The New BaseSpace

Something important is about to happen in BaseSpace. It’s really the beginning of a transformation that will be happening over the rest of the year turning BaseSpace into an genetics application platform.  In the coming days, we will be releasing a completely re-designed user experience with better data management and sharing, important new features like a fully integrated SAV, and a whole new look and feel. The data you already have in BaseSpace is still there, as is all the security and reliability you depend on us for. In this post we’ll walk through a number of the new features so you understand what’s new and how to use it.

How We Think of Data

We always knew that we would be expanding our data model to include things like projects, but we wanted to get some real world feedback before we went through that transformation.  Last spring we went back to the drawing board and completely re-architected the data model to work the way our end-users – biologists, lab managers, clinicians – want to manage their data.  Essentially what we have now are two areas focused on different types of users.  These two areas are “Runs” and “Projects”.  The diagram below shows how data from an instrument flows into these areas.



Most BaseSpace users are already familiar with runs.  This is a generic term for the process that an instrument goes through when sequencing a single flowcell.  MiSeq can do one run at a time while HiSeq can actually do two.  In this area, a lab manager or tech can, in real-time, manage the quality of their runs and the data being produced.


To enhance the run management utility of BaseSpace we have now integrated the capabilities of  “Sequence Analysis Viewer” (SAV) directly into the user interface, removing the need to install separate software but keeping the same charts and same look and feel as the current SAV. For those that don’t already know, SAV is awesome and allows for the real-time, cycle-by-cycle monitoring of the most useful primary metrics coming off the sequencing instruments.  This data is updated real-time and can be used during and after your run.


By clicking on any graph BaseSpace serves up a full screen view of those metrics. We found this particularly useful when monitoring run status in BaseSpace from a mobile device (it looks great on an iPad ).



New to BaseSpace is the concept of projects, which at their most basic are a set of samples and app results that can be flexibly managed by the data owner. In this release, projects are defined by the sample sheet and samples can be individually assigned to a project in the sample sheet. The best way to do this is with IEM (Illumina Experiment Manager).


Once a project has been associated with a sample in Illumina Experiment Manager (IEM), that sample will automatically be deposited in the project in BaseSpace at the end of your workflow.

A Project is a completely flexible entity, and can contain:

  • A single sample or up to as many samples as you choose
  • A subset of samples from a run. You can break samples from a single run out into several projects.
  • A superset of samples from multiple runs. You can assign samples from multiple runs to a single project.
  • Results from Apps
  • All samples from a run.

In this release, if a sample is not associated with a project in the sample sheet it will be given an automatically named project based on the run info.   Currently, a sample can only live in one project and cannot be moved, but additional features will change this behavior in the future.

Users can share projects the way runs can be shared. In fact, we’ve now added the ability to share content directly with an individual by entering an email address rather than sharing just by a link to your data (though that still exists!). If you want to share data with multiple email addresses, you just add more to the list.


If you share a project, the recipient only gets access to data for the samples in that project and not the whole run or runs (unless all samples from a run were added). Our thinking here was for core labs or service pro’s who have samples from multiple customers in a single run and need to separate them out so that customers see only their own data. Now with Projects, just create a project for that customer and share the project!  This also means that sharing a run will not automatically give access to the project(s).  We will be migrating existing permissions to help ease this transition, so if you had shared a run and that project doesn’t contain other run’s data we will automatically give access to those recipients, but you can always revoke or add more people to the list if you find that they lost access.


As we’ve mentioned previously, we are deep into building the app store for launch this fall. Everything that works on your data in BaseSpace, from the free secondary processing workflows to downstream commercial and academic tools, will appear as an App in the system. The results of an App (reports, variant lists, annotation, metadata, etc.) will all be stored within Projects as App Results. 


And finally there’s the new interface. Super clean look and feel, and everything critical from Projects to Runs to SAV to Applications is one click. As more people use BaseSpace we see a huge opportunity for this to become a central hub of collaboration and data sharing, and have begun work on a number of “social” features to make that easy for our users.



As a first pass we are introducing Notifications to the dashboard. Notifications allow users to passively receive updates on what’s happening in their account. The types of things we will notify you about include:

  • Updates on run status
  • When you receive an invitation to a dataset (shared with you)
  • When somebody accepts your invitation to a dataset (shared by you)
  • BaseSpace updates, including new features and new Apps

To get this new data model and new UI out we needed to “go dark” for a few months, and we’ve appreciated your patience. But from here on out we’re back to the rapid, flexible and iterative deployment ethos and you should expect to see new things in BaseSpace all the time. In fact, we have something amazing coming out in just a few weeks…


One comment

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.