FinchTalk

The Next Gen Sequencing Lab

2008-05-06T19:39:00.000-07:00

Illumina's Genome Center in a mailroom message really captures the impact of next generation sequencing technology. Each Illumina Genome Analyzer, AB SOLiD instrument, or Roche Genome Sequencer (454)...

Managing Digital Gene Expression Workflows with FinchLab

2008-04-25T06:06:00.000-07:00

Last Wed (4/23) Illumina hosted a Geospiza presentation featuring how FinchLab supports mRNA tag profiling experiments. We had a great turnout and the presentation is posted on the Illumina web...

Sneak Peak: Managing Next Gen Digital Gene Expression Workflows

2008-04-21T06:00:00.000-07:00

This Wednesday, April 23rd, Illumina will host a webinar featuring the Geospiza FinchLab. If you are interested in:Learning about Next Gen sequencing applicationsSeeing how the Illumina Genome...

Expectations Set the Rules

2008-04-16T06:21:00.000-07:00

Genetic analysis workflows are complex. Biology is non-deterministic, so we continually experience new problems. Lab processes and our data have natural uncertainty. These factors conspire against...

Digital Gene Expression with Next Gen Sequencing

2008-04-14T05:51:00.000-07:00

Next Gen Sequencing is changing how we approach problems ranging from whole genome shotgun sequencing, to variation analysis, to gene expression, to structural genomics. Next week, April 23rd,...

Exceptions are the Rule

2008-04-08T07:30:00.000-07:00

Genetic analysis workflows are complex. You can expect that things will go wrong in the laboratory. Biology also manages to interfere and make things harder than you think they should be. Your...

Lab work without data analysis and management is doo doo

2008-04-04T07:49:00.000-07:00

As we begin to contemplate next generation sequence data management, we can use Sanger sequencing to teach us important lessons. One of which, is the value of linking laboratory and data workflows to...

Working with Workflows

2008-04-02T10:00:00.000-07:00

Genetic analysis workflows involve both complex laboratory and data analysis and manipulation procedures. A good workflow management system not only tracks processes, but simplifies the work. In my...

Next Gen, Next Step

2008-03-31T07:00:00.000-07:00

Congratulations! You just got approval to purchase your next generation sequencer! What are you going to do next? Today, there is a lot being written about the data deluge accompanying Next Gen...

Color Space, Flow Space, Sequence Space or Outer Space: Part II, Uncertainty in Next Gen Data

2008-03-24T08:30:00.000-07:00

Next generation sequencing will transform sequencing assays and experiments. Understanding how the data are generated is important for interpreting results. In my last post, I discussed how all...

Color Space, Flow Space, Sequence Space, or Outer Space: Part I. Uncertainty in DNA Sequencing

2008-03-17T06:40:00.000-07:00

Next generation DNA sequencing introduces new concepts like color space, flow space, and sequence space. You might ask, what's a space? How do I deal with these spaces? Why are they important? In...

What's a Bustard?

2008-03-13T06:17:00.000-07:00

For that matter, what's a Firecrest? or a Gerald? Many with an Illumina Genome Analyzer are now learning these are the directories that have the data they may be interested in. What's in those...

Using the Finder

2008-03-09T21:02:00.000-07:00

FinchLab, iFinch, Finch Suite, and FinchLab Next Gen Edition all use a tool that we call the Finder to help you locate data by selected criteria. This video shows some quick tips on using the Finder...

Genotyping with HDF

2008-03-02T14:14:00.001-08:00

To continue our progress describing HDF and its value in bioinformatics, I present the work Geospiza and THG performed in developing a prototype application for genotyping. In this project we ...

The case for HDF

2008-02-26T20:57:00.001-08:00

As we contemplate working Next Gen data we need to think about how we are going to store data and information efficiently. You might ask, what does that mean? Common, a file is a file isn't...

Next Gen Sequencing Software

2008-02-24T12:53:00.001-08:00

In my last post, I indicated that the next generation (Next Gen) of DNA sequencers was creating a lot of excitement in DNA sequencing. In the next couple of posts I want to share some of our plans...

New Finch Best Practices Guides Available!

2008-02-21T09:42:00.000-08:00

The Geospiza Support Team has released 2 more Best Practice Guides! These guides are created for the IT professionals and system administrators responsible for your Finch server. The 2 new guides...

Entering information in iFinch via FinchTV, part I

2008-02-16T15:53:00.002-08:00

Teaching is a hard habit to break so I teach short courses now and then. This year, I've been having my students use FinchTV to enter their blast results into iFinch. This also works with FinchLab...

Conference Blogging from Marco Island and ABRF

2008-02-14T20:08:00.001-08:00

What a week! I've just returned from the AGBT and ABRF meetings in Marco Island Florida and Salt Lake City Utah. I can say the next generation of DNA sequencers are driving a renaissance in DNA ...

Geospiza and Isilon Systems find room for Next Gen sequencing data

2008-02-13T09:14:00.000-08:00

Some of you were probably wondering where we were going to put all of that Next Generation Sequencing data. We found a place. By working with Isilon Systems, we get to combine their strength in...

iFinch in education: metagenomics with JHU, part I.

2008-02-11T21:16:00.000-08:00

iFinch is the perfect bioinformatics tool to accompany a class. I used it Fall quarter in a class that I teach at Shoreline Community College (Washington) and I'm using it right now in an on-line...

Using the Finch Q >20 plots to evaluate your data

2008-02-11T06:35:00.000-08:00

All of the Finch systems: Solutions Finch, FinchLab, and iFinch; have a folder report with visual snapshots that summarize the quality of data in that folder. The Q20 histogram plot is one of...

Geospiza, ABI, and Next Generation Sequencing

2008-02-07T10:46:00.000-08:00

One of the chief complaints we hear in articles on Next Generation sequencing technologies has concerned the lack of bioinformatics support on the part of the Next Gen vendors. Lab directors have...

Uploading your data to iFinch

2008-01-22T15:56:00.000-08:00

Last fall, we introduced iFinch, a personal system for genetic analysis. Unlike our larger, industrial strength Finch systems, iFinch is designed for individual researchers, small labs, or teachers...

Welcome to 2008

2008-01-18T06:16:00.000-08:00

I'd like to start 2008 by wishing all of Geospiza's customers, collaborators, and supporters a Happy New Year! 2008 is going to be an exciting year and I'd like to share three reasons why. First, we...