FinchTalk

Bloginar: Scalable Bioinformatics Infrastructures with BioHDF. Part IV: HDF5 Benefits

2009-07-06T14:40:00.001-07:00

Now that we're back from Alaska and done with the 4th of July fireworks, it's time to present the next installment of our series on BioHDF. HDF highlightsHDF technology is designed for working with...

Sneak Peak: RNA-Seq - Global Profiling of Gene Activity and Alternative Splicing

2009-06-22T06:00:00.000-07:00

Join us June 30 at 10:00 am PDT. Eric Olson, Geospiza's VP of Product Development will present an interesting webinar on using RNA-Seq to measure gene expression and discover alternatively spliced...

Bloginar: Scalable Bioinformatics Infrastructures with BioHDF. Part III: The HDF5 Advantage

2009-06-15T05:00:00.000-07:00

The Next Generation DNA Sequencing (NGS) bioinformatics bottleneck is related to the complexity of working with the data, analysis programs, and numerous output files that are produced as the data...

Bloginar: Scalable Bioinformatics Infrastructures with BioHDF. Part II: Background

2009-06-11T17:45:00.000-07:00

Next Generation DNA Sequencing (NGS) technologies will continue to produce ever increasing amounts of complex data. In the old world of electrophoresis-based sequencing (a.k.a. Sanger) we could...

Bloginar: Scalable Bioinformatics Infrastructures with BioHDF. Part I: Introduction

2009-06-07T14:25:00.000-07:00

At the end of May, the DOE's Los Alamos National Laboratory hosted its 4th annual Sequencing, Finishing and Analysis meeting in Santa Fe, New Mexico. We participated in the conference by presenting...

Sneak Peak: Gene Expression Profiling in Cancer Research: from Raw Data to Biological Significance

2009-06-01T13:45:00.000-07:00

Join us this Wednesday, 10:00 am pacific time, for a webinar in which we present a comparative analysis of microarray and next generation DNA sequencing using data sets from skin cancer gene...

Small RNAs Get Smaller

2009-05-12T08:28:00.000-07:00

Tiny RNAs recently joined the growing list of non-coding RNA (ncRNA) molecules [1]. Their absolute function is not understood, but they are possibly a new class of ncRNA and appear to be most...

Life in the Clouds

2009-04-28T13:26:00.000-07:00

Today, the Applied Biosystems division of Life Technologies announced their partnership with us (Geospiza) to use Amazon Web Services (AWS) to use cloud-computing technologies to help customers...

What if dbEST was an NGS Experiment? Part I: dbEST

2009-04-21T12:55:00.000-07:00

Back in 1997, this alarming statement appeared in a paper [1]:“Biological research is generating data at an explosive rate. Nucleotide sequence databases along are growing at a rate of >210...

Have we been deluged?

2009-04-07T15:28:00.000-07:00

In early March, Science published a perspective “Beyond the Data Deluge [1].” Last October, Nature Biotechnology (NBT) published an editorial “Prepare for the Deluge [2].” Did we miss the...

Geospiza helps high schools get involved in bioinformatics

2009-03-31T19:27:00.000-07:00

Over the past ten years, we have seen a substantial increase in the amount of data that can be obtained from biological experiments. Where once we interrogated small pieces of DNA, we now...

Introducing BioHDF

2009-03-17T10:00:00.000-07:00

Today we released news of our funding for the BioHDF project. This project, in collaboration with The HDF Group, is focused on developing scalable bioinformatics technologies to support the many...

Grant Opportunities for Next Generation DNA Sequencing

2009-03-11T10:42:00.000-07:00

Deadlines are quickly approaching for new NIH opportunities being offered through the American Recovery and Reinvestment Act (ARRA). If you are on NIH’s mailing lists you’re getting a small flood of...

Bloginar: Next Gen Laboratory Systems for Core Facilities

2009-03-08T16:40:00.000-07:00

Geospiza kicked off February by attending the AGBT and ABRF conferences. As part of our participation at ABRF, we presented a scenario, in our poster, where a core lab provides Next Generation...

Bloginar: The Next Generation Dilemma: Large Scale Data Analysis

2009-03-04T10:00:00.000-08:00

Previous posts shared some the things we learned at the AGBT and ABRF meetings in early February. Now it is time to share the work we presented, starting with the AGBT poster, “The Next Generation...

Sneak Peak: Small RNA Analysis with Geospiza

2009-03-01T09:48:00.000-08:00

Join us this Wednesday, March 4th at 10:00 A.M. PST (1:00 P.M. EST), for a webinar focusing on small RNA analysis. Eric Olson, our VP of Product Development and principle designer of Geospiza’s...

Three Themes from AGBT and ABRF Part III: The IT Problem

2009-02-23T07:30:00.000-08:00

The power of Next Generation DNA Sequencing (NGS) technology come from the fact that a massive amount of data, sampling millions of individual molecules, is collected in a massively parallel format. ...

Three Themes from AGBT and ABRF Part II: The Bioinformatics Bottleneck

2009-02-19T07:43:00.000-08:00

In my last post, I summarized the presentations and conversations regarding Next Gen Sequencing (NGS) challenges in terms of three themes: You have to pay attention to details in the laboratory,...

Three Themes from ABRF and AGBT Part I: The Laboratory Challenge

2009-02-15T17:11:00.000-08:00

It's been an exciting week on the road at the AGBT and ABRF conferences. From the many presentations and discussions it is clear that the current and future next generation DNA sequencing (NGS)...

Next Gen Laboratory Software Systems for Core Facilities

2009-02-02T13:32:00.000-08:00

Do you have a core lab? Considering adding Next Generation DNA sequencing capacity to your lab? Then you will be interested in visiting our both and checking out our poster at the annual Association...

The Next Generation Dilemma: Large Scale Data Analysis

2009-01-28T20:04:00.000-08:00

Next week is the AGBT genome conference in Marco Island, Florida. At the conference we will present a poster on work we have been doing with Next Gen Sequencing data analysis. In this post we...

The Experts Agree

2009-01-21T10:09:00.000-08:00

It depends what you are trying to do. That is the take home message in Genome Technology’s (GT) trouble-shooting guide on picking assembly and alignment algorithms for Next-Gen sequence data.In the...

From Reads to Data Sets, Why Next Gen is not like Sanger Sequencing

2009-01-06T11:16:00.000-08:00

Time is running out! Be sure to register for the ABRF 2009 Next Generation DNA Sequencing Workshop to be held in Memphis TN Sat. Feb. 7, 2009. The day will include discussions from core lab...

Closing 2008

2008-12-31T14:25:00.000-08:00

As we bring 2008 to a close, it is a good time to reflect on our progress and think about the new year ahead. Despite the world economic news, both the genomics field in general and Geospiza...

Papers, Papers, and more Papers

2008-12-12T15:51:00.000-08:00

Next Gen Sequencing is hot, hot, hot! You can tell by the numbers and frequency in which papers are being published.A few posts ago, I wrote about a couple of grant proposals that we were preparing...