Overview of the Platform User Interface

Before you begin, set up a DNAnexus Platform account here: https://platform.dnanexus.com/login

There are several ways to interact with the platform. All of these will be covered in future lessons/ courses/ documentation.

We are going to be focused on the user interface (highlighted in green), also known as UI.

This information can also be found in the Project Section of the Documentation for the Platform

First, what is a project?

It is a collaborative workspace
The smallest unit of sharing on the platform
A place to store objects that are made on the platform
- Examples of these objects can be files, applets, and workflows
A place to contain details of running jobs/ analyses and their results

The user folder is the storage area for your output files
You can add more folders into your user folder for organization (maybe one for data, each project, etc. This is however you and your organization/ company wants to do this)

Data can be in one of 3 states

Log into the DNAnexus platform
When you login, you will see a list of projects that you are a part of.
Navigating to a project
1. We have prebuilt projects for you
2. In your project space, select "DNAnexus Academy 101"
Navigate to the users folder and use Add > New Folder

Object Classes include:

Each object receives their own unique ID

These can be file IDs or job IDs
These NEVER change
The same file can be uploaded multiple times into a project; different objects will be created. The platform DOES NOT overwrite a file. Instead, it creates a new file ID every time you upload it.
Metadata is essential to keep track of these files and their properties.

Metadata keeps your files organized

They can have

Tags: which are words to describe the file format, genome, etc.
- Examples: fastq, control, bam, vcf
Properties: are key/ value pairs
- Examples: sample_id, value= 001

Go to your project folder and find the file information. Identify the columns for the name, type/ class, and tags

You can do this in the overview of each, without selecting the file:

Or, you can do this by selecting each file individually to see a detailed view:

Now, let's try filtering

Now, let's view where the data operations are:

Select "+ New Project"
Give your project a name and following the billing/ region options that are relevant to your company/ organization
In the "more info" section, you can add descriptions and summaries for the project.
Add data to the project by using one of the options in the "Add" button in the project
Project Sharing
- Gives access to the project to individual users or groups of users (orgs)
  - Select share project
  - Add Users here
    The project Access levels are as Viewer, Uploader, Contributor, and Admin. These are outlined in the DNAnexus Documentation: Project Access Levels
    You can also remove collaborators from the project under the same share points
You will need to be manually added to a project in order to see it appear in your projects page

There are reference genomes/indices that are built on platform, so you can run jobs and analyses.
This storage is not charged to you

To create a support ticket if there are technical issues:

Go to the Help header (same section where Projects and Tools are) inside the platform
Select "Contact Support"
Fill in the Subject and Message to submit a support ticket.

Last updated 5 months ago

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