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Illumina Announces BaseSpace Correlation Engine Integration with Elsevier’s Pathway Studio

Accelerates discovery by demonstrating genetic functional relationships and validating results


Illumina and Elsevier R&D Solutions have announced a collaboration to integrate use of Pathway Studio, Elsevier’s database of experimental data and disease models, with Illumina’s BaseSpace Correlation Engine platform, offering them as one seamless solution. Under the terms of the agreement, all licensed Correlation Engine users have free access to Pathway Viewer, an application that enables researchers to quickly view a snapshot of the functional relationships among genes. In addition, researchers are able to find top scoring canonical pathways that correlate most highly with the genes list.

Correlation Engine is a suite of applications that lets users discover the relationships among their results, with billions of correlations derived from the world’s largest curated library of genomic knowledge. The applications contain over 130,000 experimental comparisons from more than a half million samples, drawn from NCBI’s Gene Expression Omnibus and other open-access or controlled-access databases.

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Upcoming BaseSpace Developer Conference in San Francisco!

We want to invite all of you to the BaseSpace Developer Conference in San Francisco!  We’ve been active with many BaseSpace Developer Conferences throughout the world this year, including Heidelberg, Singapore, Bangalore, and our most recent visit to the University of Tokyo in Japan!

First of all, we would like to thank all of our developers and speakers, you all made this possible.  We hope it was a great learning experience and look forward to the apps we can bring to BaseSpace.  Also, a big shout out to the University of Tokyo for hosting the event and our Illumina team in Japan.

developer pic

The events showcase the new Native App Engine within BaseSpace with which developers can easily adapt their command-line pipelines into the BaseSpace cloud infrastructure or an infrastructure of their choice.

During the event, developers are taken through a step-by-step walkthrough where they develop two separate BaseSpace applications by the end!  For anyone that is interested in learning more about BaseSpace App development, there is a lot of documentation available on the BaseSpace Developer Portal for both Native and Web applications.


We also spend time interacting with developers and users directly to brainstorm ideas and answer any questions they may have.

helping individual dev

We are hosting another BaseSpace Developer Conference in San Francisco on December 8th, if you are interested in attending you can sign up here.

To get an idea of whats in store for you when you attend one of our developer conferences, check us out on twitter at #basedev2014.

For any further questions about BaseSpace App development, please view or post on the developer forum or contact us through BaseSpace support.

Introducing our First BaseSpace Labs Applications – FastQC and Velvet de novo Assembly

We are excited to announce two new applications in BaseSpace, FastQC and Velvet de novo Assembly.

 denovo_assembly_100                                     FastQC_icon_100

     Velvet de novo Assembly                                      FastQC

Both applications are currently available for all users and were built using the BaseSpace Native App Engine by our internal R&D groups.  These two applications are also the first BaseSpace Labs Apps of many more to come, the concept behind BaseSpace Labs Apps is explained in more detail below.

BaseSpace Labs Apps are Illumina’s internally developed applications that extend the functionality within BaseSpace.  Some BaseSpace Labs applications will be experimental or research focused, while others will be used as a step in a greater workflow.  The Apps are reviewed regularly by our team and put through the same review process as third-party apps.

BaseSpace Labs Apps are developed using an accelerated development process in order to make them available to BaseSpace users faster than the BaseSpace Core Apps.  It is important to note that, unlike BaseSpace Core Apps, BaseSpace Labs Apps are not officially supported by Illumina Customer Service.  Support for BaseSpace Labs applications is provided at the developer’s discretion and the apps are provided as-is without any warranty of any kind.

The FastQC app can be used to provide a quality assessment of the sequence data generated using Illumina sequencers.  FastQC for BaseSpace is based on the FastQC software developed by the Bioinformatics Group at the Babraham Institute.  It provides a modular set of analyses which can be used quickly to assess if there are any problems with the sequencing data before doing any additional analysis.


The above figure shows an example output from the FastQC app depicting the quality score across all bases at a given position in the reads.  For an example of additional output generated by FastQC, please view this FastQC demo project.

The Velvet de novo Assembly app is a de novo assembly pipeline for bacterial samples using the Velvet assembler.  One of the key features of this app is that it has an adapter trimming protocol that has been optimized for the Nextera Mate-Pair library prep kit.  An application note describing the de novo assembly of 9 different bacterial using the Velvet de novo Assembly app can be found here.  In many cases, a single contig representing the entire bacterial genome can be assembled.  The figure below is an example of the output generate by the Velvet de novo Assembly app.


Example output generated by the Velvet de novo Assembly can be found here.  We hope you enjoy the FastQC and Velvet de novo Assembly apps.  For any questions, feedback, or feature requests for these applications, please send an email to and include the name of the application.  Thank you!

You Heard it Here First: Winners of the BaseSpace Killer App Contest

When we announced the BaseSpace Developer’s Meeting, we encouraged attendees to enter original ideas for the “killer” next-generation sequencing app- a utility or analysis tool to significantly advance genomic understanding. And we were not disappointed; the forward-thinking innovation in the BaseSpace development community was apparent in the 100+ ideas submitted.

Now we’re excited to reveal the two winners of the BaseSpace app contest.  The first winner is a visualization tool suggested by a Jack Lovell, a student at the Rhode Island School of Design.  In his words, “This app would be a network visualization app with a set of tools for viewing new dimensional data with the nodes.  For example, one experiment might use a network where each node contains a sequence of gene expression measurements through time.  The researcher needs to compare the sequence across multiple nodes simultaneously.  The idea is to develop visually intuitive links between the networks and proven graphical methods such as a standard line graph.”


The second winner is Terry Gaasterland from the Lab of Computational Genomics at the University of California San Diego.  The app is a simple, elegant search tool that accepts a regular expression profile and searches one or several fastq files for reads that contain the expression of interest, such as a microRNA, to build an expression reference library directly from read data. In her words: “The reason for doing this is twofold:  (a) we sequenced mRNA and microRNA from 8 tissues in eye to build an expression reference library. We need ways to peer into it for newly discovered sequence searches. Sometimes a microRNA is present but below a normal threshold cutoff, (b) many sequences of interest, e.g., a motif, a miRNA, or a short repeat, are too short to find with Blat or an alignment tool, and there are way too many such sequences to search for all of them up front.”


Congratulations to Jack and Terry! And remember, you heard about these new genomic analysis tools here first. Want to design your own killer app? More BaseSpace Developer workshops are being planned!  In the meanwhile, you can find more information about the new Native App Engine in BaseSpace here, or get started as a BaseSpace Developer here.

Announcing the first worldwide Illumina BaseSpace Developer meeting


We are excited to announce the first BaseSpace Developer Meeting in Boston, Massachusetts, on October 21, 2013.  Immediately preceding the 2013 ASHG conference, the BaseSpace Developer meeting is a great opportunity for both experienced and novice developers to network, exchange ideas, and learn more about the world’s most widely used cloud-based bioinformatics platform for next-generation sequencing. In this free, one-day forum, you can learn how to build and launch your own bioinformatics apps for BaseSpace.

Why develop for BaseSpace? 90% of the world’s next-gen sequencing data is produced on Illumina instruments, and your novel algorithms, open-source tools, or applications for BaseSpace users can directly impact the growth of genomic research. In short, you can change the way the world analyzes genomic data.

Who should attend?

  • Bioinformatics Professionals
  • Academic Researchers
  • Statisticians
  • Engineers
  • Managers
  • Computational biology and chemistry specialists from the biopharmaceutical industry


Keynote: BaseSpace: Leveraging the Cloud to Eliminate the Bioinformatics Bottleneck
Alex Dickinson, Senior Vice President, Cloud Genomics, Illumina, Inc.

The BaseSpace Ecosystem: A Growing Opportunity for End Users and Developers
Scott Kahn, Chief Information Officer, Illumina, Inc.

BaseSpace Apps — Is One Enough?
D. Matthew Landry, Chief Technology Officer, Biomatters Ltd.

GePS and the Path to BaseSpace: New BaseSpace App Developer Experience
Susan Dombrowski, Ph.D., Senior Field Applications Scientist, Genomatix Software, Inc.

Rapid App Development with BaseSpace: Hello World! App — Developed in Two Days
Scott Markel, Ph.D., Principal Bioinformatics Architect, Accelrys

Building Better Annotation and Curation Tools on BaseSpace
Srinivasan Maithreyan, Ph.D., CTO, SciGenom

BaseSpace – DNASTAR’s Chase
Tom Schwei, Vice President and CFO, DNAStar

Developer to Developer — How the BaseSpace Architecture Makes it Easy to Develop and Launch Apps
Greg Roberts, Development Leader, BaseSpace, Illumina, Inc.

Hands-on Workshop (3 hours) – How to Build an App for That

Will be followed by a Networking Reception

Link to Agenda

Event Details:

Date: Monday 21 October, 2013, 8:00-6:00 PM ET

Location: Seaport Hotel
1 Seaport Lane
Boston, MA 02210
Seaport Ballroom on Mezzanine

Cost: Free

Twitter: #basedev2013

Got a killer NGS app? Enter your original idea and win an iPad mini at the conference!

Register Here