New RNA Apps in BaseSpace

We are excited to launch the TruSeq Targeted RNA v1.0 and Small RNA v1.0 Core Apps in BaseSpace, which are some of the most feature-rich Apps we have launched to date.


TruSeq Targeted RNA v1.0

Small RNA v1.0

A high level overview of the Apps is provided below. More detailed information about the Apps can be found in their respective Core Apps application guides.

Read More…

Illumina Informatics at Bio-IT World 2015

We are excited to be part of the Bio-IT World Conference & Expo 2015 starting today at the Seaport World Trade Center in Boston, MA.  Representatives from the BaseSpace and NextBio teams will be at the conference, and are looking forward to engage with Bio-IT attendees. Stop by our booth #129, or connect through Twitter (@BaseSpace) to discuss our portfolio of cloud and on-site genomic storage, analysis and interpretation solutions: BaseSpace cloud, BaseSpace On-site, NextBio Research, & NextBio Clinical.

We will have an in-booth demo of the NextBio Clinical platform at 10.05am (as part of the ‘Best of Show’ program).

Plus, join us for our lunchtime presentations on Wednesday, April 22.

  • Track 5 (12:40pm):  “Sample Aggregation and Analytics in the Post-$1,000 Genome Era” 12:40 PM presented by John Shon, VP, Bioinformatics & Data Sciences
  • Track 9 (1:10 PM): “Enterprise Informatics: A High-Performance Application Development Platform for Collaborative Genomics Research” presented by Paul Flook, Ph.D., Sr. Director, Enterprise Informatics

And stay an extra day in Boston for the BaseSpace developers conference at The Broad Institute. Register here.

See you all in Boston!

New Download Experience

With our newest release today, we are happy to introduce a revamped download experience from our run details and analysis details page.  This new experience takes advantage of the existing BaseSpace Downloader, with a couple new filtering options.

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Introducing the ability to Launch Apps via the API!

We are happy to announce the introduction of API-driven App launch capabilities on BaseSpace. We are now extending the BaseSpace API to include app launch, so that with a call to a RESTful API endpoint, you can launch a BaseSpace app on your data. With the new feature in the API, you can now:

  • Configure and launch multiple Apps in succession or in parallel using a script, this ensures consistency of configuration and reduces the possibility of human error through manual launch
  • Automatically launch Apps in the background, without direct intervention by a human user. This allows the possibility of unattended sets of app launches, such as apps that launch in the middle of the night as soon as sequencing data is ready, rather than waiting for a manual launch
  • Create scripts to automate testing of your app for developers

BaseSpaceLaunchAPI (1)

The apps are launched in exactly the same underlying BaseSpace environment as the web UI, so you can check the status of API-launched apps and look at generated reports through the web UI.  In addition, the ability to launch the apps on a locally configured machine or a local virtual machine are also supported via this API.

There are several ways to make use of the API-driven app launch. One is to use the API directly, using any HTTP compatible toolchain such as curl or the Chrome plugin Postman. The documentation for using this API can be found in the API Reference.  To make this process more convenient and hide the details of authentication, we have also exposed the relevant APIs as part of the Python SDK. You can find details of the Python SDK method here.

Example App Launch Script

To demonstrate the power of API-driven app launch, we have made available a set of prototype tools to automate some of the analysis needs of a sequencing facility using BaseSpace.  These tools are open source and available on github at,  The scripts are designed to be run on a Unix host using cron, the command scheduling application that comes with all modern Unix flavors. Cron can run command line tools at regular intervals so that a server machine can be periodically polling BaseSpace to look for the arrival of new data.

When that data arrives, the tools configure and launch an app run using the BaseSpace API. Further tools, also run with cron, poll BaseSpace to keep track of that app as it runs to completion and then check and download the results. All of this happens without intervention from the user, as cron tools continues to work on the samples as they arrive in BaseSpace. Further command line tools are provided to keep track of the status of app runs and intervene in problem samples.

The scripts are written in Python and make use of the BaseSpace Python SDK for interaction with the BaseSpace API. The github repo has been carefully documented so that you should be able to not only use them as they are, but also extend and modify them for your own needs. The developers of the tools will also be monitoring the BaseSpace forums (!forum/basespace-developers) to answer any questions you might have or help with using and adapting the tools to your needs. For more information on these tools and to try them for yourself, go here.

API Rate Limiting

Along with this new API we are also introducing the concept of API Rate limiting.  While any API can have a limit, we are currently focused on the App launch API.  You will notice new http headers being returned on this API described below and in more detail API Reference:

  • X-RateLimit-Policy – The name of the policy/rule that applied for this API request
  • X-RateLimit-Limit – For the applicable policy, the maximum number of requests that the user is permitted to make in the current rate limit window before usage is restricted
  • X-RateLimit-Remaining -The number of requests remaining in the current rate limit window
  • X-RateLimit-Reset – The UTC date/time when the rate limit usage for this policy will be reset

App Launch API Restrictions

  • API Rate Limiting: There are limitations on how many requests can be made to the app launch API for each user.
  • Only Native applications can be launched using this API: This is primarily because Native applications have a pre-defined set of input fields that a user may configure, whereas non-Native applications (Web/Desktop) are more open-ended.
  • Only free applications can be launched with this API.
  • Only Apps that you have access to and that are in Beta or Published state can be launched and run on our platform.
  • Apps that are in development can use this API to send to your local agent, but cannot be run on the platform until they are in Beta or Published

MiSeq Analysis Reports Upgrade

We are happy to announce newly revamped reports for all MiSeq based analyses.  BaseSpace automatically runs an analysis package called MiSeq Reporter, similar to what is available on instrument, upon completion of MiSeq run uploads. With the advent of the rich reporting tools available in the Native App Engine, we felt these analysis reports needed an upgrade.  While the underlying analysis result data has not been altered, the visualizations and reports on our site have been upgraded to this new style for all MiSeq analyses in the past 2 years.

Here are some example reports and charts:




Even with these upgraded reports, we also encourage our MiSeq users to try out all of the latest apps in the app store!

BaseSpace 2015 WWDC @ The Broad



Space is limited, so please register early.

Create your own Apps in BaseSpace!

Publish your favorite novel algorithms or applications on BaseSpace.

At this free event, you will learn how to build and launch your own bioinformatics Apps in BaseSpace.
Make an impact on the analysis and interpretation of genomic information by publishing your own BaseSpace App!

Friday, April 24, 8:00 AM to 5:00 PM |  The Broad Institute

415 Main Street Cambridge, MA 02142 | Monadnock Meeting Room, 2nd Floor

Who should attend?

● Engineers
● Researchers
● Software Developers with a focus in Bioinformatics
● Managers
● Academics
● Statisticians
● Computational biology and chemistry professionals
● Biopharma industry professionals
● Commercial Bioinformatics professionals


Space is limited, so please register early.

Support for Internet Explorer 9

Coinciding with the release of BaseSpace v3.16, we are officially discontinuing support for Internet Explorer 9 (IE9). After April 17, 2015, users will no longer be able to run BaseSpace on IE9.

With the IE browser having undergone two major upgrades (latest version is IE11), we only have a small number of users accessing BaseSpace via IE9. More importantly, with rapid evolution of browser features, the technical burden of supporting old browsers slows down development of newer features.

We apologize for any inconvenience, but encourage you to either upgrade to the latest version of Internet Explorer (IE11), or choose other supporter browsers such as Chrome, Firefox, or Safari.