GenomeQuest Industry » NGS

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

Cloud now?

admin — Mon, 19 Oct 2009 13:38:55 +0000

At the CHI NGS conference, I chaired a roundtable of key managers and influencers discussing the opportunity and challenges to adoption of “cloud computing” for NGS applications. As a first observation, the session was well attended and people are thinking deeply about cloud issues. About 16 participated including representatives from major pharmaceuticals, agroscience, major medical research core labs, and the NIH.

Here is a transcript of my notes from the roundtable:

Some felt end-users increasingly accept the privacy of their data in the hands of a secure cloud provider. Others remarked it remains uncomfortable for some end users who worry when they “don’t know where their data lives”. The roundtable agreed that more end-user education is needed.
Data transfer from the location of data generation to where it is processed remains a bottleneck. However, the problem is more on the upload side since cloud providers tend to have unlimited bandwidth. Corporate and Institution wide networks will have to improve to remedy this bottleneck.
Software application providers will have to develop metering metrics for licensing their applications on cloud resources that can be de-commissioned.
Cloud resources should allow for moving data between desktop applications and the centralized resources.
Commissioning and de-commissioning fixed resources such as databases can be an issue.
From a clinical applicability perspective, cloud providers (and those who run applications on cloud resources) will have to consider how to make their solution suitable for regulatory approval and auditing.
Finally, if an application provider such as GenomeQuest uses a commercial cloud provider such as Amazon EC2, the participants agreed that the application provider and not Amazon is accountable for the security, privacy, and over all robustness of the IT.

My takeaways? Cloud computing is becoming viable in the minds of the industry. A few solvable roadblocks remain. With infinite computing and infinite data, managing the data and turning it into insight remains the challenge and the opportunity.

What are you best at?

admin — Wed, 02 Sep 2009 16:19:10 +0000

Recently I met with a genomics executive at a Biotech who expressed frustration that by appearances, NGS software vendors appear similar. I agree with his assessment if you just look at the web sites. Customers can play a role in helping the vendor community communicate (and compete) better by asking this simple question: “What are you best at?” Why? Because everybody appreciates and accepts that you cannot “be all things to all people” and it therefore forces choice, on the part of the vendor and the customer.

At this stage, vendors are probably best at 1 or 2 things, like SDM, LIMS, client side visualization, or assembly. I’m skeptical that any vendor in the field is really best at ALL the needs for an NGS infrastructure, including GenomeQuest.

For customers, asking the question forces a different consideration: “what key requirement is necessary for us to solve FIRST?” This brings clarity to the trial activity and helps the vendors prioritize and communicate better the value of their offerings, instead of trying to solve all the customer problems for which they may not be most well suited.

Science Advisory Board

admin — Thu, 27 Aug 2009 12:00:20 +0000

I’m excited to start our advisory board, with the appointment of Dr. Mark Boguski. Since our initial financing in 2005, our investors have urged us to build the science advisory board.

So what took so long? Until now, it wasn’t necessary. We provided clear business value to pharma for a well-defined use case. An advisory board might have even been a distraction.

So what’s changed? As we build out the sequence data management (SDM) platform, we want to see beyond this year’s application of next generation sequencing (NGS), and make sure we understand where the industry is going.

Dr. Mark Boguski

Mark is a perfect advisor for this initiative. His practical experience at NCBI, Rosetta, and Novartis, and his current vantage point at Harvard Medical School and Beth Israel, places him squarely with a view to the future uses of sequence data in a clinical setting, and with firm grounding in the practical applications of sequence data for the past 20 years.

It’s an honor to have Mark join us as a scientific advisor. We hope to build a diverse advisory team to complement him with skills and experiences that reflect the diversity of talents converging on the digital revolution in biology.

CHI Conference

GenomeQuest — Wed, 26 Aug 2009 15:50:56 +0000

The Next Generation Sequencing Data Analysis conference in Providence in September looks like it’s shaping up to be a good one. Plenty of GenomeQuesters will be there as will I. We’re sponsoring a roundtable – NGS Five Years Down The Road. In five years time, NGS will have gone from “sexy new technology” to “established and mainstream.” The price of sequencing and analysis will come down, the complexity and volume of experiments will go up. What will remain from our efforts today, and what will NGS analysis look like?

Dr. Henk Heus from GenomeQuest will represent us and I’ll hope to be there personally. Stop by and participate, and introduce yourself!

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.