Tag Archive | Illumina

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!

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!

Proteomics? There are Apps for that!

Hello. Aaron from AB SCIEX here, and we are adding Proteomics to BaseSpace. I bet you weren’t expecting that! But about a year ago we started working with the very nice people at Illumina and together we began to map out a grand vision of how we could better enable systems biology/translational medicine/functional genomics (did I miss one?). Both teams recognized that to really help our customers make revolutionary discoveries in biological research we needed to expand beyond our individual core competencies. For too long the omics technologies had been compartmentalized, and that really isn’t how it works in living cells.

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In parallel, mass spectrometry-based proteomics was growing up. With the new AB SCIEX next-gen proteomics technology (a.k.a. SWATH Proteomics), we can quantify thousands of proteins in many, many samples reproducibly for the first time, so integration with genomics and transcriptomics would be more meaningful.

I am proud to announce the launch of OneOmics – an exclusive partnership to bring together AB SCIEX next-gen proteomics (NGP) and Illumina next-generation sequencing (NGS) tools in the BaseSpace cloud computing environment. There are four BaseSpace Apps in the AB SCIEX next-gen proteomics toolkit:

•             Protein Expression Extractor – for processing raw mass spectrometry data

•             Protein Expression Assembler – for protein fold-change analysis

•             Protein Expression Browser – to visualize results in biological context

•             Protein Expression Analytics – for data quality review

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The Protein Expression Extractor and Assembler have some really fancy algorithms generating the results, and the high-powered distributed computing in BaseSpace delivers results up to 50x faster than on the usual high-end desktop computer (from 3 days down to a couple of hours!). Also the ‘don’t try this at home’ paradigm normally associated with mass spec proteomics is a thing of the past, and you don’t have to be a bioinformatics expert to process the data. It’s virtually parameter free. I told you the algorithms are fancy.

But the Protein Expression Browser is the really cool App. There’s not a mass spectrum in sight, and you don’t have to worry about any of the usual impenetrable jargon associated with mass spec proteomics. Just great visuals of showing your results in biological context.

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Having proteomics and genomics data in the same place/cloud is a huge step forward in itself, but the AB SCIEX and Illumina teams wanted to take this a step further and integrate NGP and NGS. One of the main benefits of using BaseSpace is that there is already a community of bioinformatics developers publishing new apps, and we are really excited about the applications that our collaborators at the Institute for Systems Biology (ISB), Yale, NextBio and Advaita have been developing. Rob Moritz and his team at ISB have developed the SWATHAtlas Ion Library Generator App that can generate standard and modified SWATH Proteomics Libraries as part of their SWATHAtlas project. This means that researchers have easy access to human, yeast and MtB libraries currently, but more are on the way.

 

There are obviously many ways to combine genomics information with proteomics information.  You could simply do your gene expression with Illumina’s TopHat, Cufflinks or RNA Express Apps, and then your protein expression with AB SCIEX’s next-gen proteomics toolkit, and then integrate the results (parallel analysis). But Chris Colangelo and Rob Kitchen at Yale University are developing the RNA-Seq Translator App that takes the output from Cufflinks and converts it to protein FASTA files. That App will be available soon. These files can then be converted into an NGP library and be used as the basis for proteomics analysis (serial analysis). The transcriptomics and proteomics results can be loaded into Advaita’s iPathwayGuide, or mapped onto the genome using NextBio, and differential transcript or gene expression can be compared with differential protein expression.

OneOmics

I hope you are as excited about the possibilities as we are here at AB SCIEX and Illumina. This is only the beginning…

Related Content:
6 Ways SWATH Cloud Toolkit will help you
Illumina Press release
Genome Web Proteomonitor article
FierceBiotechIT article
GeneticEngineering & Biotechnology News article

 

FASTQ upload is now available in BaseSpace

We are excited to announce the availability of a data upload feature for FASTQ files that were previously generated on Illumina sequencing instruments. This simple-to-use feature is accessible from any project to which the user has write access by first clicking on the project and then selecting the Import tab shown below.

ProjectTab

The user will then be prompted to select their import type. The user can upload a single sample by clicking on “Sample” as shown below.

Samples

The user can then either “Drag and drop” one or more files into the webpage or click on “select files” and select which files they would like to upload from a file browser. Note that the FASTQ files need to adhere to Illumina standards, as specified below.  Data for a single sample can constitute multiple files. The total number of files per sample and their combined size are limited to 16 and 25 GB respectively. It will take 1-2 hours to upload a 25GB sample on a network with a relatively fast internet connection.

dranganddrop

The user will then see a progress bar as the file/s are uploaded. Once the progress bar completes, the user can add additional files. The user can also set the sample name and associate a genome with the sample in the upper left hand corner of the screen.

upload_screen

Once the user has imported all of the files and the files complete uploading, the user will need to click on the  “Complete Import” button (shown above) to complete the session.

FASTQ file standards

  • The uploader will only support gzipped FASTQ files generated on Illumina instruments
  • The name of the FASTQ files must conform the following convention:
    • SampleName_SampleNumber_Lane_Read_FlowCellIndex.fastq.gz (i.e. SampleName_S1_L001_R1_001.fastq.gz / SampleName_S1_L001_R2_001.fastq.gz)
  • The read descriptor in the FASTQ files must conform to the following convention:
    • @Instrument:RunID:FlowCellID:Lane:Tile:X:Y ReadNum:FilterFlag:0:SampleNumber:
      • Read 1 descriptor would look like this:
        @M00900:62:000000000-A2CYG:1:1101:18016:2491 1:N:0:13
      • Read 2 would have a 2 in the ReadNum field, like this:
        @M00900:62:000000000-A2CYG:1:1101:18016:2491 2:N:0:13

Quality considerations

  • The number of base calls for each read must equal the number of quality scores
  • The number of entries for Read 1 must equal the number of entries for Read 2
  • The uploader will determine if files are paired-end based on the matching file names in which the only difference is the ReadNum
  • For paired-end reads, the descriptor must match for every entry for both reads 1 and 2
  • Each read has passed filter

Upload parameters

  • Only one sample can be uploaded at a time
  • A maximum of 16 files can be uploaded in a session
  • The size of the uploaded files cannot exceed 25 GB
  • A detailed description of how to use the uploader can be found in the BaseSpace user guide