simplify

Author: nsheff

Diff for: docs/pephub/user/getting-started.md

@@ -7,42 +7,38 @@ Just like GitHub allows you to share and edit projects that you are tracking wit
 - **Upload** your metadata to a central database
 - **Edit** your metadata in a web interface
 - **Share** your metadata with collaborators
+- **Validate** your metadata using a schema
+- **Access** and update metadata programmatically through an API, from Python or R.
 
 ## What is a PEP?
 
-Portable Encapsulated Projects (PEPs) are standard format for biological sample metadata.  A PEP is simply a **yaml** + **csv** file (or just csv) -- the CSV file is a sample table, while the YAML file provides project-level metadata and sample modifiers. PEPs are a common input for running workflows using tools such as [Snakemake](https://snakemake.readthedocs.io/en/stable/), [Common Workflow Language](https://www.commonwl.org/), [Looper](http://pep.databio.org/looper), and other workflow systems. For more details, read the [PEP specification](http://pep.databio.org/spec/simple-example).
+Portable Encapsulated Projects (PEPs) are standard format for biological sample metadata.  A PEP is simply a **csv** file representing a sample table, plus an *optional* **YAML** file for project-level metadata and sample modifiers.  For more details, read the [PEP specification](http://pep.databio.org/spec/simple-example).
 
-## How PEPhub and PEPs work together
+PEPhub gives you a platform to store and collaborate on your PEPs. This makes it easier to work together for large or small teams. Instead of relying on local files that you send back-and-forth, PEPhub provides a centralized interface and API that simplifies sharing and collaboration.
 
-PEPhub gives you a central location to store and collaborate on your PEPs. This makes it easier to work together for large or small teams. Instead of relying on local files that you send back-and-forth, PEPhub provides a centralized interface and API that simplifies sharing and collaboration.
+## Your first PEP on PEPhub
 
-In short, PEPs are the standard format for biological metadata, and PEPhub is the platform that allows you to store, edit, and share these PEPs. Through the API, one can easily access and retrieve PEPs for use in workflows and analyses.
+### Logging in
 
-## Logging into PEPhub
-
-PEPhub accounts are linked to GitHub. This allows us to leverage GitHub's OAuth system for secure authentication and namespacing. Once you have a [GitHub account](https://github.com/signup), you can log in to PEPhub. Just click the "Login" button in the top right corner of the [PEPhub home page](https://pephub.databio.org). 
+You log in to PEPhub using your [GitHub account](https://github.com/signup). Just click the "Log in" button in the top right corner of the [PEPhub home page](https://pephub.databio.org). 
 
 ![PEPhub login button](../img/login.png)
 
 You will be redirected to GitHub to authorize the PEPhub application. You are now logged in and can upload your first PEP! There are two mains ways to add a PEP to your PEPhub namespace: you can either [upload a PEP directly](#uploading-a-pep), or you can [create a new PEP from scratch](#creating-a-new-pep-from-scratch) using the web interface. This guide will walk you through both methods.
 
-## Uploading a PEP
+### Uploading a PEP
 
 Navigate to your PEPhub namespace (`https://pephub.databio.org/{github username}`) and click the "Add" button in the top right. Click the "Upload PEP" tab. You will be prompted to select a PEP file from your local machine. Fill in the details about your PEP and then either drag files to the drop zone or click the drop zone to select files from your computer. Click "Submit" to add the PEP to your namespace.
 
-## Creating a new PEP from scratch
+### Creating a new PEP from scratch
 
 Navigate to your PEPhub namespace (`https://pephub.databio.org/{github username}`) and click the "Add" button in the top right. Click the "Blank PEP" tab. Again, fill in the details about your PEP and then you can start filling in the sample table. Click "Submit" to add the PEP to your namespace.
 
 ![Submission form for a new PEP](../img/add-pep-form.png)
 
-## Ready to edit your PEP
-
-Once you have uploaded or created a PEP, you can now start using it in pipelines!
-
 ## Editing a PEP
 
-Editing a PEP is easy; just make changes in the table and click `Save` when you are finished.
+Once you have uploaded or created a PEP, you can edit it. Editing a PEP is easy; just make changes in the table and click `Save` when you are finished.
 
 ## Sharing your PEP