DNAnexus Navigation and UI Changes

To keep the DNAnexus platform easy enough for anyone to use and powerful enough for expert users, our team has made some layout and user interface (UI) changes. While these updates are relatively minor, they make the platform look different than you might be used to, so we’ve outlined them below to help you find your way around and see what’s new.

New Look

The first thing you’ll probably notice is that the user interface looks cleaner, flatter, and more modern. The visual updates to the interface make it easier to look at and faster to find what you’re looking for. Primary actions will be on the right of the screen and be immediately noticeable. Certain areas of the site won’t have this updated look yet, but every part of the site is getting revamped in the next few months, so if it hasn’t changed yet, it will soon.


Projects UI

We have redesigned the Project list page with an easily filterable list of all your projects. A new “pin” feature allows you to mark your favorite projects and they will remain on top of the list! 

Project List

Projects now display a line of summary text in the main list. You can add even longer text in the Descriptions section of the Info panel.

Reference Data List

Info Panel

We have added a new “info” panel which allows you to quickly inspect any project when you select its row. The info panel can be opened by clicking the “i” icon in the upper right. This shows information (metadata, project settings, project size, etc.) which is also available in the Project Settings. Now you can access this information directly from the Project list page. The info panel also lets you easily copy the project ID.

Pin Project

The context (three-dots) menu in each row gives you a shortcut to Leave or Delete a project (depending on your access level), share, pin and view project settings.

To view the contents of a project, click the project name and you will enter the Data Manager section.

Data Manager: Manage Tab 

The Manage section has many enhancements. Next to the Project name there is now a menu for quick access to common tasks such as Sharing projects. Also task such as Leaving or Deleting a project (tasks formerly found in Settings) are in the menu.

Data Manager

Project navigation has been enhanced with a collapsible tree as well as fully functional breadcrumbs.

Project Folder Tree

All action buttons have been consolidated to the right side of the screen (New Folder, New Workflow, Upload Data, Add Data, Copy data from project, Start Analysis)

Start Analysis Add Button

The filter bar has been redesigned and now defaults to searching within a project. 

Project Folders

Data Manager: Manage Tab: New “info” panel

We have added a new “info” panel which allows you to quickly inspect any file. The info panel can be opened by clicking the “i” icon in the upper right. You can then select any item, or multiple items, to display their properties. This shows information previously found in the info pop up window.

You can easily copy a file or path ID from this side panel by clicking the copy icon. 

Project Info Panel

Tables are now paginated.

New folders will now be created and show at the top of the list. After you enter a name, it will move to the appropriate place in the sort order.

Project Folder Rename

Projects can be renamed in the Settings tab or in the Info panel on the main project list page.

Data Uploading

The data uploading dialog has been split into three discrete functions.

Data Uploader

The ability to apply tags and properties in the dialog has been removed. Tags and properties can easily be added in the new Info panel. Select multiple items to apply the same tag or property to multiple objects at once.

Note: Settings & Visualize tabs are the same with minor visual updates.

Featured Projects

The Featured projects section has been removed and the projects in Resources have been updated to have useful reference files and demo data.

Featured Projects Section

Data Selection Dialog

The Data Selection dialog appears when you copy data, select projects or paths during app runs, and select inputs for workflows. It now allows you to filter, add/remove columns, and view pinned items.

Platform Data Selection

Within a project, filters allow for easier filtering to find files.

Platform Folder Selection

Start Analysis 

The start analysis dialog has enhanced to improve usability. It has the familiar filtering mechanism to easily locate an app, applet workflow or global workflow. You can now see the category and the author of the analysis tool. By selecting a row and opening the “i” Info panel, you can still view the inputs and outputs. 

Starting Analysis

Version can be toggled in the dropdown:

Allele Frequency Calculator

Open the tools details to see full information provided by the tool developer.

Tool Details Button

Tool Runner

The Tool Runner has been enhanced with a graphical representation of the analysis process. Each app or workflow has three areas that a you can configure: Settings, Analysis Inputs, Stage Settings.

Settings includes execution name, project location, output folder and optional advanced features.

Analysis inputs is where you can select appropriate inputs and can toggle to batch mode. Also, you can now view all inputs in one location.

Stage Settings contains information about each stage of a workflow, including app version, instance type and output folder. You can change these as desired.

Tool Runner

Data Manager: Monitor Tab

The Monitor Tab also has a fresh look with updated filter bar UI and action buttons consolidated to the right side. 

Monitor Tab

On the monitor details page, several actions have been moved or temporarily removed.

  • View info in not currently visibility (coming in our next release)
  • View input is removed as the inputs and outputs all shown on the page details.
  • Save as New Workflow has been removed.
  • Monitor tab is not indicating that a job is running (coming in next release)
  • Tags not showing on the Monitor table (coming in next release as its own column)

You can copy an execution ID to the clipboard by clicking the icon next to the ID.

Logs have a new Download button feature: 

Logs Download Feature

From Manhattan Plot to BigTop: DNAnexus Makes Data Visualization a (Virtual) Reality

BigTop Team Members

Drowning in a deluge of data? What if there was a better way to grasp the information — literally?

Enter BigTop, an innovative virtual reality platform that allows you to interact with your data in a totally new way. Thousands of data points, three dimensions, unlimited possibilities.

It takes this:

2D Manhattan Plot

And turns it into this:

VR Manhattan Plot

BigTop is the brainchild of Senior Program Manager and resident microbiome expert Sam Westreich, Principal Software Engineer Christopher Meyer, and former Data Visualization Team Lead Maria Nattestad.

An avid gamer, Meyer had been searching for a way to take scientific data visualization into the virtual world, and Westreich was similarly interested in VR, 3D programming, and building better tools for the scientific community.

Scientists have been comfortably plodding along with scatter plots for decades. But the medium is limited to two dimensions, and is insufficient to handle the vast amounts and the depth of data being generated in the era of genomics and precision medicine.

The Manhattan plots often used to visualize genome-wide association study (GWAS) data can allow you to map out associations between disease risk and chromosome locations, for instance. But what if you want to throw in another variable, such as age, race or mutation frequency?

“Scatter plots provide a good way to get an overall glimpse, but you can’t really drill down into the data,” Westreich said.

BigTop widens the field of possibilities — by literally widening the field.

“Computer screens are relatively small. Large amounts of data won’t always fit,” Meyer said. “One of the luxuries of virtual reality is the space to set up an entire world. A lot more data can be presented that way.”

BigTop takes three different qualities of each data point, plotting them in three different dimensions. If you find a point of interest, you don’t have to remember the coordinates and type them into a browser to investigate further — you can just turn around and select the point. That action brings up even more information culled from the originating dataset or other records.  

The program not only enhances the data analysis process for professional users, but it makes it more accessible for a wider audience, who may find the physical interaction to be more intuitive and easier to understand.

“It presents data in a way that we are better equipped to deal with,” Westreich said. “The dataset is not just a file that sits somewhere. It’s turned into a bright, vibrant, multicolored thing that people are curious to explore. You can literally walk through the data. You no longer have to try to conceptualize it in your head.”

Frontier Fridays

BigTop was born one Friday afternoon in March 2018 during a session of Science Frontiers,  time allocated to DNAnexus science and engineering teams to get creative on projects not directly related to their day-to-day customer work. Every week, about a dozen people participate.

Nattestad and Meyer came up with the concept and Westreich was soon brought in to “begin sticking toothpicks into paper plates” to develop a prototype. Soon, Meyer was lugging his huge gaming computer and Oculus headset into work each Friday as they delved into the brave new world. They experimented with different platforms — one of which was abruptly taken off the market — and settled on A-Frame.  

“It’s a relatively new environment, so there’s not years worth of documentation and user questions and answers,” Westreich said. “It’s been challenging, but it’s also exciting. We are really getting in on the ground floor and contributing to the evolution of this completely new media.”

BigTop works with a variety of VR headsets. With the headset on, you can walk around to explore the data, using your right-hand controller to project a laser that can be used to select points: simply aim the laser at a point and pull the trigger on the controller to get info on it. Your left controller will present a virtual hand; this currently does nothing, but you can use it to wave or give a thumbs-up to your data, as the team notes in their QuickStart guide.

The program can also be played like a video game using a phone, computer screen, keyboard and mouse, making it accessible to those who may not have more advanced equipment.

After demonstrating the program to colleagues at DNAnexus, the company invested in VR equipment, and Nattestad and Westreich have taken it on the road to several conferences, where BigTop has been a big hit.

“It’s a lot of fun and attracts a lot of attention. And it shows how we, as a company, are experimenting with new modalities and thinking out of the box,” Westreich said.

BigTop is currently available for free on Github, where it comes pre-loaded with a GWAS dataset from the GIANT consortium with associations between SNPs and height, and a second dataset on breast cancer. The program can also be used to visualize other datasets — Westreich presented an interactive rice genome at this year’s Plant and Animal Genome Conference, for instance.

After experiencing BigTop at the last DNAnexus Connect user group meeting, customers have been eager to get the program integrated into their DNAnexus packages. Westreich and Meyer said the program is already optimized for use as a DNAnexus file viewer. Users have to put their data in the right format themselves, which may not be a straightforward process depending on the data.

But Meyer thinks the payoff will be worth it.

“Virtual reality is still very new. This sort of biological data exploration has not been available before, and scientists are not nearly as cutting edge as you might think when it comes to data visualization,” Meyer said. “Although they may be slow to adopt new methods, when they do start and realize the potential, they embrace it.”