Overview of the Platform User Interface

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

Basic Structure

The Platform

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.

Projects

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

Folder Usage

  • 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)

Status of a Data Object

Data can be in one of 3 states

  • Open: initial, empty state, awaits upload

  • Closing: uploading, not instantaneous

  • Closed: Finalization completed, available for next steps

Creating Folders

  1. Log into the DNAnexus platform

  2. When you login, you will see a list of projects that you are a part of.

  3. Navigating to a project

    1. We have prebuilt projects for you

    2. In your project space, select "DNAnexus Academy 101"

  4. Navigate to the users folder and use Add > New Folder

Data Object Classes

Object Classes include:

  • Data files

  • Apps

  • Workflows

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.

Object Metadata

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

  • In this example, you can filter by Type, Class, and the Tags, for example

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

  • Archive

  • Copy

  • Delete

  • Download

Copying Files

  • Copying means from one project to another project

  • You cannot copy within the same project because of the file ID.

Project Administration

Creating a Project

  1. Select "+ New Project"

  2. Give your project a name and following the billing/ region options that are relevant to your company/ organization

  3. In the "more info" section, you can add descriptions and summaries for the project.

  4. Add data to the project by using one of the options in the "Add" button in the project

  5. Project Sharing

    • Gives access to the project to individual users or groups of users (orgs)

      • Select share project

      • Add Users here

  6. You will need to be manually added to a project in order to see it appear in your projects page

Public Projects

  • There are reference genomes/indices that are built on platform, so you can run jobs and analyses.

  • This storage is not charged to you

Resources

Key Concepts

User Interface QuickStart Guide

Full Documentation

To create a support ticket if there are technical issues:

  1. Go to the Help header (same section where Projects and Tools are) inside the platform

  2. Select "Contact Support"

  3. Fill in the Subject and Message to submit a support ticket.

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