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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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

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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:

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msr-report-2

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