Introducing App Versioning

We’re excited to announce support for versions of BaseSpace apps. The App Store has been very successful, and with this success comes the need to publish improved versions of apps.

Every app will now have a single entry in the App Store, and you may choose the version on each App Description page.

app-launch-menu

Each app version will have two new sections on the App Description page. The “Release Notes” section will list the changes since the last version. And the optional “What’s New” section can contain the latest updates about a version, such as bugs discovered since publication or changes to the version’s price.

isaac-enrichment

It’s important that once app versions are published, they can no longer be changed. This way apps can be used to analyze many samples in exactly the same way.

We’ve added some features to ensure that samples can be analyzed consistently during experiments. If you navigate to the App Description page of an app you’ve launched before, your default view will be the version that you launched the last time. Also, once an app version is published, it can no longer be changed by developers. Bug fixes and improvements can be added in new versions.

We’ll let you know if a new version is available. If you are on the App Description page of an older version, you will be notified that a new version is available.

app-launch-notification

App developers will notice some nice improvements to our developer portal, which include a new page to create and view app versions.

devportal

We hope you find these changes useful, and we all look forward to improved versions of apps!

Overhaul of SAV Charts

As part of the latest release of BaseSpace, we have made some changes to the Run charts by adding interactive functionalities such as zoom, pan, and scale for certain charts.

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MethylSeq v1.0 App for DNA Methylation Calling

DNA methylation is one of the most studied epigenetic modifications in human cells. Changes in DNA methylation patterns play a critical role in development, differentiation and diseases such as multiple sclerosis, diabetes, schizophrenia, aging, and multiple forms of cancer. Over the past decade, interest in DNA methylation has grown rapidly and expanded across multiple areas of research. Consequently, DNA methylation analysis methods have undergone dramatic changes. Bisulfite-treatment and next-generation sequencing (NGS) have increasingly become the tools of choice to profile DNA methylation levels. Here, we announce a bioinformatics solution for analyzing NGS methylation data: BaseSpace® MethylSeq v1.0 app.

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MethylSeq v1.0 app

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Submit Data from BaseSpace to NCBI’s Sequence Read Archive

When sequencing data supports a new finding that is reported to the scientific community, it is common practice to share the sequencing data that generated the result, through an archive such as NCBI’s Sequence Read Archive. How would a BaseSpace user do this? Until now, a BaseSpace user would have to download their data locally, and then prepare an SRA submission through NCBI’s published guidelines.

SRA Submission App

Since BaseSpace already stores some of the metadata that go into a submission, we felt we could make this process easier. Today, we’re excited to announce the release of the SRA Submission App, a BaseSpace Labs release. Built in collaboration with NCBI, the app prepares your submission XML and transfers the data directly to SRA from BaseSpace. Read More…

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.

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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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