tag:blogger.com,1999:blog-32189326456254156042008-05-13T10:11:21.047-07:00Sandra Porternoreply@blogger.comBlogger28125tag:blogger.com,1999:blog-3218932645625415604.post-79492300583893797372008-05-06T19:39:00.000-07:002008-05-06T20:13:45.727-07:00

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) has the per run capacity of a Genome Center's daily output. More importantly this is possible because you can do your DNA prep work on a single lab bench. Of course you'll have to find someplace to

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-60654318971317343032008-04-25T06:06:00.000-07:002008-04-25T06:25:08.761-07:00

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 site. In the webninar we talked about: Next Gen sequencing applicationsHow the Illumina Genome Analyzer makes mRNA Tag Profiling more sensitive by looking at some features of mRNA Tag Profiling data sets

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-19389951517255432342008-04-21T06:00:00.000-07:002008-04-21T06:12:33.245-07:00

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 Analyzer makes mRNA Tag Profiling more sensitiveUnderstanding the flow of data and information as samples are converted into resultsOvercoming the significant data management challenges that accompany

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-8410839687544433092008-04-16T06:21:00.000-07:002008-04-16T16:30:44.166-07:00

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 us to make our world rich in variability and processes less than perfect. That keeps things interesting. In a previous post, I was able to show how sequence quality values could be used to summarize

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-50305860457064436262008-04-14T05:51:00.000-07:002008-04-14T06:16:13.173-07:00

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, Geospiza will present a webinar on managing Digital Gene Expression experiments and data with FinchLab. The webinar is hosted by Illumina as part of their ongoing webinar series on Next Gen sequencing.

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-86601096311180646972008-04-08T07:30:00.000-07:002008-04-08T07:40:02.343-07:00

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 workflow management system needs to show the relevant data, allow you to observe trends, and have flexible points were procedures can be repeated. In the last few posts, I introduced genetic analysis

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-4036968325259370792008-04-04T07:49:00.000-07:002008-04-04T08:01:50.801-07:00

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 be able to view information in the context of our assays and experiments. I have been fortunate to hear J. Michael Bishop speak on a couple of occasions. He ended these talks by quoting one of his

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-54205602470210097332008-04-02T10:00:00.000-07:002008-04-02T06:55:10.285-07:00

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 last post , I introduced the concept of workflows in describing the issues one needs to think about as they prepare their lab for Next Gen sequencing. To better understand these challenges, we can

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-89650498241672266762008-03-31T07:00:00.000-07:002008-04-01T08:22:00.446-07:00

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 sequencers. It's true, they produce a lot of data. But even more important are the questions about how you plan to set up the lab and data workflows to turn those precious samples into meaningful

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-20164026089317132972008-03-24T08:30:00.000-07:002008-03-24T08:33:04.187-07:00

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 measurement systems have uncertainty (error) and how error probability is determined in Sanger sequencing. In this post, I discuss the current common next generation (Next Gen) technologies and their

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-37088165640229646422008-03-17T06:40:00.000-07:002008-03-17T06:36:57.207-07:00

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 this two part blog, I will first talk about error analysis in DNA sequencing. Next I will talk about how we might think about error analysis in next generation sequencing. Last week I came across a

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-53919616591968833682008-03-13T06:17:00.000-07:002008-03-13T07:01:32.206-07:00

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 directories? In this post, we explore some of the data in the directories, talk about what data might be important, and use FinchLab Next Gen Edition (FinchLab NG) to look at some of the files. In the

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-68361966021073074872008-03-09T21:02:00.000-07:002008-03-11T12:45:57.466-07:00

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 with iFinch as an example. Using the finder from Sandra Porter on Vimeo.

Sandra Porternoreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-15152138488711875672008-03-02T14:14:00.001-08:002008-03-02T15:14:28.402-08:00

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 implemented a data model, based on polyPhred, in HDF5 to demonstrate HDF5's data organization capabilities. We further demonstrated HDF5's strengths for compressing and accessing data by adding HapMap

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-91934876510699373702008-02-26T20:57:00.001-08:002008-03-30T11:01:27.416-07:00

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 it?WrongWhen one considers ways to work with data on a computer two problems must be solved: The first is how to structure the data. This is also known as defining the data model or format. The second is

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-44741048747723291922008-02-24T12:53:00.001-08:002008-03-09T21:05:17.411-07:00

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 for supporting Next Gen by discussing the poster that we presented at the AGBT and ABRF conferences. The general goal of the poster was to share our thoughts on how Next Gen data will have to be dealt

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-19544442219439595682008-02-21T09:42:00.000-08:002008-02-21T09:49:29.011-08:00

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 are: 1) Stopping and Starting your Finch Server's Services. This guide reviews the proper way to start and stop your Finch server's services and discusses some known problems that you might encounter

Sandra Porternoreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-56412567994173170222008-02-16T15:53:00.002-08:002008-02-21T09:28:00.896-08:00

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 and other Finch systems, too. This has been pretty helpful. The data get stored for each chromatogram and we can all view the results (I'll address this part in a later post.) How does this work?

Sandra Porternoreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-87042748736619149102008-02-14T20:08:00.001-08:002008-02-21T09:29:10.682-08:00

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 sequencing. In the past people would ask me if DNA sequencing was going to be replaced by another technology. I always thought, what a silly thing to say, many of the other technologies are used

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-28842102184559914112008-02-13T09:14:00.000-08:002008-02-21T09:30:15.495-08:00

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 data storage with our expertise in data management. It's a wonderful match! From the press release: Geospiza Announces OEM Agreement with Isilon Systems to Integrate Isilon X-Series Clustered

Sandra Porternoreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-1174185997650024972008-02-11T21:16:00.000-08:002008-02-21T09:32:06.828-08:00

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 class that I teach at Austin Community College (Texas). We cover several different topics in the class, but I have a fondness for long projects where we can use multiple techniques and tie everything

Sandra Porternoreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-28445976121350742782008-02-11T06:35:00.000-08:002008-02-21T09:33:49.413-08:00

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 those tools and in these next two posts, I'll describe what we can learn from these plots. First, we'll talk about the values on the x axis. When we use the term "Q> 20 bases," we're referring to the

Sandra Porternoreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-84930749386072717352008-02-07T10:46:00.000-08:002008-02-21T09:30:15.498-08:00

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 described feeling like they've been left on their own to when it comes to solutions for handling the enormous amount of data produced by Next Gen instruments. I suspect that the people at Applied

Sandra Porternoreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-57116703326801787502008-01-22T15:56:00.000-08:002008-01-22T16:36:18.299-08:00

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 who want a trouble-free system for managing and working with genetic data. I call iFinch "bioinformatics in a box." I've been using it this year in two bioinformatics courses and it's been

Sandra Porternoreply@blogger.comtag:blogger.com,1999:blog-3218932645625415604.post-60617392710755547432008-01-18T06:16:00.000-08:002008-02-21T09:30:15.499-08:00

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 are building on work we began in 2007, which was our 10th year of business! In the last half of 2007 we added two new products. Along with FinchTV, Geospiza now has four discrete products that are

Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com