GenomeQuest Industry » GenomeQuest 6.0Beta

Announcing ChIP-Seq Support

GenomeQuest — Mon, 09 Nov 2009 13:30:19 +0000

We’ve released our ChIP-Seq workflow this week, available to anyone with a Free Basic Account inside of GenomeQuest. Like all of our NGS workflows, it runs in two basic steps: a mapping step and a downstream analysis step. In this case, of course, the downstream analysis is a peak-finding algorithm. We chose the MACS modeling software for peak modeling. (You can see the entire workflow’s documentation here.) Integrated into the GenomeQuest Sequence Data Management platform, it outputs a heavily annotated sequence database, which can then be interactively filtered, grouped, sorted, and mined for peaks of interest. And this can all be connected to your RNA-Seq and resequencing data to get the global picture.

So now researchers can go from their ChIP-Seq NGS runs directly to gene-based annotation of the peaks found by their biology. Select regions of interest, or genes of interest, or peaks of a certain class, and drill down to see the actual evidence that backs up the call.

We’re giving away free ChIP-Seq runs to the first 100 people to sign up.

As always, feel free to leave a comment – we read every one.

Richard J. Resnick
VP Software and Services

Guiding Principle of GenomeQuest 6.0Beta Platform

GenomeQuest — Fri, 18 Sep 2009 12:30:24 +0000

The guiding principle of the development of the GenomeQuest 6.0Beta platform is to support the complete “sequence cycle” – from uploading raw reads, to mapping them to an arbitrary reference, to generating knowledge through a variety of workflows, and then ultimately through to the assembly of those reads for use as the reference for tomorrow’s experiment. In this way, investments in sequencing are not one-off, but rather continually augment each other over long periods of research.

We’re getting very close to releasing a new point version of GenomeQuest 6.0Beta that includes, among other things, support for the Velvet assembly tool. This is one more step in supporting the sequence cycle – a powerful, easy to use, widely adopted assembly package. In addition to the release of the Velvet tool inside of GenomeQuest 6.0Beta, we’re going to be releasing the full “how-to” of its implementation inside of GenomeQuest 6.0Beta for those bioinformaticists and developers that want to get a close-up look at how anyone can integrate virtually any tool into the GenomeQuest 6.0Beta platform.

Richard J. Resnick
VP Software and Services

GenomeQuest 6.0Beta Launch Update

GenomeQuest — Wed, 19 Aug 2009 19:07:14 +0000

The past few weeks have been exciting! The rush of users to the 6.0Beta product has kept us on our toes trying to ensure that everyone can find their way around. Our users’ ingenuity is thrilling to watch. The heart of the company beats in rhythm with users who take a few hundred million reads in color space and do RNA-Seq over a time series. It’s a really fun time to be at GenomeQuest – there are lots of discoveries waiting to be made in the pent up unanalyzed NGS data that has been pouring in.

Coming soon… ChIP-Seq, Velvet, much more…

Richard J. Resnick
VP Software and Services

GenomeQuest 6.0Beta in Bio-IT World

admin — Wed, 19 Aug 2009 13:47:41 +0000

I was recently interviewed for an article by Kevin Davies at Bio-IT World on our GenomeQuest 6.0Beta launch. He immediately connected our story to “NGS” and “Cloud” computing. We have deliberately not over-played the “cloud” aspect of our offering, but as the response from the article shows, there is a lot of interest in the potential economics of the cloud and customer are actively evaluating its potential.

From my view, cloud vendors such as Amazon and others will follow the commodity pricing curve of the instruments and become a way to process larger and larger data sets with fewer and fewer dollars. For us, cloud computing is an opportunity to offer more customers more services at lower costs. However, the winning strategy will require value added software, knowledge and skills to harness those resources for organizations and their end-users.

Thrilled About GenomeQuest 6.0Beta

GenomeQuest — Wed, 22 Jul 2009 12:21:47 +0000

I’m thrilled about our launch of GenomeQuest 6.0Beta because I believe it’ll really have an impact on researchers’ abilities to make sense of their NGS data. We’ve overlayed a web-based toolkit of NGS analyses on top of our world-class NGS-scale sequence data management engine, and have included all of the world’s reference data. In just a few clicks, your reads are mapped, classified, and summarized against whatever genome you’re researching. Our variant calling capability allows for such powerful global mining that you can ask questions like, “show me all of the SNPs and indels that truncate a protein and are previously undiscovered.” To be able to do that in a few clicks in your web browser is pretty cool. And while our RNA-Seq workflow of course computes RPKMs, it also gets you into discovery by letting you examine splice variants all the way down to the level of individual reads. The ability to change the scale up and down so drastically gives researchers huge insights.

My favorite aspect of GenomeQuest 6.0Beta is its openness. Bioinformaticians can plug in their own algorithms and make their own workflows, while at the same time leveraging all of the power of the centrally managed reference data. Researchers can share their results at the click of a button. And the whole thing is available and open to try by anyone who wants to use it.

We’ll keep making GenomeQuest better and better with your help, and I look forward to hearing your feedback on the product.

Richard Resnick
VP Software and Professional Services

Why are we doing this?

admin — Mon, 20 Jul 2009 14:55:28 +0000

Putting GenomeQuest 6.0Beta on the web for free use is a pretty radical step. Our servers could get over-run with data and our queues can get backed up with requests. We could face denial of service attacks from deviant users lurking on the web. Our competitors (who we consider partners and collaborators) will come to the site and look for weak points in performance or our algorithms. So why are we doing this?

Because a picture is worth 1000 words and simply, because we can. The best way to find us out is to use the product. The resources here are ample and they are scalable. If we get too many users and data, then we have a “high class problem” of needing to add more servers. What better proof-point for scalability?

By making our data, computation, and easy-to-use resources freely available we hope to unlock the data deluge and help the industry move beyond alignment technology to the real biology hidden in the data. As a side effect, we hope that GQ6.0 becomes a destination where newcomers can learn about NGS technology and Sequence Data Management in general.

If you are are researcher, we hope you will be so pleased that you will encourage your collaborators to use the system.

If you are a core lab manager and you want to run this in-house, please let us know.

If you are a software vendor, please contact us so that we can discuss ways to integrate your solutions to our platform and help our common customers find cures for cancer and discover new sources of clean energy.