FinchTalk

Expeditiously Exponential: Data Sharing and Standardization

2009-11-08T15:25:00.001-08:00

We can all agree that our ability to produce genomics and other kinds of data is increasing at exponential rates. Less clear, is understanding the consequences for how these data will be shared and...

GeneSifter Laboratory Edition Update

2009-11-01T18:13:00.000-08:00

GeneSifter Laboratory Edition has been updated to version 3.13. This release has many new features and improvements that further enhance its ability to support all forms of DNA sequencing and...

Yardsticks and Sequencers

2009-10-23T06:22:00.000-07:00

A recent question to the ABRF discussion forum, about quality values and Helicos data, led to an interesting conversation about having yardsticks to compare between Next Generation Sequencing (NGS)...

Sneak Peak: Gene Expression Profiling in Cancer Research: Microarrays, Tag Profiling and Whole Transcriptome Analysis

2009-10-19T04:54:00.000-07:00

Join us this Wednesday (October 21, 2009 10:00 am Pacific Daylight Time) to learn about how GeneSifter is used to measure transcript abundance as well as discover novel transcripts and isoforms of...

Super Computing 09 and BioHDF

2009-10-13T19:51:00.000-07:00

Next month, Nov 16-20, we will be in Portland for Super Computing 09 - SC09. Join us at a Birds of a Feather (BoF) session to learn about developing bioinformatics applications with BioHDF. The...

Resequencing and Cancer

2009-10-08T06:55:00.001-07:00

Yesterday we released news about new funding from NIH for a project to work on ways to improve how variations between DNA sequences are detected using Next Generation Sequencing (NGS) technology. The...

From Blue Gene to Blue Genome? Big Blue Jumps In with DNA Transistors

2009-10-06T11:38:00.000-07:00

Today, IBM announced that are getting into the DNA sequencing business and race for the $1,000 dollar genome by winning a research grant to explore new sequencing technology based on nanopore devices...

GeneSifter in Current Protocols

2009-09-23T06:19:00.000-07:00

This month we are pleased to report Geospiza's publication of the first standard protocols for analyzing Next Generation Sequencing (NGS) data. The pulication, appearing in the September issue of...

Sneak Peak: Sequencing the Transcriptome: RNA Applications for Next Generation Sequencing

2009-09-12T12:21:00.000-07:00

Join us this coming Wednesday, September 16, 2009 10:00 am Pacific Daylight Time (San Francisco, GMT-07:00), for a webinar on whole transcriptome analysis. In the presentation you will learn...

Open or Closed

2009-09-06T14:22:00.000-07:00

A key aspect of Geospiza’s software development and design strategy is to incorporate open scientific technologies into the GeneSifter products to deliver user friendly access to best-of-breed tools...

BioHDF on the Web

2009-08-16T17:46:00.000-07:00

During the past spring and early part of summer, we presented our initial work using HDF5 technology to make next generation DNA sequencing data management scalable. The presentations are posted on...

Researchers get hands-on practice using GeneSifter to analyze Next Gen data and SNPs at the UT-ORNL-KBRIN 2009 summit

2009-07-26T12:21:00.000-07:00

As the recently-published meeting report attests (1), while the much of the genomics world was bemoaning the challenge of working with Next Generation DNA sequence (NGS) data, attendees at the...

Bloginar: Scalable Bioinformatics Infrastructures with BioHDF. Part V: Why HDF5?

2009-07-12T15:58:00.001-07:00

Through the course of this BioHDF bloginar series, we have demonstrated how the HDF5 (Hierarchical Data Format) platform can successfully meet current and future data management challenges posed by...

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...