reference](api-reference/api.md) - Detailed API documentation for developers.
 
 ### Quilt Ecosystem and Integrations
 
 The **Quilt Ecosystem** extends the platform with integrations and plugins to
 fit your workflow. Whether you're managing scientific data or automating
 packaging tasks, Quilt can be tailored to your needs with these tools:
 
-- [Benchling
-  Packager](https://open.quiltdata.com/b/quilt-example/packages/examples/benchling-packager)
-  - Package biological data from Benchling.
+- [Benchling Packager](examples/benchling.md) - Package electronic lab notebooks
+  from Benchling.
 - [Nextflow Plugin](examples/nextflow.md) - Integrate with Nextflow pipelines
   for bioinformatics.
 
@@ -89,18 +108,7 @@ administrator, Quilt helps streamline your data management workflows.
   better insights.
 - **Discover**: Use metadata and search tools to explore data relationships
   across projects.
-- **Model**: Version and manage large data sets that don't fit traditional git
-  repositories.
+- **Model**: Version and manage large data sets that don't fit traditional git repositories.
 - **Decide**: Empower your team with auditable data for better decision-making.
 
 ---
-
-## How to Get Started
-
-To dive deeper into the capabilities of Quilt, start with our [Quick Start
-Guide](Quickstart.md) or explore the [Installation
-Instructions](Installation.md) for setting up your environment.
-
-If you have any questions or need help, join our [Slack
-community](https://slack.quiltdata.com/) or visit our full [documentation
-site](https://docs.quiltdata.com/).

docs/SUMMARY.md

@@ -38,13 +38,7 @@
   * [GxP for Security & Compliance](advanced-features/good-practice.md)
   * [Organizing S3 Buckets](advanced-features/s3-bucket-organization.md)
 
-## Quilt Ecosystem Integrations
-
-* [Benchling Packager](https://open.quiltdata.com/b/quilt-example/packages/examples/benchling-packager)
-* [Event-Driven Packaging](advanced-features/event-driven-packaging.md)
-* [Nextflow Plugin](examples/nextflow.md)
-
-## Quilt Python SDK Developers
+## Quilt Python SDK
 
 * [Installation](Installation.md)
 * [Quick Start](Quickstart.md)
@@ -73,3 +67,9 @@
   * [Contributing](CONTRIBUTING.md)
   * [Frequently Asked Questions](FAQ.md)
   * [Troubleshooting](Troubleshooting.md)
+
+## Quilt Ecosystem Integrations
+
+* [Benchling Packager](examples/benchling.md)
+* [Event-Driven Packaging](advanced-features/event-driven-packaging.md)
+* [Nextflow Plugin](examples/nextflow.md)

docs/examples/benchling.md

@@ -0,0 +1,32 @@
+<!-- markdownlint-disable-next-line first-line-h1 -->
+The Benchling Packager is a lambda you can deploy in your own AWS private cloud
+to process [Benchling](https://benchling.com/) events in order to create (and
+link back, if possible) a dedicated [Quilt](https://quiltdata.com/) package for
+every Benchling notebook.
+
+The CloudFormation template is available as a package on
+[open.quiltdata.com](https://open.quiltdata.com/b/quilt-example/packages/examples/benchling-packager).
+
+## Prerequisites
+
+In order to install the benchling packager, you will need to know, and have
+administrative access to:
+
+- Your Benchling tenant domain (e.g., `<YOUR_TENANT>` from
+  `<YOUR_TENANT>.benchling.com`), for ßconfiguring event subscriptions and
+  metadata schemas.
+- The AWS Account ID (e.g. 12345689123) and AWS Region (e.g., us-west-2) used by
+  your Quilt stack, for configuring the CloudFormation stack and lambdas.
+
+## Installation
+
+Go to the [Benchling Packager
+package](https://open.quiltdata.com/b/quilt-example/packages/examples/benchling-packager)
+on open.quiltdata.com and follow the instructions in the README.
+
+## References
+
+- [AWS CloudFormation templates](https://aws.amazon.com/cloudformation/resources/templates/)
+- [AWS Lambda functions](https://aws.amazon.com/lambda/)
+- [Benchling EventBridge events](https://docs.benchling.com/docs/events-getting-started#event-types)
+- [Benchling Schemas](https://help.benchling.com/hc/en-us/articles/9684227216781)